Friday, August 28, 2015

Nature Methods Contents: September 2015 Volume 12 pp 795 - 893

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TABLE OF CONTENTS

September 2015 Volume 12, Issue 9

In This Issue
Editorial
This Month
Correspondence
Research Highlights
Technology Feature
News and Views
Brief Communications
Articles
Corrigendum
Errata
Application Note
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In This Issue

Top

In This Issue   

Editorial

Top

Empowering citizen scientists   p795
doi:10.1038/nmeth.3577
Scientists should consider engaging more with the DIYbio community.

This Month

Top

The Author File: Daniel J. Muller   p797
Vivien Marx
doi:10.1038/nmeth.3557
A new way to quantify ligand-binding interactions of individual membrane proteins.

Points of Significance: Bayesian networks   pp799 - 800
Jorge López Puga, Martin Krzywinski and Naomi Altman
doi:10.1038/nmeth.3550

Correspondence

Top

Validating subcellular thermal changes revealed by fluorescent thermosensors   pp801 - 802
Shigeki Kiyonaka, Reiko Sakaguchi, Itaru Hamachi, Takashi Morii, Takenao Yoshizaki et al.
doi:10.1038/nmeth.3548

See also: Correspondence by Suzuki et al. | Correspondence by Baffou et al.

The 105 gap issue between calculation and measurement in single-cell thermometry   pp802 - 803
Madoka Suzuki, Vadim Zeeb, Satoshi Arai, Kotaro Oyama and Shin'ichi Ishiwata
doi:10.1038/nmeth.3551

See also: Correspondence by Baffou et al. | Correspondence by Kiyonaka et al.

Reply to: "Validating subcellular thermal changes revealed by fluorescent thermosensors" and "The 105 gap issue between calculation and measurement in single-cell thermometry"   p803
Guillaume Baffou, Hervé Rigneault, Didier Marguet and Ludovic Jullien
doi:10.1038/nmeth.3552

See also: Correspondence by Suzuki et al. | Correspondence by Kiyonaka et al.

Research Highlights

Top

Building lasers inside cells
Optical microresonators form stand-alone intracellular lasers.

Algae are the best engineers of optogenetic inhibitors
Anion channelrhodopsins, recently discovered in cryptophyte algae, can be used as highly efficient optogenetic tools to inhibit neurons.

Where the G-quadruplexes are
A new sequencing method identifies G-quadruplexes genome wide.

Navigating the negative-mode proteome
A negative-mode mass spectrometry approach characterizes intractable parts of the proteome.

Stop the presses
A self-cleaving degradation tag allows researchers to quickly and reversibly shut down protein production.

Micro-C maps of genome structure
A method using micrococcal nuclease for chromatin fragmentation gives a high-resolution view of 3D genome structure.

RNA catch and release
The binding of single RNA molecules to individual proteins can be observed in the subcellular compartments of living cells.

Methods in Brief

Deep learning to predict sequence specificity | Universal parts | Cardiovascular progenitors from human stem cells | Wireless pharmacology and optogenetics

Tools in Brief

Finding more ribozymes | Fluorescent proteins for diverse environments | A light switch for microtubule dynamics | Introducing the BioPlex network

Methods
JOBS of the week
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Technology Feature

Top

Mapping proteins with spatial proteomics   pp815 - 819
Vivien Marx
doi:10.1038/nmeth.3555
A number of techniques address the location of proteins within cells.

News and Views

Top

Removing roadblocks to deep sequencing of modified RNAs   pp821 - 822
Jeremy E Wilusz
doi:10.1038/nmeth.3516
By removing modified nucleotides that block reverse transcriptase, two methods have now made tRNAs amenable to RNA-seq.

See also: Brief Communication by Zheng et al. | Article by Cozen et al.

Brief Communications

Top

Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach   pp823 - 826
Raj Chari, Prashant Mali, Mark Moosburner and George M Church
doi:10.1038/nmeth.3473
Assessing the activity of >1,000 single guide RNAs (sgRNAs) on >1,000 genetic loci with two Cas9 orthologs provides insight into sgRNA design and epigenetic parameters for optimal activity.

Ultrafast, temporally stochastic STED nanoscopy of millisecond dynamics   pp827 - 830
Jale Schneider, Jasmin Zahn, Marta Maglione, Stephan J Sigrist, Jonas Marquard et al.
doi:10.1038/nmeth.3481
Temporally stochastic STED nanoscopy with electro-optical deflector-based scanning allows ultrafast super-resolution imaging. The method was used to monitor vesicles and viruses moving at ~2 μm/s with no motion blur.

EEG and functional ultrasound imaging in mobile rats   pp831 - 834
Lim-Anna Sieu, Antoine Bergel, Elodie Tiran, Thomas Deffieux, Mathieu Pernot et al.
doi:10.1038/nmeth.3506
Functional ultrasound imaging and electroencephalography are combined to assess brain activity in mobile rats. The methodology is applied to the analysis of theta rhythms in a maze task and of epileptic seizures.

Efficient and quantitative high-throughput tRNA sequencing   pp835 - 837
Guanqun Zheng, Yidan Qin, Wesley C Clark, Qing Dai, Chengqi Yi et al.
doi:10.1038/nmeth.3478
The combination of an engineered demthylase and a highly processive reverse transcriptase during tRNA library preparation for high-throughput sequencing allows comprehensive profiling of the small RNAs.

See also: News and Views by Wilusz

Inferring transient particle transport dynamics in live cells   pp838 - 840
Nilah Monnier, Zachary Barry, Hye Yoon Park, Kuan-Chung Su, Zachary Katz et al.
doi:10.1038/nmeth.3483
Single-particle dynamics are analyzed with hidden Markov modeling in combination with Bayesian model selection. This method can annotate both diffusive and directed motion states with single-step resolution.

Phenolyzer: phenotype-based prioritization of candidate genes for human diseases   pp841 - 843
Hui Yang, Peter N Robinson and Kai Wang
doi:10.1038/nmeth.3484
The Phenolyzer software provides prioritized candidate gene lists based on disease and phenotype terms that are entered by users as free text.

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Articles

Top

Imaging G protein-coupled receptors while quantifying their ligand-binding free-energy landscape   pp845 - 851
David Alsteens, Moritz Pfreundschuh, Cheng Zhang, Patrizia M Spoerri, Shaun R Coughlin et al.
doi:10.1038/nmeth.3479
A force-distance curve-based atomic force microscopy method is developed and applied to both image and quantify the ligand-binding free-energy landscape of single protease-activated receptor-1 (PAR1) molecules under physiologically relevant conditions.

Photoactivatable genetically encoded calcium indicators for targeted neuronal imaging   pp852 - 858
Shai Berlin, Elizabeth C Carroll, Zachary L Newman, Hitomi O Okada, Carson M Quinn et al.
doi:10.1038/nmeth.3480
The photoactivatable calcium sensors reported in this paper allow simultaneous highlighting of cellular morphology and recording of calcium activity, which is demonstrated in neuronal cultures, in Drosophila and in zebrafish.

ProteoPlex: stability optimization of macromolecular complexes by sparse-matrix screening of chemical space   pp859 - 865
Ashwin Chari, David Haselbach, Jan-Martin Kirves, Juergen Ohmer, Elham Paknia et al.
doi:10.1038/nmeth.3493
ProteoPlex optimizes buffer conditions for the isolation and purification of macromolecular complexes. The concurrent complex stabilization is beneficial for structure determination using X-ray crystallography or cryo-electron microscopy.

Mutational interference mapping experiment (MIME) for studying RNA structure and function   pp866 - 872
Redmond P Smyth, Laurence Despons, Gong Huili, Serena Bernacchi, Marcel Hijnen et al.
doi:10.1038/nmeth.3490
Functionally important residues in a long RNA can be identified by mutational interference mapping experiment (MIME), a method which uses random mutagenesis of RNA followed by selection for function and high-throughput sequencing.

Real-time imaging of brain activity in freely moving rats using functional ultrasound   pp873 - 878
Alan Urban, Clara Dussaux, Guillaume Martel, Clément Brunner, Emilie Mace et al.
doi:10.1038/nmeth.3482
A miniaturized ultrasound probe enables functional brain imaging in freely behaving rats. The large field of view and deep penetration makes this technique complementary to optical imaging approaches.

ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments   pp879 - 884
Aaron E Cozen, Erin Quartley, Andrew D Holmes, Eva Hrabeta-Robinson, Eric M Phizicky et al.
doi:10.1038/nmeth.3508
ARM-seq enables enhanced sequencing of modified tRNAs and tRNA fragments. Treatment of RNA with the demethylase AlkB prior to reverse transcription removes three 'hard-stop' modifications, allowing for discovery of modified tRNA fragments and their precursors by RNA sequencing.

See also: News and Views by Wilusz

Automated, high-throughput derivation, characterization and differentiation of induced pluripotent stem cells   pp885 - 892
Daniel Paull, Ana Sevilla, Hongyan Zhou, Aana Kim Hahn, Hesed Kim et al.
doi:10.1038/nmeth.3507
A modular, robotic system for reprogramming to induced pluripotent stem cells in high-throughput and automated fashion.

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Corrigendum

Top

Corrigendum: Drosophila Brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns   p893
Stefanie Hampel, Phuong Chung, Claire E McKellar, Donald Hall, Loren L Looger et al.
doi:10.1038/nmeth0915-893a

Errata

Top

Erratum: Rational design of a high-affinity, fast, red calcium indicator R-CaMP2   p893
Masatoshi Inoue, Atsuya Takeuchi, Shin-ichiro Horigane, Masamichi Ohkura, Keiko Gengyo-Ando et al.
doi:10.1038/nmeth0915-893b

Erratum: Whole-body immunoPET reveals active SIV dynamics in viremic and antiretroviral therapy-treated macaques   p893
Philip J Santangelo, Kenneth A Rogers, Chiara Zurla, Emmeline L Blanchard, Sanjeev Gumber et al.
doi:10.1038/nmeth0915-893c

Erratum: Multitarget super-resolution microscopy with high-density labeling by exchangeable probes   p893
Tai Kiuchi, Makio Higuchi, Akihiro Takamura, Masahiro Maruoka and Naoki Watanabe
doi:10.1038/nmeth0915-893d

Erratum: Power and sample size   p893
Martin Krzywinski and Naomi Altman
doi:10.1038/nmeth0915-893e

Application Note

Top

InnoStamp 40™ and InnoScan 1100AL™: a complete automated platform for microstructured cell arrays   
Adriana Lagraulet, Julie Foncy, Benjamin Berteloite, Aurore Esteve, Marie-Charline Blatche et al.

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