Nature Methods Contents: February 2012 Volume 9 pp 111 - 208

Advertisement Apoptosis Detection: A streamlined approach.  New BD FACSuite™ software on the BD FACSVerse™ flow cytometry system provides predefined research assays matched with reagent kits, making it easy to achieve reproducible, consistent results. Download a free application note on apoptosis detection and see the exciting innovations behind the new BD FACSVerse. bdbiosciences.com/go/verse TABLE OF CONTENTS February 2012 Volume 9, Issue 2 In This Issue Editorial This Month Correspondence Research Highlights Tools in Brief Methods in Brief Technology Feature News and Views Review Perspective Analysis Brief Communications Articles Advertisement Infinite® M1000 PRO with AlphaScreen® • 10 detection modes • Including • AlphaScreen®/AlphaLISA® • Excitation, emission, absorbance, • luminescence and 3D scans • Flexible wavelength selection • Adjustable fluorescence bandwidth • settings • Free definition of plate formats up • to 1536-wells • NanoQuant Plate™ compatible Click here for details Subscribe   Facebook   RSS   Recommend to library   Twitter   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 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 All things being equal p111 doi:10.1038/nmeth.1891 Direct comparisons of tool or method performance under standardized experimental conditions yield highly valuable information for both method users and developers. Full Text | PDF This Month Top The author file: Susan Cox p113 Monya Baker doi:10.1038/nmeth.1866 Using Bayesian statistics to speed super-resolution microscopy Full Text | PDF Points of view: Networks p115 Nils Gehlenborg and Bang Wong doi:10.1038/nmeth.1862 We describe graphing techniques to support exploration of networks. Full Text | PDF Correspondence Top Improved Mos1-mediated transgenesis in C. elegans  pp117 - 118 Christian Frøkjær-Jensen, M Wayne Davis, Michael Ailion and Erik M Jorgensen doi:10.1038/nmeth.1865 Full Text | PDF Generating transgenic nematodes by bombardment and antibiotic selection pp118 - 119 Jennifer I Semple, Laura Biondini and Ben Lehner doi:10.1038/nmeth.1864 Full Text | PDF Research Highlights Top Fatherless stem cells p121 Two independent research groups derive haploid mouse embryonic stem cells and propose their use for genetic screens. Timing an intron's departure pp122 - 123 An in vitro RNA-labeling technique with single-molecule resolution offers a look into the kinetics and the location of splicing. Optimal stoichiometry for pluripotency pp122 - 123 Different ratios of reprogramming factors affect the epigenetic state of cells. Better resolution for structured-illumination microscopy p124 The use of a photoswitchable fluorescent protein allows nonlinear structured-illumination microscopy of cellular structures at 50 nanometer resolution. Bearing the mark p127 Arabinosyl nucleosides are an addition to the toolkit of DNA-labeling methods. A microscopic endoscope p128 Microscopic optical devices make their way into living cells. High-resolution chromatin immunoprecipitation p130 Exonuclease digestion of immunoprecipitated chromatin sharpens protein binding peaks and improves signal. Methods JOBS of the week Quality Assurance Manager – Medical Paramount Recruitment Postdoc (f / m) as an instrument officer for the neutron powder diffractometer Forschungszentrum Juelich GmbH Scholarship for Postdoctoral studies in Bioinformatics Karolinska Institutet 3D Imaging Process Engineer Paramount Recruitment 101701-Medical Director (MD) Genentech 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 Tools in Brief Top De novo short read assembler  | Watching protein synthesis  | A database of yeast mutant phenotypes | Switchable infrared dyes  Methods in Brief Top Targeted structural variations  | In vivo detection of protein binding in the transcriptome  | Clearing the way to spinal cord regeneration  | Ribosome profiling in bacteria  Technology Feature Top Structural variation: the genome's hidden architecture pp133 - 137 Monya Baker doi:10.1038/nmeth.1858 Next-generation sequencing is uncovering more variants than ever before, but it also faces limitations. Full Text | PDF News and Views Top Super resolution for common probes and common microscopes pp139 - 141 Keith A Lidke doi:10.1038/nmeth.1863 A sophisticated analysis approach based on the concept of fluorophore localization provides dynamic super-resolution data of GFP-labeled live cells using a common, arc lamp-based wide-field fluorescence microscope. Full Text | PDF See also: Article by Cox et al. Making sense out of nonsense to visualize editing in the fly nervous system pp141 - 143 Chammiran Daniel and Marie Öhman doi:10.1038/nmeth.1860 In vivo methods to capture processing events such as RNA editing in specific cell types are sparse. Researchers have now developed a method to visualize adenosine-to-inosine editing activity in individual fruit fly neurons using a reverse-engineered fluorescent reporter. Full Text | PDF See also: Article by Jepson et al. Review Top DNA methylome analysis using short bisulfite sequencing data pp145 - 151 Felix Krueger, Benjamin Kreck, Andre Franke and Simon R Andrews doi:10.1038/nmeth.1828 In this Review, the authors take the reader through the steps needed to analyze bisulfite-treated DNA, pointing out different considerations for data in base or color space, to ensure high-quality methylome analysis. Abstract | Full Text | PDF Perspective Top Immunolabeling artifacts and the need for live-cell imaging pp152 - 158 Ulrike Schnell, Freark Dijk, Klaas A Sjollema and Ben N G Giepmans doi:10.1038/nmeth.1855 In this Perspective the authors highlight and discuss the artifacts that can arise when using immunolabeling to examine protein localization in cell culture. They call for using both alternative fixation and permeabilization protocols and live-cell imaging of fluorescent protein fusions to reliably study subcellular protein localization. Abstract | Full Text | PDF Analysis Top Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins pp159 - 172 Joanna Mattis, Kay M Tye, Emily A Ferenczi, Charu Ramakrishnan, Daniel J O'Shea, Rohit Prakash, Lisa A Gunaydin, Minsuk Hyun, Lief E Fenno, Viviana Gradinaru, Ofer Yizhar and Karl Deisseroth doi:10.1038/nmeth.1808 In this Analysis, the authors directly experimentally compare microbial opsins used for the control of neural activity. They extract essential principles and key parameters that can help end users with the design and interpretation of optogenetic experiments and guide tool developers in the characterization of future tools. Abstract | Full Text | PDF Brief Communications Top HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment pp173 - 175 Michael Remmert, Andreas Biegert, Andreas Hauser and Johannes Söding doi:10.1038/nmeth.1818 HHblits is a protein sequence search tool that works by iterative pairwise comparison of profile hidden Markov models. It outperforms existing tools in terms of speed, sensitivity and alignment quality. Abstract | Full Text | PDF Detection of structural variants and indels within exome data pp176 - 178 Emre Karakoc, Can Alkan, Brian J O'Roak, Megan Y Dennis, Laura Vives, Kenneth Mark, Mark J Rieder, Debbie A Nickerson and Evan E Eichler doi:10.1038/nmeth.1810 The Splitread algorithm uses a split-read strategy to detect structural variants and small insertions and deletions (indels) in whole-exome and whole-genome sequence datasets at high sensitivity. It maps the breakpoints at single-base-pair resolution, even in low-complexity regions, and can detect novel processed pseudogenes. Abstract | Full Text | PDF A linear complexity phasing method for thousands of genomes pp179 - 181 Olivier Delaneau, Jonathan Marchini and Jean-François Zagury doi:10.1038/nmeth.1785 An efficient haplotype-estimation algorithm that features linear complexity allows the rapid and accurate phasing of diploid genomes from trios, duos and unrelated samples. Abstract | Full Text | PDF Blotting protein complexes from native gels to electron microscopy grids pp182 - 184 Roland Wilhelm Knispel, Christine Kofler, Marius Boicu, Wolfgang Baumeister and Stephan Nickell doi:10.1038/nmeth.1840 A simple, general procedure for transferring protein complexes directly from native gels to electron microscopy grids for structural analysis is reported. Abstract | Full Text | PDF Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton pp185 - 188 Ke Xu, Hazen P Babcock and Xiaowei Zhuang doi:10.1038/nmeth.1841 The use of dual-objective detection with astigmatism-based three-dimensional stochastic optical reconstruction microscopy (STORM) imaging improves resolution more than twofold and removes noise in resulting super-resolution images. This allowed detailed fluorescence imaging of distinctive features of the three-dimensional actin cytoskeleton ultrastructure with single-filament resolution in cells. 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 Visualizing adenosine-to-inosine RNA editing in the Drosophila nervous system pp189 - 194 James E C Jepson, Yiannis A Savva, Kyle A Jay and Robert A Reenan doi:10.1038/nmeth.1827 Adenosine-to-inosine RNA editing modifies expressed sequences and enhances functional protein diversity. The authors report an in vivo fluorescent reporter that provides a readout of adenosine deaminase RNA-editing activity in Drosophila melanogaster neurons, showing evidence of inter-individual variability in editing activity. Abstract | Full Text | PDF See also: News and Views by Daniel & Ohman Bayesian localization microscopy reveals nanoscale podosome dynamics pp195 - 200 Susan Cox, Edward Rosten, James Monypenny, Tijana Jovanovic-Talisman, Dylan T Burnette, Jennifer Lippincott-Schwartz, Gareth E Jones and Rainer Heintzmann doi:10.1038/nmeth.1812 Bayesian analysis of fluorophore blinking and bleaching in image data collected from simple xenon arc lamp illumination and high-speed wide-field imaging of standard fluorescent proteins allows localization microscopy in living cells with a 50 nm spatial and a 4 s temporal resolution. Abstract | Full Text | PDF See also: News and Views by Lidke Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes pp201 - 208 Gergely Katona, Gergely Szalay, Pál Maák, Attila Kaszás, Máté Veress, Dániel Hillier, Balázs Chiovini, E Sylvester Vizi, Botond Roska and Balázs Rózsa doi:10.1038/nmeth.1851 An acousto-optic two-photon microscope with continuous three-dimensional trajectory and random-access scanning modes can scan near-cubic-millimeter volumes of tissue at sub-millisecond temporal resolution in vivo. The system can be used to image both sub-cellular as well as network-scale neuronal activity. Abstract | Full Text | PDF Top Advertisement Miami 2012 Winter Symposium: Nanotechnology in Biomedicine February 26-29, 2012 • Miami, FL, USA The 45th Miami Winter Symposium will bring together leaders in the field to discuss breakthroughs in new nanomaterials and the challenges in translating these materials into products for the clinic and laboratory. For more information and to register, visit: www.nature.com/natureconferences/miami/mws2012   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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