Volume 12 Issue 9, September 2015

Editorial

Empowering citizen scientists

Scientists should consider engaging more with the DIYbio community.

Editorial 28 Aug 2015

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This Month

Daniel J. Müller

A new way to quantify ligand-binding interactions of individual membrane proteins.

Vivien Marx
This Month 28 Aug 2015
Bayesian networks

Jorge López Puga
Martin Krzywinski
Naomi Altman

Collection:

Statistics for Biologists
This Month 28 Aug 2015

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Correspondence

Validating subcellular thermal changes revealed by fluorescent thermosensors

Shigeki Kiyonaka
Reiko Sakaguchi
Yasuo Mori
Correspondence 28 Aug 2015
The 10⁵ gap issue between calculation and measurement in single-cell thermometry

Madoka Suzuki
Vadim Zeeb
Shin'ichi Ishiwata
Correspondence 28 Aug 2015
Reply to: "Validating subcellular thermal changes revealed by fluorescent thermosensors" and "The 10⁵ gap issue between calculation and measurement in single-cell thermometry"

Guillaume Baffou
Hervé Rigneault
Ludovic Jullien
Correspondence 28 Aug 2015

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Research Highlights

Building lasers inside cells

Optical microresonators form stand-alone intracellular lasers.

Rita Strack
Research Highlights 28 Aug 2015
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.

Nina Vogt
Research Highlights 28 Aug 2015
Where the G-quadruplexes are

A new sequencing method identifies G-quadruplexes genome wide.

Tal Nawy
Research Highlights 28 Aug 2015
Navigating the negative-mode proteome

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

Allison Doerr
Research Highlights 28 Aug 2015

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Methods in Brief

Deep learning to predict sequence specificity

Methods in Brief 28 Aug 2015
Universal parts

Methods in Brief 28 Aug 2015
Cardiovascular progenitors from human stem cells

Methods in Brief 28 Aug 2015
Wireless pharmacology and optogenetics

Methods in Brief 28 Aug 2015

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Tools in Brief

Finding more ribozymes

Tools in Brief 28 Aug 2015
Fluorescent proteins for diverse environments

Tools in Brief 28 Aug 2015
A light switch for microtubule dynamics

Tools in Brief 28 Aug 2015
Introducing the BioPlex network

Tools in Brief 28 Aug 2015

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Research Highlights

Stop the presses

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

Michael Eisenstein
Research Highlights 28 Aug 2015
Micro-C maps of genome structure

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

Natalie de Souza
Research Highlights 28 Aug 2015
RNA catch and release

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

Stéphane Larochelle
Research Highlights 28 Aug 2015

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Technology Feature

Mapping proteins with spatial proteomics

A number of techniques address the location of proteins within cells.

Vivien Marx

Collection:

NatureTech
Technology Feature 28 Aug 2015

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News & Views

Removing roadblocks to deep sequencing of modified RNAs

By removing modified nucleotides that block reverse transcriptase, two methods have now made tRNAs amenable to RNA-seq.

Jeremy E Wilusz
News & Views 28 Aug 2015

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Brief Communication

Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach

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.

Raj Chari
Prashant Mali
George M Church
Brief Communication 13 Jul 2015
Ultrafast, temporally stochastic STED nanoscopy of millisecond dynamics

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.

Jale Schneider
Jasmin Zahn
Stefan W Hell
Brief Communication 27 Jul 2015
EEG and functional ultrasound imaging in mobile rats

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.

Lim-Anna Sieu
Antoine Bergel
Ivan Cohen
Brief Communication 03 Aug 2015
Efficient and quantitative high-throughput tRNA sequencing

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.

Guanqun Zheng
Yidan Qin
Tao Pan

Collection:

Methods for studying noncoding RNA
Brief Communication 27 Jul 2015
Inferring transient particle transport dynamics in live cells

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.

Nilah Monnier
Zachary Barry
Mark Bathe
Brief Communication 20 Jul 2015
Phenolyzer: phenotype-based prioritization of candidate genes for human diseases

The Phenolyzer software provides prioritized candidate gene lists based on disease and phenotype terms that are entered by users as free text.

Hui Yang
Peter N Robinson
Kai Wang
Brief Communication 20 Jul 2015

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Article

Imaging G protein–coupled receptors while quantifying their ligand-binding free-energy landscape

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.

David Alsteens
Moritz Pfreundschuh
Daniel J Müller
Article 13 Jul 2015
Photoactivatable genetically encoded calcium indicators for targeted neuronal imaging

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.

Shai Berlin
Elizabeth C Carroll
Ehud Y Isacoff
Article 13 Jul 2015
ProteoPlex: stability optimization of macromolecular complexes by sparse-matrix screening of chemical space

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.

Ashwin Chari
David Haselbach
Holger Stark
Article 03 Aug 2015
Mutational interference mapping experiment (MIME) for studying RNA structure and function

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.

Redmond P Smyth
Laurence Despons
Roland Marquet
Article 03 Aug 2015
Real-time imaging of brain activity in freely moving rats using functional ultrasound

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.

Alan Urban
Clara Dussaux
Gabriel Montaldo
Article 20 Jul 2015
ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments

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.

Aaron E Cozen
Erin Quartley
Todd M Lowe

Collection:

Methods for studying noncoding RNA
Article 03 Aug 2015
Automated, high-throughput derivation, characterization and differentiation of induced pluripotent stem cells

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

Daniel Paull
Ana Sevilla
Scott A Noggle
Article 03 Aug 2015