Nature Methods Contents: November 2014 Volume 11 pp 1077 - 1181

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Advertisement Complete Genome Editing Solutions GeneCopoeia provides complete genome editing solutions, including CRISPR products & services TALEN & TALE-TF construction services Donor construction service & cloning vectors Safe harbor knockin kits and clones Stable cell line services Transgenic mouse services Register our FREE webinar to learn more.  TABLE OF CONTENTS November 2014 Volume 11, Issue 11 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Perspective Review Brief Communications Articles Advertisement Greiner Bio-One Microplates for Intelligent Sample Storage High performance chemical/thermal resistant cycloolefin & polypropylene microplates for acoustic dispensing 384 & 1536 well polypropylene microplates for high-throughput drug discovery 96 well polypropylene microplates for classical applications with enhanced resistance and well-volume capacity Read more: http://www.gbo.com/microplates Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Optimize your SPR results — Tap Reichert's Knowledge! Check out articles on setting up successful SPR experiments including: Minimize the Influence of Mass Transport, Reduce Non-specific Binding, Overcome Regeneration Problems. Or, contact Reichert about your research to see how SPR can get results for you.  ReichertSPR.com   Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast on: A Closer Look at Cell Death with Imaging Flow Cytometry Wednesday, November 5th at 9AM PST, 12PM EST, 5PM GMT, 6PM CET  Register for the webcast and live Q and A session  Sponsored by: EMD Millipore      In This Issue Top InThisIssue    Editorial Top No money, no research   p1077 doi:10.1038/nmeth.3171 For innovations in basic science to continue at the pace of previous decades, a solid funding strategy is needed. This Month Top The Author File: Alexei Vyssotski   p1079 Vivien Marx doi:10.1038/nmeth.3150 An avian backpack for discerning individual zebra finches' songs and studying cognition comes to Switzerland via Novosibirsk, Russia. Correspondence Top In vivo imaging of oligodendrocytes with sulforhodamine 101   pp1081 - 1082 Robert A Hill and Jaime Grutzendler doi:10.1038/nmeth.3140 DeeZ: reference-based compression by local assembly   pp1082 - 1084 Faraz Hach, Ibrahim Numanagic and S Cenk Sahinalp doi:10.1038/nmeth.3133 Research Highlights Top Versatile clusters formed by light As a tool for light-dependent protein clustering, cryptochrome offers many opportunities to manipulate and query processes in the cell. Voltage sensors revisited Imaging of electrical activity in vivo in Caenorhabditis elegans is possible with the improved genetically encoded voltage sensors Archer1 and Archer2. Probing the protein structure-ome Protein structure changes can be charted on a global scale with a method that couples limited proteolysis with mass spectrometry-based proteomics. Cleaving RNA with Cas9 CRISPR-Cas9 is not just for DNA anymore: RNA targeting is also achievable. Protein interactions in situ A twist on the MAPPIT method enables studying protein-protein interactions within living mammalian cells. Rereading familiar messages Two surveys of the transcriptome hint at unexpected diversity in the breadth of mRNA modifications. Prostate cancer in 3D Researchers grow genetically stable organoids from mouse and human prostate cells in the lab and establish patient-derived lines that model prostate cancer. Methods in Brief Single-molecule protein interaction detection | Super-resolution imaging in live animals | Phosphohistidine proteomics | Large-scale transcription factor binding prediction Tools in Brief Improved guide RNA design | A mass cytometry activity-based probe | Seeking genetic variants that affect splicing | A universal voltage indicator Methods JOBS of the week Informatics and Computational Toxicology Post-doctoral Fellow at NCATS National Center for Advancing Translational Science, NIH Four-Year Science PhD Studentships Institute of Cancer Research (ICR) Post-doctoral position in Computational Biology University of British Columbia (UBC) Bioinformatician (m / f) Institute of Molecular Biology gGmbH Bioinformatics Focus: Pluripotent Stem Cell Laboratory University of California-San Diego More Science jobs from Methods EVENT Hybrid Methods in Structural Biology 4th - 8th March 2015 Tahoe City, USA More science events from Technology Feature Top Neurobiology: rethinking the electrode   pp1099 - 1103 Vivien Marx doi:10.1038/nmeth.3149 Electrodes and electrode arrays to record from neurons come in an increasing number of shapes and sizes, and engineers are continuously adding capabilities. News and Views Top Expanding the synthetic ribonucleoprotein world in cells   pp1105 - 1106 Kei Endo, Callum Parr and Hirohide Saito doi:10.1038/nmeth.3148 Protein-responsive ribozymes generated by a streamlined design process will expand the plug-and-play toolbox for synthetic biologists. See also: Article by Auslander et al. Perspective Top Onco-proteogenomics: cancer proteomics joins forces with genomics   pp1107 - 1113 Javier A Alfaro, Ankit Sinha, Thomas Kislinger and Paul C Boutros doi:10.1038/nmeth.3138 Tumor-specific peptides missed in standard mass spectrometry-based workflows can be identified by integrating genomic information to interpret proteomic data. As discussed in this Perspective, an onco-proteogenomic approach to study tumor biology could have a substantial impact on cancer research. Also in this issue, Nesvizhskii reviews proteogenomic technology. Review Top Proteogenomics: concepts, applications and computational strategies   pp1114 - 1125 Alexey I Nesvizhskii doi:10.1038/nmeth.3144 A proteogenomic approach to analyzing mass spectrometry-based proteomic data enables the discovery of novel peptides, provides peptide-level evidence of gene expression, and assists in refining gene models. Strategies for building custom sequence databases, applications benefitting from a proteogenomic approach, and challenges in interpreting data are discussed in this Review. Also in this issue, Alfaro et al. discuss the use of proteogenomic approaches for studying cancer biology. Brief Communications Top From genes to protein mechanics on a chip   pp1127 - 1130 Marcus Otten, Wolfgang Ott, Markus A Jobst, Lukas F Milles, Tobias Verdorfer et al. doi:10.1038/nmeth.3099 A microfluidic chip is used to construct a microarray of proteins, each labeled with a dockerin tag, for high-throughput single-molecule force spectroscopy experiments using a single cohesin-modified cantilever. Time-resolved crystallography using the Hadamard transform   pp1131 - 1134 Briony A Yorke, Godfrey S Beddard, Robin L Owen and Arwen R Pearson doi:10.1038/nmeth.3139 A method based on the Hadamard transform is shown to enable time-resolved X-ray crystallography measurements of protein dynamics at standard synchrotron sources. Reconstruction of vocal interactions in a group of small songbirds   pp1135 - 1137 Victor N Anisimov, Joshua A Herbst, Andrei N Abramchuk, Alexander V Latanov, Richard H R Hahnloser et al. doi:10.1038/nmeth.3114 Communications between animals such as zebra finches can be discriminated with back-attached acceleration recorders. In contrast to microphones, these devices record the carrier's signals only, allowing a more precise analysis of individual vocalizations during social interactions. Comprehensive analysis of DNA methylation data with RnBeads   pp1138 - 1140 Yassen Assenov, Fabian Muller, Pavlo Lutsik, Jörn Walter, Thomas Lengauer et al. doi:10.1038/nmeth.3115 RnBeads facilitates user-friendly analysis of large-scale DNA methylation data and fosters reproducibility and data sharing. 3D genome reconstruction from chromosomal contacts   pp1141 - 1143 Annick Lesne, Julien Riposo, Paul Roger, Axel Cournac and Julien Mozziconacci doi:10.1038/nmeth.3104 ShRec3D (shortest-path reconstruction in 3D) converts sparse chromosome contact maps into spatial distances followed by 3D reconstruction. Binning metagenomic contigs by coverage and composition   pp1144 - 1146 Johannes Alneberg, Brynjar Smári Bjarnason, Ino de Bruijn, Melanie Schirmer, Joshua Quick et al. doi:10.1038/nmeth.3103 The CONCOCT software performs unsupervised binning of metagenomic contigs across multiple samples to allow better genome reconstruction from microbial communities. Advertisement News Alert: Empirical Bioscience provides the purest reagents, assayed for the right concentrations and components and vigorously tested. Their products are manufactured using proprietary technology and rigorous lot controls. Researchers say Empirical reagents yield "outstanding results they don't see using other reagents." Click for a FREE SAMPLE and Observe the Difference.   Articles Top A quantitative framework for the forward design of synthetic miRNA circuits   pp1147 - 1153 Ryan J Bloom, Sally M Winkler and Christina D Smolke doi:10.1038/nmeth.3100 A model that incorporates the quantitative relationship between microRNA and the expression of its target gene achieves predictable and robust genetic circuits. A general design strategy for protein-responsive riboswitches in mammalian cells   pp1154 - 1160 Simon Ausländer, Pascal Stücheli, Charlotte Rehm, David Ausländer, Jörg S Hartig et al. doi:10.1038/nmeth.3136 Designer ribozymes show protein-responsive translational control and can be combined with transcriptional control elements to program complex gene circuits. See also: News and Views by Endo et al. Intracellular autofluorescence: a biomarker for epithelial cancer stem cells   pp1161 - 1169 Irene Miranda-Lorenzo, Jorge Dorado, Enza Lonardo, Sonia Alcala, Alicia G Serrano et al. doi:10.1038/nmeth.3112 This paper reports an autofluorescent signal in cancer stem cells within epithelial tumors and describes its use as a marker to isolate and study these cells. Small molecules facilitate rapid and synchronous iPSC generation   pp1170 - 1176 Ori Bar-Nur, Justin Brumbaugh, Cassandra Verheul, Effie Apostolou, Iulian Pruteanu-Malinici et al. doi:10.1038/nmeth.3142 This paper reports a combination of two small molecules for very efficient mouse cell reprogramming to induced pluripotency, achieving close to 100% reprogramming within a few days for some cell types. Nanoparticle vesicle encoding for imaging and tracking cell populations   pp1177 - 1181 Paul Rees, John W Wills, M Rowan Brown, James Tonkin, Mark D Holton et al. doi:10.1038/nmeth.3105 Quantum dots sequentially loaded into cells are used to generate barcodes that can identify thousands of individual cells within a population and that can be used to track cells over many hours. Advertisement The QX200™ AutoDG™ Droplet Digital™ PCR system is here. The new automated droplet generator simplifies the ddPCR™ workflow, making digital PCR both scalable and practical. Learn more.   Top Advertisement Poster & Webcast on CRISPR-Cas technology from Nature Publishing Group Nature Reviews Microbiology  FREE POSTER CRISPR-Cas: extraordinary editing  Presented by Nature Biotechnology  Webcast and live Q&A: A practical guide to CRISPR technology Date: November 25, 2014 Poster and Webcast produced with support from  OriGene, Your Gene Company      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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