Nature Methods Contents: November 2012 Volume 9 pp 1127 - 1225

TABLE OF CONTENTS December 2012 Volume 9, Issue 12 In This Issue Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Commentaries Resource Brief Communications Articles Application Note Advertisement Exciting New Insights into the Interior of Specimens with 3View from Carl Zeiss 3View enables the acquisition of high resolution 3D data from resin embedded cell and tissue samples in the shortest possible time. The integrated ultramicrotome from Gatan Inc. is offered in several versions: SIGMA 3View, MERLIN 3View and MERLIN Compact 3View. Click here to view stunning images of the retina and cornea taken with 3View. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Macro to Micro Fluorescence In Vivo Imaging iBox Explorer2 Imaging Microscope facilitates small animal in vivo imaging. Detects fluorescent markers (UV to NIR 800 nm wavelengths) from whole mouse to individual cell for tumor, metastases, biodistribution studies. Simplifies workflow process, easily navigates through magnification ranges and captures high resolution images.   In This Issue Top In This Issue Editorial Top Bio-cinema verité?   p1127 doi:10.1038/nmeth.2284 Animations of biological processes are superb tools for science outreach and communication and can be useful in research too. But we need better ways to tell which parts of an animation are based on data. This Month Top Author File: Jerome Mertz   p1129 Vivien Marx doi:10.1038/nmeth.2260 Microscopy without fluorescence to peek under the tissue surface Points of view: Visualizing biological data   p1131 Bang Wong doi:10.1038/nmeth.2258 Data visualization is increasingly important, but it requires clear objectives and improved implementation. Correspondence Top Fluorescence and super-resolution standards based on DNA origami   pp1133 - 1134 Jürgen J Schmied, Andreas Gietl, Phil Holzmeister, Carsten Forthmann, Christian Steinhauer, Thorben Dammeyer and Philip Tinnefeld doi:10.1038/nmeth.2254 Flaws in evaluation schemes for pair-input computational predictions   pp1134 - 1136 Yungki Park and Edward M Marcotte doi:10.1038/nmeth.2259 Research Highlights Top Predicting PPIs An algorithm to predict protein-protein interactions using structural information yields results comparable in accuracy to those of high-throughput experiments. A genetically encoded probe for EM Electron microscopy welcomes a versatile genetically encoded protein tag. Honing in on the niche Cultures of mouse spermatogonial stem cells on primary testis feeder cells model the in vivo niche. Tagging newborn proteins: version 2.0 Newly synthesized proteins of interest can be visualized with a tag by fluorescence imaging or electron microscopy. Mapping microbes on the move A low-cost imaging strategy gives scientists the 'big picture' on locomotive behavior of microorganisms in solution. Synthetic polarization Simple two- and three-component circuits induce polarization in yeast cells. Dye shines bright A tiny lightning rod made of two gold particles and a DNA pillar creates a hotspot that brightens fluorescent signals in zeptoliter volumes. Methods JOBS of the week Postdoc in Bioinformatics Qatar Computing Research Institute Postdoctoral / Research Associate position in Computational Genomics Wayne State University (WSU) School of Medicine Postdoctoral fellow Division of Biostatistics, University of Texas School of Public Health Postdoctoral fellow to study the intestinal microbiota from C. difficile – Ref: 81303 Wellcome Trust Sanger Institute PhD Position: Control of meiotic DNA break formation Vader Lab-Max Planck Institute of Molecular Physiology More Science jobs from Methods EVENT International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2013) 11th Feb - 14th Feb 2013 Barcelona, Spain More science events from Methods in Brief Top Invisible excited-state RNA structures | Genome-driven metabolome identification | Cell monolayer mechanics | Buffered synthetic circuits Tools in Brief Top GCaMP transgenic mice | Measuring phosphorylation-site stoichiometry | Probing the matrix | Trapping a shape-shifting bacterium Technology Feature Top Digging deep and wide into single cells   pp1151 - 1155 Vivien Marx doi:10.1038/nmeth.2261 Instruments maximize the yield in high-content single-cell imaging, which calls for carefully planned experiments and data analysis. News and Views Top Six steps closer to FRET-driven structural biology   pp1157 - 1158 Timothy D Craggs and Achillefs N Kapanidis doi:10.1038/nmeth.2257 A new toolbox for structural biology that combines single-molecule fluorescence and molecular modeling is used to generate high-precision structures of protein complexes. See also: Article by Kalinin et al. GEM: crystal-clear DNA alignment   pp1159 - 1160 Gregory G Faust and Ira M Hall doi:10.1038/nmeth.2256 The Genome Multitool (GEM) mapper rapidly and accurately provides all alignments of a read within a user-defined number of mismatches. See also: Brief Communication by Marco-Sola et al. Commentaries Top Lost in presumption: stochastic reactions in spatial models   pp1163 - 1166 Anel Mahmutovic, David Fange, Otto G Berg and Johan Elf doi:10.1038/nmeth.2253 Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems. Measuring behavior of animal models: faults and remedies   pp1167 - 1170 Ehud Fonio, Ilan Golani and Yoav Benjamini doi:10.1038/nmeth.2252 Widely used behavioral assays need re-evaluation and validation against their intended use. We focus here on measures of chronic anxiety in mouse models and posit that widely used assays such as the open-field test are performed at the wrong time, for inadequate durations and using inappropriate mouse strains. We propose that behavioral assays be screened for usefulness on the basis of their replicability across laboratories. Resource Top Two-photon optogenetic toolbox for fast inhibition, excitation and bistable modulation   pp1171 - 1179 Rohit Prakash, Ofer Yizhar, Benjamin Grewe, Charu Ramakrishnan, Nancy Wang, Inbal Goshen, Adam M Packer, Darcy S Peterka, Rafael Yuste, Mark J Schnitzer and Karl Deisseroth doi:10.1038/nmeth.2215 A collection of opsins for two-photon modulation of neuronal activity in vitro and in vivo is presented in this resource. The opsins have kinetic, expression and spectral properties ideally suited to typical raster-scanning two-photon microscopy. Also online, Packer et al. use the red-shifted opsin C1V1T and simple raster-scanning illumination to stimulate individual spines and dendrites and map synaptic circuits. Brief Communications Top Ultrabright photoactivatable fluorophores created by reductive caging   pp1181 - 1184 Joshua C Vaughan, Shu Jia and Xiaowei Zhuang doi:10.1038/nmeth.2214 The resolution achievable with single-molecule-based super-resolution fluorescence imaging is increased via a fluorophore caging procedure that uses a reducing agent to convert dyes to a long-lived dark state from which they can be activated with UV light and emit high numbers of photons. The GEM mapper: fast, accurate and versatile alignment by filtration   pp1185 - 1188 Santiago Marco-Sola, Michael Sammeth, Roderic Guigó and Paolo Ribeca doi:10.1038/nmeth.2221 A sequence read mapper for versatile searching of genome space that returns all matches with precision and speed. See also: Brief Communication by Marco-Sola et al. Membrane-protein binding measured with solution-phase plasmonic nanocube sensors   pp1189 - 1191 Hung-Jen Wu, Joel Henzie, Wan-Chen Lin, Christopher Rhodes, Zhu Li, Elodie Sartorel, Jeremy Thorner, Peidong Yang and Jay T Groves doi:10.1038/nmeth.2211 Silica-coated silver nanocube suspensions provide an easy, rapid and label-free way to quantify protein binding to supported lipid bilayers by localized plasmon resonance measurement with a standard laboratory UV spectrophotometer. Systematic reconstruction of RNA functional motifs with high-throughput microfluidics   pp1192 - 1194 Lance Martin, Matthias Meier, Shawn M Lyons, Rene V Sit, William F Marzluff, Stephen R Quake and Howard Y Chang doi:10.1038/nmeth.2225 Binding studies with systematically mutagenized RNA and RNA-binding proteins allow insight into the relationship between an RNA sequence, its structure and its function. Phase-gradient microscopy in thick tissue with oblique back-illumination   pp1195 - 1197 Tim N Ford, Kengyeh K Chu and Jerome Mertz doi:10.1038/nmeth.2219 A method for phase contrast imaging of unstained thick tissue samples is presented. It is based on oblique back-illumination and can image at depths of several tens of microns. Staining and embedding the whole mouse brain for electron microscopy   pp1198 - 1201 Shawn Mikula, Jonas Binding and Winfried Denk doi:10.1038/nmeth.2213 A method for staining and embedding the entire mouse brain for electron microscopy is reported. The method results in uniform myelin staining and will allow reconstructions of myelinated long-range axons using serial block-face electron microscopy. Two-photon optogenetics of dendritic spines and neural circuits   pp1202 - 1205 Adam M Packer, Darcy S Peterka, Jan J Hirtz, Rohit Prakash, Karl Deisseroth and Rafael Yuste doi:10.1038/nmeth.2249 Using the red shifted opsin C1V1T and simple raster-scanning illumination, this work shows two-photon optogenetic stimulation of single cells, dendrites and spines. The method is also applied to map synaptic circuits in mouse brain slices and, using holographic photostimulation, for the simultaneous activation of two neurons located in different planes. Also online, Prakash et al. present a collection of opsins for two-photon excitation, inhibition and bistable control of neuronal activity in vitro and in vivo. Advertisement FULL POWER ACROSS THE SPECTRUM Chroma is a proven leader and innovator in optics technologies. We are a team of employee-owners committed to producing the world's finest precision sputtered optics. BP/LP/SP • Multiband • Notch • Dichroic Mirrors • Polychroic Mirrors • UV/VIS/N-IR • AR Coatings • Hot/Cold Mirrors • ND/Ag-Al Mirrors • Laser Grade   Articles Top De novo derivation of proteomes from transcriptomes for transcript and protein identification   pp1207 - 1211 Vanessa C Evans, Gary Barker, Kate J Heesom, Jun Fan, Conrad Bessant and David A Matthews doi:10.1038/nmeth.2227 Integration of transcriptomic and proteomic data allows more detailed annotation of proteomes of model and non-model species. Membrane-protein structure determination by solid-state NMR spectroscopy of microcrystals   pp1212 - 1217 Shakeel Ahmad Shahid, Benjamin Bardiaux, W Trent Franks, Ludwig Krabben, Michael Habeck, Barth-Jan van Rossum and Dirk Linke doi:10.1038/nmeth.2248 The structure of the membrane anchor domain of the bacterial autotransporter YadA is solved by a solid-state NMR spectroscopy approach using a uniformly 13C- and 15N-labeled microcrystalline sample. A toolkit and benchmark study for FRET-restrained high-precision structural modeling   pp1218 - 1225 Stanislav Kalinin, Thomas Peulen, Simon Sindbert, Paul J Rothwell, Sylvia Berger, Tobias Restle, Roger S Goody, Holger Gohlke and Claus A M Seidel doi:10.1038/nmeth.2222 A collection of simulation tools and workflow for single-molecule Forster resonance energy transfer (smFRET) allows highly quantitative structural modeling. This hybrid approach yields a model of reverse-transcriptase binding to DNA at sub-angstrom accuracy when benchmarked against a crystal structure and can resolve a flexible single-stranded template overhang. See also: News and Views by Craggs & Kapanidis Advertisement High quality BD reagents are now more affordable Lower pricing on BD Biosciences reagents means that you don't have to sacrifice quality. Now the consistency and reliability of BD flow cytometry reagents are more affordable, including thousands of proven products and innovative new brilliant dyes. Find the right product for your needs here. bdbiosciences.com/reagents   Application Note Top SENSE: a fast RNA-seq library preparation protocol with superior strand specificity    Courtney Nadeau and Alexander Seitz Top Advertisement The good, the bad, the ugly - when it comes to finding antibodies, Antibodypedia wants to hear it all! Like us on Facebook and tell us how your research is going and how we can help you find the right antibody for the right application.   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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