Nature Methods Contents: February 2015 Volume 12 pp 93 - 160

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Advertisement Hamamatsu, Living Image It is undeniable: Biological research is increasingly multidisciplinary. And as more powerful and computationally complex imaging methods are integrated into life science research, the need for deeper understanding and increased dialogue among biologists, physicists, engineers, mathematicians and statisticians grows. Please visit The Living Image and join us in celebrating science and technology that pushes the limits of what is possible. And, above all, we invite you to do what comes naturally...Explore! TABLE OF CONTENTS February 2015 Volume 12, Issue 2 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature Perspective Brief Communications Articles Corrigenda Errata Application Note Advertisement   PhotoFluor LM-75 A low-cost, high power and ultra-stable direct-mounted metal halide light source. No liquid light guide, mounts directly to your microscope. Powerful white light source with high UV output, no flickering and small footprint. Best for routine fluorescence, FISH and other clinical applications.  www.89north.com Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement CRISPR Human sgRNA Libraries (Starting from $1400) Sets of single guide RNAs (sgRNAs) cloned into lentiviral vectors for dual-use (transfection or transduction) delivery methods. These libraries are designed for large-scale functional screens, such as gene discovery, genome-scale functional interrogation, and drug discovery. Individually constructed, sequence-verified, pooled sgRNA libraries ensure high quality and good sgRNA representation for selected target gene families. Pre-made or custom sets 2 or more sgRNAs per target gene Flexible delivery formats such as pooled sgRNA plasmids, bacteria stocks, or lentiviral particles Learn more   Advertisement Nature Reviews Microbiology  CRISPR CALENDAR 2015 One of the most exciting recent developments in microbiology has been the discovery and characterization of the CRISPR—Cas adaptive immune system in bacteria and archaea. This special Calendar brings together CRISPR related images from a range of Nature Publishing Group journals. Produced with support from  OriGene, Your Gene Company     In This Issue Top In This Issue    Editorial Top Communication matters   p93 doi:10.1038/nmeth.3282 Is social media a new 4mat 4 science in UR community? It may be time to sign up. This Month Top The Author File: Wesley P. Wong   p95 Vivien Marx doi:10.1038/nmeth.3260 Brainstorming leads to an invention that makes a lab workhorse gallop. Points of view: Temporal data   p97 Marc Streit and Nils Gehlenborg doi:10.1038/nmeth.3262 Use inherent properties of time to create effective visualizations. Correspondence Top Aquaria: simplifying discovery and insight from protein structures   pp98 - 99 Se´n I O'Donoghue, Kenneth S Sabir, Maria Kalemanov, Christian Stolte, Benjamin Wellmann et al. doi:10.1038/nmeth.3258 Research Highlights Top All-optical electrophysiology in behaving animals Three different optical strategies enable the manipulation and imaging of neural activity in awake mice. Cryo-EM strikes gold Gold supports nearly eliminate unwanted specimen motion in cryo-electron microscopy, enabling high-resolution structure determination of challenging proteins. CRISPR gain-of-function screens An engineered dCas9-guide RNA complex containing three different transcriptional activation domains achieves consistently high expression of endogenous genes in a genome-wide screen. Community organizers Electrochemical sensors monitor communication between bacterial aggregates. An expanded human interactome An expanded catalog of binary biophysical interactions between human proteins. XFELs probe protein dynamics A new study shows that time-resolved serial femtosecond crystallography can reveal high-resolution intermediates of photoactive yellow protein. Methods in Brief Timed CRISPR action enhances homology-driven repair | Reprogramming methods compared | Bacterial ghosts for cryo-electron tomography | RNA caps in bacteria stabilize transcripts Tools in Brief Nanopore sequencing for bacterial trouble spots | Retinal analogs for optogenetics | A multifocal approach to whole-cell super-resolution imaging | Wireless electrophysiology in behaving animals Methods JOBS of the week Postdoctoral in Bioinformatics Dartmouth College Postdoctoral Fellow in Environmental Metabolomics University of Toronto PhD Students in Molecular Medicine Institute for Molecular Medicine Finland (FIMM) Post-doc Associate in Computational Biology University of Southern California PhD students ETH Zurich More Science jobs from Methods EVENT EMBO Practical Course: Current Methods in Cell Biology 14th Sept - 22nd Sept 2015 Heidelberg, Germany More science events from Technology Feature Top Stem cells: disease models that show and tell   pp111 - 114 Vivien Marx doi:10.1038/nmeth.3263 Perspective Top Orchestrating high-throughput genomic analysis with Bioconductor   pp115 - 121 Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson et al. doi:10.1038/nmeth.3252 A Perspective on the open-source and open-development software project Bioconductor provides an overview for prospective users and developers dealing with high-throughput data in genomics and molecular biology. Brief Communications Top DNA nanoswitches: a quantitative platform for gel-based biomolecular interaction analysis   pp123 - 126 Mounir A Koussa, Ken Halvorsen, Andrew Ward and Wesley P Wong doi:10.1038/nmeth.3209 A DNA nanoswitch platform enables inexpensive kinetic and thermodynamic analysis of a range of biomolecular interactions using a simple gel electrophoresis readout. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data   pp127 - 130 Gábor Bunkóczi, Airlie J McCoy, Nathaniel Echols, Ralf W Grosse-Kunstleve, Paul D Adams et al. doi:10.1038/nmeth.3212 An improved analysis approach for single-wavelength anomalous diffraction (SAD)-based macromolecular X-ray structure determination expands the applicability of this phasing method for macromolecules with weak anomalous signals. Fast native-SAD phasing for routine macromolecular structure determination   pp131 - 133 Tobias Weinert, Vincent Olieric, Sandro Waltersperger, Ezequiel Panepucci, Lirong Chen et al. doi:10.1038/nmeth.3211 A native-SAD (single-wavelength anomalous diffraction) data collection strategy enables phasing using anomalous signal from a single native crystal, facilitating straightforward macromolecular X-ray structure determination. Conformal nanopatterning of extracellular matrix proteins onto topographically complex surfaces   pp134 - 136 Yan Sun, Quentin Jallerat, John M Szymanski and Adam W Feinberg doi:10.1038/nmeth.3210 Patterning on topography printing allows nano- to microscale patterning of extracellular matrix proteins onto topologically complex surfaces. Genetic targeting of chemical indicators in vivo   pp137 - 139 Guoying Yang, Fernanda de Castro Reis, Mayya Sundukova, Sofia Pimpinella, Antonino Asaro et al. doi:10.1038/nmeth.3207 Snap-tag reporter mice allow flexible yet efficient targeting of chemical indicators to genetically labeled cells in vivo. With this strategy, cells can either be labeled fluorescently or ablated using the same reporter. Articles Top Simultaneous all-optical manipulation and recording of neural circuit activity with cellular resolution in vivo   pp140 - 146 Adam M Packer, Lloyd E Russell, Henry W P Dalgleish and Michael Häusser doi:10.1038/nmeth.3217 Here, the authors present an approach for the simultaneous optogenetic manipulation and recording of neural activity at cellular resolution using two-photon microscopy and apply their strategy in the mouse barrel cortex. Quantitative profiling of initiating ribosomes in vivo   pp147 - 153 Xiangwei Gao, Ji Wan, Botao Liu, Ming Ma, Ben Shen et al. doi:10.1038/nmeth.3208 QTI-seq (quantitative translation initiation sequencing) maps the position of the start codon and thus allows the determination of initiation efficiency in response to various stimuli, such as starvation, in cell culture and in vivo. Selecting causal genes from genome-wide association studies via functionally coherent subnetworks   pp154 - 159 Murat Taşan, Gabriel Musso, Tong Hao, Marc Vidal, Calum A MacRae et al. doi:10.1038/nmeth.3215 The prix fixe strategy and software uses cofunction networks to identify causal genes among candidate genes in disease-associated loci from genome-wide association studies. Corrigenda Top Corrigendum: From genes to protein mechanics on a chip   p160 Marcus Otten, Wolfgang Ott, Markus A Jobst, Lukas F Milles, Tobias Verdorfer et al. doi:10.1038/nmeth0215-160a Corrigendum: Mining the O-glycoproteome using zinc-finger nuclease-glycoengineered SimpleCell lines   p160 Catharina Steentoft, Sergey Y Vakhrushev, Malene B Vester-Christensen, Katrine T-B G Schjoldager, Yun Kong et al. doi:10.1038/nmeth0215-160d Corrigendum: Time-resolved crystallography using the Hadamard transform   p160 Briony A Yorke, Godfrey S Beddard, Robin L Owen and Arwen R Pearson doi:10.1038/nmeth0215-160e Errata Top Erratum: Onco-proteogenomics: cancer proteomics joins forces with genomics   p160 Javier A Alfaro, Ankit Sinha, Thomas Kislinger and Paul C Boutros doi:10.1038/nmeth0215-160b Erratum: Light microscopy with lattices   p160 Nina Vogt doi:10.1038/nmeth0215-160c Application Note Top Fast and convenient 5-hydroxymethylcytosine enrichment workflow for next-generation sequencing    Milda Kaniušaite, Eimantas Astromskas, Gediminas Alzbutas, Renata Bružaitė and Arūnas Lagunavičius Top Advertisement Nature Collections  NOBEL PRIZE IN CHEMISTRY 2014  The 2014 Nobel Prize in Chemistry was awarded for the development of super-resolution fluorescence microscopy. 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