Thursday, June 27, 2013

Nature Methods Contents: July 2013 Volume 10 pp 591 - 682

Nature Methods

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TABLE OF CONTENTS

July 2013 Volume 10, Issue 7

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

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InThisIssue   

Editorial

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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.

This Month

Top

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.

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.

Correspondence

Top

NetGestalt: integrating multidimensional omics data over biological networks   pp597 - 598
Zhiao Shi, Jing Wang and Bing Zhang
doi:10.1038/nmeth.2517

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

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

Research Highlights

Top

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.

Methods
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Methods in Brief

Top

Multiplex mouse genetic engineering with CRISPR | Tissue molding in the dish | Profiling transcriptional heterogeneity | Functional thymic progenitors from stem cells

Tools in Brief

Top

Imaging when cells get together | Visualizing high-dimensional data | Hyperpolarized silicon particles for MRI | Active T cells on the run

Technology Feature

Top

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.

News and Views

Top

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.

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.

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.

Analysis

Top

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.

Brief Communications

Top

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.

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

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

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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

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.

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.

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

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.

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.

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

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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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