Nature Methods Contents: January 2015 Volume 12 pp 1 - 91

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Advertisement Free Trial Program: The DeNovix DS-11 Spectrophotometer is the next generation UV-Vis system for rapid quantification of 1uL nucleic acid and protein samples. The Android™ based stand-alone instrument includes intuitive apps, full-spectrum (190-840 nm) analysis, a 7" HD touchscreen and Wi-Fi, USB and ethernet connectivity. Trade-in programs available. TABLE OF CONTENTS January 2015 Volume 12, Issue 1 In This Issue Special Feature Editorial This Month Correspondence Research Highlights News Feature Commentaries Methods to Watch Technology Feature News and Views Brief Communications Articles Subscribe   Facebook   RSS   Recommend to library   Twitter   In This Issue Top InThisIssue    Special Feature Top Method of the Year 2013 Contents Editorial News Feature Commentary Methods to Watch Our Method of the Year 2014 goes to light-sheet fluorescence microscopy. This series of papers discusses how this technology, in combination with increasingly sophisticated cameras and powerful computing, is dramatically changing and enabling the imaging of living biological samples from developing embryos to functioning brains. We also highlight methods worth watching in the upcoming years. Editorial Top Special feature: Method of the Year 2014 Method of the Year 2014   p1 doi:10.1038/nmeth.3251 Light-sheet fluorescence microscopy can image living samples in three dimensions with relatively low phototoxicity and at high speed. This Month Top The Author File: Graham Johnson   p3 Vivien Marx doi:10.1038/nmeth.3221 An illustrator drops the barriers between work and play with software to model and explore cells. Points of significance: Sources of variation   pp5 - 6 Naomi Altman and Martin Krzywinski doi:10.1038/nmeth.3224 Correspondence Top The I-TASSER Suite: protein structure and function prediction   pp7 - 8 Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson et al. doi:10.1038/nmeth.3213 Research Highlights Top Transparency in large tissue samples Recent improvements in tissue 'clearing' techniques permit their application to a variety of tissues and their combination with immunohistochemistry. MinION takes center stage One of the first genome sequences produced on a handheld nanopore sequencer shows the platform's potential as well as its challenges. Bacterial recall Bacterial populations get outfitted with stable analog genetic memory. A bumpy, holey method to probe proteins A 'bump-and-hole' strategy probes individual BET bromodomains. A global look at local translation Proximity-specific ribosome profiling reveals the exquisite specificity of translation at the endoplasmic reticulum and mitochondrial outer membrane. Methods in Brief A high-resolution look at DNA demethylation | A powerful haploid tool for plant genetics | Proteins masquerading as DNA for efficient delivery | Solutions for structural heterogeneity in diffractive imaging Tools in Brief Chemical decaging in live cells | A microscope with two arms | Finding new RNA mimics of GFP | Controlled protein degradation in bacteria Methods JOBS of the week Postdoctoral position “Coordinator Biodiversity Informatics” m / f Senckenberg Gesellschaft fuer Naturforschung Faculty Positions Chemical Science King Abdullah University of Science and Technology (KAUST) Postdoctoral Researcher Cornell University Bioinformatics Speacialist I Massachusetts General Hospital Laboratory Technician Cardiocentro Ticino - Swiss Institute for Regenerative Medicine More Science jobs from Methods EVENT 2015 Joint ICTP-IAEA Advanced School and Workshop on Modern Methods in Plasma Spectroscopy 16th March - 27th March 2015 Trieste, Italy More science events from News Feature Top Special feature: Method of the Year 2014 Pump up the volume   pp19 - 22 doi:10.1038/nmeth.3220 Light-sheet fluorescence microscopy techniques are enabling researchers to achieve dynamic, long-term imaging and three-dimensional reconstruction of specimens ranging from single cells to whole embryos. Commentaries Top Special feature: Method of the Year 2014 Light-sheet fluorescence microscopy for quantitative biology   pp23 - 26 Ernst H K Stelzer doi:10.1038/nmeth.3219 In light sheet-based fluorescence microscopy (LSFM), optical sectioning in the excitation process minimizes fluorophore bleaching and phototoxic effects. Because biological specimens survive long-term three-dimensional imaging at high spatiotemporal resolution, LSFM has become the tool of choice in developmental biology. Special feature: Method of the Year 2014 Light-sheet imaging for systems neuroscience   pp27 - 29 Philipp J Keller, Misha B Ahrens and Jeremy Freeman doi:10.1038/nmeth.3214 Developments in electrical and optical recording technology are scaling up the size of neuronal populations that can be monitored simultaneously. Light-sheet imaging is rapidly gaining traction as a method for optically interrogating activity in large networks and presents both opportunities and challenges for understanding circuit function. Special feature: Method of the Year 2014 Guide to light-sheet microscopy for adventurous biologists   pp30 - 34 Emmanuel G Reynaud, Jan Peychl, Jan Huisken and Pavel Tomancak doi:10.1038/nmeth.3222 Ten years of development in light-sheet microscopy have led to spectacular demonstrations of its capabilities. The technology is ready to assist biologists in tackling scientific problems, but are biologists ready for it? Here we discuss the interdisciplinary challenges light-sheet microscopy presents for biologists and highlight available resources. Methods to Watch Top Special feature: Method of the Year 2014 DIA mass spectrometry   p35 Allison Doerr doi:10.1038/nmeth.3234 Data-independent acquisition (DIA) mass spectrometry may change how proteomic data are generated. Special feature: Method of the Year 2014 Understanding noncoding RNAs   p35 Nicole Rusk doi:10.1038/nmeth.3235 Methods to profile and characterize the function of noncoding RNAs will emerge. Special feature: Method of the Year 2014 In vivo voltage sensors   p36 Nina Vogt doi:10.1038/nmeth.3236 Genetically encoded voltage indicators are on the brink of allowing neuronal activity to be directly imaged in vivo. Special feature: Method of the Year 2014 Next-generation CRISPRs   p36 Nicole Rusk doi:10.1038/nmeth.3237 As the CRISPR-Cas system matures, specificity, efficacy and maybe even a eukaryotic nuclease are being considered. Special feature: Method of the Year 2014 Structures from tiny crystals   p37 Allison Doerr doi:10.1038/nmeth.3238 Protein structures can be determined from microcrystals using X-ray and electron diffraction. Special feature: Method of the Year 2014 Super-resolution CLEM   p37 Natalie de Souza doi:10.1038/nmeth.3239 Correlated light and electron microscopy (CLEM) is particularly powerful when applied in super-resolution. Special feature: Method of the Year 2014 Nanopores for proteins   p38 Tal Nawy doi:10.1038/nmeth.3240 Nanopores hold promise for single-protein characterization. Special feature: Method of the Year 2014 Imaging at depth   p38 Nina Vogt doi:10.1038/nmeth.3241 A closer look into the depths of organs such as the brain is within reach. Technology Feature Top Biophysics: using sound to move cells   pp41 - 44 Vivien Marx doi:10.1038/nmeth.3218 Moving and sorting cells with sound are a few of the possible applications for this no-contact technique. News and Views Top Toward high-throughput biomechanical phenotyping of single molecules   pp45 - 46 David Alsteens, Savaş Tay and Daniel J Müller doi:10.1038/nmeth.3216 Two high-throughput single-molecule force spectroscopy platforms expand the reach of this technology for biomechanical molecular phenotyping. See also: Brief Communication by Sitters et al. Brief Communications Top Acoustic force spectroscopy   pp47 - 50 Gerrit Sitters, Douwe Kamsma, Gregor Thalhammer, Monika Ritsch-Marte, Erwin J G Peterman et al. doi:10.1038/nmeth.3183 Acoustic force spectroscopy applies acoustic forces across a large dynamic range for highly multiplexed single-molecule measurements in a simple, compact setup. See also: News and Views by Alsteens et al. Directed evolution of APEX2 for electron microscopy and proximity labeling   pp51 - 54 Stephanie S Lam, Jeffrey D Martell, Kimberli J Kamer, Thomas J Deerinck, Mark H Ellisman et al. doi:10.1038/nmeth.3179 A genetically encoded peroxidase with improved sensitivity, APEX2, is reported for electron microscopy and proximity labeling at low expression levels. LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification   pp55 - 58 Pitter F Huesgen, Philipp F Lange, Lindsay D Rogers, Nestor Solis, Ulrich Eckhard et al. doi:10.1038/nmeth.3177 The Archaea metalloproteinase LysargiNase increases proteome coverage, identifies more C-terminal peptides from proteins and improves methylated peptide identification. Fast and sensitive protein alignment using DIAMOND   pp59 - 60 Benjamin Buchfink, Chao Xie and Daniel H Huson doi:10.1038/nmeth.3176 The open-source DIAMOND software provides protein alignment that is 20,000 times faster on short reads than BLASTX at similar sensitivity, for rapid analysis of large metagenomics data sets on a desktop computer. Grease matrix as a versatile carrier of proteins for serial crystallography   pp61 - 63 Michihiro Sugahara, Eiichi Mizohata, Eriko Nango, Mamoru Suzuki, Tomoyuki Tanaka et al. doi:10.1038/nmeth.3172 Serial femtosecond crystallography experiments with diverse protein microcrystal suspensions are facilitated using a grease matrix as a carrier medium for sample injection. Articles Top Rational design of a high-affinity, fast, red calcium indicator R-CaMP2   pp64 - 70 Masatoshi Inoue, Atsuya Takeuchi, Shin-ichiro Horigane, Masamichi Ohkura, Keiko Gengyo-Ando et al. doi:10.1038/nmeth.3185 An improved genetically encoded red calcium sensor enables the monitoring of neuronal activity in cell culture and in vivo. R-CaMP2 has fast kinetics and a high affinity to calcium and can follow action potentials up to 40 Hz. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes   pp71 - 78 Wenxiu Ma, Ferhat Ay, Choli Lee, Gunhan Gulsoy, Xinxian Deng et al. doi:10.1038/nmeth.3205 Targeted DNase Hi-C uses DNase I instead of restriction enzymes for chromatin fragmentation and improves the resolution of chromatin interaction maps. In silico prediction of physical protein interactions and characterization of interactome orphans   pp79 - 84 Max Kotlyar, Chiara Pastrello, Flavia Pivetta, Alessandra Lo Sardo, Christian Cumbaa et al. doi:10.1038/nmeth.3178 This paper presents FpClass, a prediction method for physical protein-protein interactions. The method is benchmarked against experimental data and is used to predict, among others, partners of interactome 'orphans'. cellPACK: a virtual mesoscope to model and visualize structural systems biology   pp85 - 91 Graham T Johnson, Ludovic Autin, Mostafa Al-Alusi, David S Goodsell, Michel F Sanner et al. doi:10.1038/nmeth.3204 Software to model, pack and integrate biological structures at the scale of macromolecular complexes and cellular organelles is described. It is applied in several contexts, including hypothesis generation and testing. Top   Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. 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