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TABLE OF CONTENTS
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July 2013 Volume 10, Issue 7 |
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| In This Issue Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Analysis Brief Communications Articles Application Note
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In This Issue | Top |
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InThisIssue |
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Editorial | Top |
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Sharing blueprints for better research p591 doi:10.1038/nmeth.2554 Like software before it, open-source hardware promises to encourage collaborative tinkering and promote access to innovative technologies.
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This Month | Top |
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The author file: Chris Toumazou p593 Vivien Marx doi:10.1038/nmeth.2550 Inspired by his son, an electrical engineer brings microchip technology and portability to biology.
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Points of view: Multidimensional data p595 Martin Krzywinski and Erica Savig doi:10.1038/nmeth.2531 Visually organize complex data by mapping them onto familiar representations of biological systems.
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Correspondence | Top |
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NetGestalt: integrating multidimensional omics data over biological networks pp597 - 598 Zhiao Shi, Jing Wang and Bing Zhang doi:10.1038/nmeth.2517
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OpenSPIM: an open-access light-sheet microscopy platform pp598 - 599 Peter G Pitrone, Johannes Schindelin, Luke Stuyvenberg, Stephan Preibisch and Michael Weber et al. doi:10.1038/nmeth.2507
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OpenSpinMicroscopy: an open-source integrated microscopy platform pp599 - 600 Emilio J Gualda, Tiago Vale, Pedro Almada, Jose A Feijo and Gabriel G Martins et al. doi:10.1038/nmeth.2508
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Research Highlights | Top |
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Embryos under the X-ray X-ray imaging using synchrotron radiation reveals the cellular choreography of a developing frog embryo in spectacular detail. | Fly walk Two methodological advances enable tracking of the walking behavior of fruit flies at single-leg resolution. | Matching marks with mechanisms Reagents that recognize specific chemical modifications while ignoring the surrounding protein offer valuable proteomic insights. | Human stem cells from cloned embryos Methodological optimization makes possible the long-awaited derivation of human embryonic stem cells from embryos obtained with somatic cell nuclear transfer. | Peptides aplenty A large library of peptides and phosphopeptides, along with their tandem mass spectra, serves as a resource for the proteomics field. | Assembling genomes in microbial communities Binning based on differential read coverage, rather than sequence composition, allows separation of metagenomic sequence reads into species-level clusters that can be assembled into single chromosomes. |
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Methods in Brief | Top |
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Multiplex mouse genetic engineering with CRISPR | Tissue molding in the dish | Profiling transcriptional heterogeneity | Functional thymic progenitors from stem cells |
Tools in Brief | Top |
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Imaging when cells get together | Visualizing high-dimensional data | Hyperpolarized silicon particles for MRI | Active T cells on the run |
Technology Feature | Top |
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Data visualization: ambiguity as a fellow traveler pp613 - 615 Vivien Marx doi:10.1038/nmeth.2530 Being sure is good; being uncertain is not necessarily bad. Research teams are working to render uncertainty visual.
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News and Views | Top |
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Another transistor-based revolution: on-chip qPCR pp617 - 618 Carlotta Guiducci and Fabio M Spiga doi:10.1038/nmeth.2525 More than 40 years after the invention of semiconductor pH microtransducers known as ISFETs, this transistor-based technology may revolutionize quantitative PCR.
See also: Article by Toumazou et al. |
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Building a better stop sign: understanding the signals that terminate transcription pp618 - 619 Rachel Anne Mooney and Robert Landick doi:10.1038/nmeth.2527 A synthetic biology terminator toolkit enables more sophisticated circuit design and gives insight into the mechanism of transcriptional termination.
See also: Article by Chen et al. |
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Eavesdropping on PTM cross-talk through serial enrichment pp620 - 621 Kristofor Webb and Eric J Bennett doi:10.1038/nmeth.2526 Two approaches to serially enrich protein post-translational modifications allow the detection of multiple modifications in a single biological sample using mass spectrometry.
See also: Brief Communication by Mertins et al. | Article by Swaney et al. |
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Analysis | Top |
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Comparative analysis of RNA sequencing methods for degraded or low-input samples pp623 - 629 Xian Adiconis, Diego Borges-Rivera, Rahul Satija, David S DeLuca and Michele A Busby et al. doi:10.1038/nmeth.2483 This comparison of five RNA-seq library preparation methods highlights metrics for assessing the suitability of the methods for samples with low amounts of RNA and/or those with low-quality RNA.
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Brief Communications | Top |
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MicroRNA target site identification by integrating sequence and binding information pp630 - 633 William H Majoros, Parawee Lekprasert, Neelanjan Mukherjee, Rebecca L Skalsky and David L Corcoran et al. doi:10.1038/nmeth.2489 The integration of microRNA target sequence features and data from cross-linking and immunoprecipitation of Argonaute proteins, implemented in the hidden Markov model-based framework MUMMIE, provides accurate prediction of microRNA targets.
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Integrated proteomic analysis of post-translational modifications by serial enrichment pp634 - 637 Philipp Mertins, Jana W Qiao, Jinal Patel, Namrata D Udeshi and Karl R Clauser et al. doi:10.1038/nmeth.2518 A mass spectrometry-based method using serial enrichments of different post-translational modifications (SEPTM) enables high-coverage proteomic analysis of multiple PTMs from a single biological sample.
See also: News and Views by Webb & Bennett |
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Whole-rat conditional gene knockout via genome editing pp638 - 640 Andrew J Brown, Daniel A Fisher, Evguenia Kouranova, Aaron McCoy and Kevin Forbes et al. doi:10.1038/nmeth.2516 Conditional genetic knockout is achieved in the rat by using zinc-finger nucleases to place loxP sites at specific genomic locations and introducing Cre recombinase under the control of a native promoter.
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Articles | Top |
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Simultaneous DNA amplification and detection using a pH-sensing semiconductor system pp641 - 646 Christofer Toumazou, Leila M Shepherd, Samuel C Reed, Ginny I Chen and Alpesh Patel et al. doi:10.1038/nmeth.2520 A semiconductor chip, coupled to an ion-sensitive field effect transistor (ISFET) pH sensor, can amplify and quantitate DNA in real time without dyes, cameras and external heating devices.
See also: News and Views by Guiducci & Spiga |
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Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides pp647 - 652 Cosimo Ducani, Corinna Kaul, Martin Moche, William M Shih and Bjorn Hogberg doi:10.1038/nmeth.2503 A method for enzymatically producing long, high-purity, single-stranded DNA oligonucleotides should find many applications in basic research, in DNA nanotechnology and in clinical fields.
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Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms pp653 - 658 Fang Huang, Tobias M P Hartwich, Felix E Rivera-Molina, Yu Lin and Whitney C Duim et al. doi:10.1038/nmeth.2488 Algorithms that account for and overcome the intrinsic pixel-dependent readout noise from scientific complementary metal-oxide semiconductor (sCMOS) cameras prevent localization artifacts and avoid substantial compromises in localization uncertainty in single-molecule imaging. When combined with multi-emitter fitting, sCMOS cameras allow video-rate single-molecule switching nanoscopy.
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Characterization of 582 natural and synthetic terminators and quantification of their design constraints pp659 - 664 Ying-Ja Chen, Peng Liu, Alec A K Nielsen, Jennifer A N Brophy and Kevin Clancy et al. doi:10.1038/nmeth.2515 For genetically engineered circuits, the movement of RNA polymerase across the DNA during transcription needs to be tightly controlled. A large library of strong terminators will make circuit design easier and more efficient.
See also: News and Views by Mooney & Landick |
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The Caenorhabditis elegans Lifespan Machine pp665 - 670 Nicholas Stroustrup, Bryne E Ulmschneider, Zachary M Nash, Isaac F Lopez-Moyado and Javier Apfeld et al. doi:10.1038/nmeth.2475 Automated methods are described for the determination of survival curves in C. elegans, enabling rapid and statistically rigorous studies of lifespan in this organism.
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High-throughput tetrad analysis pp671 - 675 Catherine L Ludlow, Adrian C Scott, Gareth A Cromie, Eric W Jeffery and Amy Sirr et al. doi:10.1038/nmeth.2479 Barcode-enabled sequencing of tetrads (BEST) allows isolation and genotyping of individual yeast spores while maintaining their tetrad relationships.
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Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation pp676 - 682 Danielle L Swaney, Pedro Beltrao, Lea Starita, Ailan Guo and John Rush et al. doi:10.1038/nmeth.2519 Two methods for identifying protein isoforms that are concurrently phosphorylated and ubiquitylated are applied in yeast to identify phosphorylation sites that regulate ubiquitin proteasome-mediated proteome degradation.
See also: News and Views by Webb & Bennett |
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Application Note | Top |
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Improved RNA-seq of blood-derived RNA increases gene discovery and coverage Jim Pease and Cris Kinross RNA-seq of blood-derived RNA can aid discovery of the cause of disease, as well as preclinical research. However, the high content of globin mRNA and ribosomal RNA (rRNA) in blood samples limits the detection of rare transcripts and splice variants. The ScriptSeq™ Complete Kit (Blood) is a new method to prepare directional RNA-seq libraries that are virtually free of globin mRNA and rRNA contamination and exhibit high detection of reference and novel genes.
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