Friday, August 28, 2015

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

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Nature Methods

Nikon's A1rMP+ multiphoton system is now available with a New Dual IR beam option. With dual IR beams, users can now simultaneously excite two different fluorophores such as GFP and mCherry. This capability enables ultra-fast two-color multiphoton imaging, ideal for dynamic specimens.

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September 2015 Volume 12, Issue 9

In This Issue
This Month
Research Highlights
Technology Feature
News and Views
Brief Communications
Application Note

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In This Issue


In This Issue   



Empowering citizen scientists   p795
Scientists should consider engaging more with the DIYbio community.

This Month


The Author File: Daniel J. Muller   p797
Vivien Marx
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



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

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

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

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

Research Highlights


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

JOBS of the week
Environmental Chemistry
University of Windsor
Translational Bioinformatics Postdoc positions
University of Hawaii Cancer Center
Postdoctoral Position in Genomics and Molecular Biology at UCLA
Advanced Research Assistant - Bespoke Gene Targeting
Wellcome Trust Sanger Institute
Assistant / Associate Professor, Bioinformatics
The University of Nevada School Of Medicine
More Science jobs from
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12th Oct - 27th Oct 2015
Cold Spring Harbor, USA
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Technology Feature


Mapping proteins with spatial proteomics   pp815 - 819
Vivien Marx
A number of techniques address the location of proteins within cells.

News and Views


Removing roadblocks to deep sequencing of modified RNAs   pp821 - 822
Jeremy E Wilusz
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


Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach   pp823 - 826
Raj Chari, Prashant Mali, Mark Moosburner and George M Church
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.
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.
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.
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.
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
The Phenolyzer software provides prioritized candidate gene lists based on disease and phenotype terms that are entered by users as free text.

Are you sure that your CO2 incubator provides active humidity control?

Technologies to provide precise, user-defined control of temperature and CO2 are widely available, but methods to control relative humidity (while preventing condensation) are still evolving. 

Click the Baker logo to learn more about the available active humidity control technologies in CO2 incubators.



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.
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.
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.
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.
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.
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.
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.
A modular, robotic system for reprogramming to induced pluripotent stem cells in high-throughput and automated fashion.

Droplet Digital™ PCR (ddPCR™) is leading the way 

More than 200 peer-reviewed publications have benefited from Droplet Digital PCR's unmatched ability to detect rare nucleic acid species. From tracking cancer biomarkers to quantifying rare mutations, gene expression, and miniscule viral loads, Droplet Digital PCR has led to more discoveries than any other digital PCR platform. Visit our ddPCR page for application guides, publication lists, and webinars that explore the world of ddPCR.



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.



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.

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.

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

Erratum: Power and sample size   p893
Martin Krzywinski and Naomi Altman

Application Note


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.

Nature Plants: Call for Papers

Nature Plants
launched in January and covers all aspects of plants be it their evolution, genetics, development or metabolism, their interactions with the environment, or their societal significance. The journal welcomes high quality submissions and encourages you and your colleagues to consider submitting your next research paper to the journal. 

Submit your next research paper to the journal.
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