Nature Methods Contents: March 2012 Volume 9 pp 209 - 309

Advertisement Enhanced biological safety for flow cytometry Biosafety cabinets developed for BD flow cytometry instruments provide a high standard of safety, protecting people, products, and the environment. Learn more about the innovations from BD that can improve your workflow, results, and provide the highest level of safety in your lab. bdbiosciences.com/go/biosafety TABLE OF CONTENTS March 2012 Volume 9, Issue 3 In This Issue Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Perspective Brief Communications Articles Application Notes Advertisement See the Light. Make the Switch. Stop Cloning! The LightSwitch Luciferase Assay System provides everything you need for reporter assays: pre-cloned human promoters and 3'UTRs in luciferase reporter vectors plus optimized luciferase reagents to measure promoter induction and miRNA target validation. Visit SwitchGear Genomics and explore our genome-wide collections and validated pathway sets. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Amnis introduces the revolutionary new FlowSight, a 12 channel imaging flow cytometer that is priced for every lab. The FlowSight can be upgraded with up to four lasers, a 96 well AutoSampler, and image analysis package. For more demanding requirements, Amnis' ImageStreamX imaging cytometer delivers the ultimate in image quality and image-based applications in flow.   In This Issue Top PDF Editorial Top On being second p209 doi:10.1038/nmeth.1926 Early adopters of new methods have a crucial role in validating them and defining their limits. They deserve more formal recognition of this role. Full Text | PDF This Month Top The author file: Yi Yang p211 Monya Baker doi:10.1038/nmeth.1901 Engineering light-induced gene expression Full Text | PDF Points of view: Heat maps p213 Nils Gehlenborg and Bang Wong doi:10.1038/nmeth.1902 Heat maps are useful for visualizing multivariate data but must be applied properly. Full Text | PDF Correspondence Top ChromHMM: automating chromatin-state discovery and characterization pp215 - 216 Jason Ernst and Manolis Kellis doi:10.1038/nmeth.1906 Full Text | PDF Research Highlights Top Reporting plant hormone levels: a disappearing act p219 A fluorescent protein fusion reports levels of the plant hormone auxin by succumbing to its degradation signal. Prokaryotic RNAi pp220 - 221 Rationally designed RNAs that work with the bacterial immune response allow targeted gene silencing in prokaryotes. A bird's-eye view of disease pp220 - 221 The integration of protein-protein interaction networks with structural information about the interacting protein partners creates a three-dimensional scaffold on which are mapped mutations involved in human disease. How TAL effectors bind DNA p222 Structure of modular DNA-recognition domain is revealed. A broader palette for luciferase p225 Engineered firefly enzymes use new substrates and emit at redder wavelengths. Single-molecule circuits p226 An electronic circuit enables analysis of dynamic processivity of single molecules. Degrading proteins with intracellular antibodies p228 Researchers develop a genetic method for degradation of GFP protein fusions in cells and living flies. Methods JOBS of the week PhD in chemistry R&D team of advanced research reactor Belgian nuclear research centre (SCK-CEN) Genomics Specialist Nestle Institute of Health Sciences Head of Production - Ireland - Pharmaceutical Paramount Recruitment Postdoctoral Fellowship in Skeletal and Stem Cell Biology University of California - San Francisco Development Scientist III (Technical Department) 1917 Millipore (U.K.) Ltd. 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 Studying fine visual perception using rats  | Personalized models of virus infection  | Improved Bessel beam light sheets  | In vitro self-renewing cells from the adult human eye  Tools in Brief Top Channelrhodopsin's crystal structure  | Exploding nanodroplets  Timing DNA repair  | Screening for potent viral RNA interference  Technology Feature Top Reprogramming: faithful reporters pp231 - 234 Monya Baker doi:10.1038/nmeth.1899 Researchers are finding efficient ways to pick the most promising pluripotent stem cells. Full Text | PDF News and Views Top Establishing homology between monkey and human brains pp237 - 239 Tor D Wager and Tal Yarkoni doi:10.1038/nmeth.1869 Neuroimaging methods are beginning to provide promising ways of understanding the functional organization of the brain across species. Full Text | PDF See also: Article by Mantini et al. Modeling cellular signaling: taking space into the computation pp239 - 242 Michael W Sneddon and Thierry Emonet doi:10.1038/nmeth.1900 In living systems, chemical reactions and the geometry of cells feed back on each other. Methods for computational modeling are beginning to take this complexity into account. Full Text | PDF See also: Article by Angermann et al. Small is beautiful pp242 - 243 Keith Moffat doi:10.1038/nmeth.1895 Using two independent methods, researchers show that in vivo-grown crystals of soluble proteins and of membrane proteins grown in the lipidic sponge phase can be analyzed by serial femtosecond crystallography on an X-ray free electron laser. Full Text | PDF See also: Brief Communication by Koopmann et al. | Brief Communication by Johansson et al. Perspective Top OMERO: flexible, model-driven data management for experimental biology pp245 - 253 Chris Allan, Jean-Marie Burel, Josh Moore, Colin Blackburn, Melissa Linkert, Scott Loynton, Donald MacDonald, William J Moore, Carlos Neves, Andrew Patterson, Michael Porter, Aleksandra Tarkowska, Brian Loranger, Jerome Avondo, Ingvar Lagerstedt, Luca Lianas, Simone Leo, Katherine Hands, Ron T Hay, Ardan Patwardhan, Christoph Best, Gerard J Kleywegt, Gianluigi Zanetti and Jason R Swedlow doi:10.1038/nmeth.1896 The Open Microscopy Environment Remote Objects (OMERO) software platform provides a server-based system for managing and analyzing microscopy images and non-image data. Abstract | Full Text | PDF Brief Communications Top Serial two-photon tomography for automated ex vivo mouse brain imaging pp255 - 258 Timothy Ragan, Lolahon R Kadiri, Kannan Umadevi Venkataraju, Karsten Bahlmann, Jason Sutin, Julian Taranda, Ignacio Arganda-Carreras, Yongsoo Kim, H Sebastian Seung and Pavel Osten doi:10.1038/nmeth.1854 Automated tissue sectioning and two-photon imaging of fluorescently labeled and fixed mouse brains allows high-resolution tomographic imaging of the entire brain. The authors demonstrate performance using multiple GFP mouse lines, dye-based retrograde tracing and viral anterograde tracing. Abstract | Full Text | PDF In vivo protein crystallization opens new routes in structural biology pp259 - 262 Rudolf Koopmann, Karolina Cupelli, Lars Redecke, Karol Nass, Daniel P DePonte, Thomas A White, Francesco Stellato, Dirk Rehders, Mengning Liang, Jakob Andreasson, Andrew Aquila, Sasa Bajt, Miriam Barthelmess, Anton Barty, Michael J Bogan, Christoph Bostedt, Sébastien Boutet, John D Bozek, Carl Caleman, Nicola Coppola, Jan Davidsson, R Bruce Doak, Tomas Ekeberg, Sascha W Epp, Benjamin Erk, Holger Fleckenstein, Lutz Foucar, Heinz Graafsma, Lars Gumprecht, Janos Hajdu, Christina Y Hampton, Andreas Hartmann, Robert Hartmann, Günter Hauser, Helmut Hirsemann, Peter Holl, Mark S Hunter, Stephan Kassemeyer, Richard A Kirian, Lukas Lomb, Filipe R N C Maia, Nils Kimmel, Andrew V Martin, Marc Messerschmidt, Christian Reich, Daniel Rolles, Benedikt Rudek, Artem Rudenko, Ilme Schlichting, Joachim Schulz, M Marvin Seibert, Robert L Shoeman, Raymond G Sierra, Heike Soltau, Stephan Stern, Lothar Strüder, Nicusor Timneanu, Joachim Ullrich, Xiaoyu Wang, Georg Weidenspointner, Uwe Weierstall, Garth J Williams, Cornelia B Wunderer, Petra Fromme, John C H Spence, Thilo Stehle, Henry N Chapman, Christian Betzel and Michael Duszenko doi:10.1038/nmeth.1859 Expression of a protein in Sf9 insect cells at high concentration triggers formation of in vivo crystals that can be analyzed by serial femtosecond X-ray crystallography. Abstract | Full Text | PDF See also: News and Views by Moffat Lipidic phase membrane protein serial femtosecond crystallography pp263 - 265 Linda C Johansson, David Arnlund, Thomas A White, Gergely Katona, Daniel P DePonte, Uwe Weierstall, R Bruce Doak, Robert L Shoeman, Lukas Lomb, Erik Malmerberg, Jan Davidsson, Karol Nass, Mengning Liang, Jakob Andreasson, Andrew Aquila, Saša Bajt, Miriam Barthelmess, Anton Barty, Michael J Bogan, Christoph Bostedt, John D Bozek, Carl Caleman, Ryan Coffee, Nicola Coppola, Tomas Ekeberg, Sascha W Epp, Benjamin Erk, Holger Fleckenstein, Lutz Foucar, Heinz Graafsma, Lars Gumprecht, Janos Hajdu, Christina Y Hampton, Robert Hartmann, Andreas Hartmann, Günter Hauser, Helmut Hirsemann, Peter Holl, Mark S Hunter, Stephan Kassemeyer, Nils Kimmel, Richard A Kirian, Filipe R N C Maia, Stefano Marchesini, Andrew V Martin, Christian Reich, Daniel Rolles, Benedikt Rudek, Artem Rudenko, Ilme Schlichting, Joachim Schulz, M Marvin Seibert, Raymond G Sierra, Heike Soltau, Dmitri Starodub, Francesco Stellato, Stephan Stern, Lothar Strüder, Nicusor Timneanu, Joachim Ullrich, Weixiao Y Wahlgren, Xiaoyu Wang, Georg Weidenspointner, Cornelia Wunderer, Petra Fromme, Henry N Chapman, John C H Spence and Richard Neutze doi:10.1038/nmeth.1867 Lipidic sponge phase crystallization yields membrane protein microcrystals that can be injected into an X-ray free electron laser beam, yielding diffraction patterns that can be processed to recover the crystal structure. Abstract | Full Text | PDF See also: News and Views by Moffat Spatiotemporal control of gene expression by a light-switchable transgene system pp266 - 269 Xue Wang, Xianjun Chen and Yi Yang doi:10.1038/nmeth.1892 A light-inducible dimerization domain is used to create a genetically encoded, light-switchable transactivator of gene expression. The system allows rapid blue light-mediated activation of transgenes containing an appropriate activation sequence with low background and high induction. Abstract | Full Text | PDF Library-free methylation sequencing with bisulfite padlock probes pp270 - 272 Dinh Diep, Nongluk Plongthongkum, Athurva Gore, Ho-Lim Fung, Robert Shoemaker and Kun Zhang doi:10.1038/nmeth.1871 The pairing of bisulfite padlock probes with a probe-design algorithm, library-free sequencing and an analysis pipeline provides a flexible and scalable method for quantifying cytosine methylation. Abstract | Full Text | PDF An artery-specific fluorescent dye for studying neurovascular coupling pp273 - 276 Zhiming Shen, Zhongyang Lu, Pratik Y Chhatbar, Philip O'Herron and Prakash Kara doi:10.1038/nmeth.1857 The authors report Alexa Fluor 633 hydrazide to be artery-specific and use it to measure arteriole dilation dynamics in vivo in response to visual stimuli in mouse, rat and cat neocortex. They find that sensory stimulus-evoked arteriole dilation reduces the fluorescence recorded from underlying neurons. 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 Interspecies activity correlations reveal functional correspondence between monkey and human brain areas pp277 - 282 Dante Mantini, Uri Hasson, Viviana Betti, Mauro G Perrucci, Gian Luca Romani, Maurizio Corbetta, Guy A Orban and Wim Vanduffel doi:10.1038/nmeth.1868 To examine functional correspondences between monkey and human brain areas, a method based on the temporal correlation of sensory-evoked functional magnetic resonance imaging responses is proposed. The study reveals putative homologous regions that have shifted to topologically unexpected locations during evolution. Abstract | Full Text | PDF See also: News and Views by Wager & Yarkoni Computational modeling of cellular signaling processes embedded into dynamic spatial contexts pp283 - 289 Bastian R Angermann, Frederick Klauschen, Alex D Garcia, Thorsten Prustel, Fengkai Zhang, Ronald N Germain and Martin Meier-Schellersheim doi:10.1038/nmeth.1861 Molecular processes in cells are not spatially homogenous. Reported here is an approach, implemented in the Simmune toolset, for modeling cellular processes within their dynamic spatial context. Abstract | Full Text | PDF See also: News and Views by Sneddon & Emonet Controlling airborne cues to study small animal navigation pp290 - 296 Marc Gershow, Matthew Berck, Dennis Mathew, Linjiao Luo, Elizabeth A Kane, John R Carlson and Aravinthan D T Samuel doi:10.1038/nmeth.1853 A device for generating precise spatial and temporal patterns of airborne odorants is reported. In combination with machine vision tracking software, the authors use the device to monitor navigation of freely moving Drosophila melanogaster larvae. Abstract | Full Text | PDF Chronic in vivo imaging in the mouse spinal cord using an implanted chamber pp297 - 302 Matthew J Farrar, Ida M Bernstein, Donald H Schlafer, Thomas A Cleland, Joseph R Fetcho and Chris B Schaffer doi:10.1038/nmeth.1856 An imaging chamber implanted over the mouse spinal cord enables long-term longitudinal two-photon microscopy of cellular dynamics in normal or pathological conditions. Abstract | Full Text | PDF Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling pp303 - 309 Joshua J Sims, Francesco Scavone, Eric M Cooper, Lesley A Kane, Richard J Youle, Jef D Boeke and Robert E Cohen doi:10.1038/nmeth.1888 Sensor proteins that exploit principles of linkage-specific avidity reveal topology-related functions of polyubiquitin in diverse cell types and pathways. Abstract | Full Text | PDF Application Notes Top A rapid, directional RNA-seq library preparation workflow for Illumina® sequencing  Jim Pease and Roy Sooknanan Abstract | Full Text | PDF Expresso® CMV system: effortless mammalian expression cloning  Saurabh Sen, Heather Sternard, Eric Steinmetz and Ronald Godiska Abstract | Full Text | PDF Top Advertisement Scientific Reports published the most downloaded paper on nature.com in December. Downloaded over 100,000 times and counting... Make your paper seen. Make your paper open. 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