Table of contents


Top

Editorial

Software with impact p211

doi:10.1038/nmeth.2880

The usefulness of computational methods can be improved by releasing code and designing software that supports reproducible research.


Top

This Month

The author file: Erik Meijering p213

Vivien Marx

doi:10.1038/nmeth.2853

A bass guitar helps a scientist-engineer promote transparency for bioimage analysis.


Points of significance: Comparing samples—part I pp215 - 216

Martin Krzywinski & Naomi Altman

doi:10.1038/nmeth.2858

Robustly comparing pairs of independent or related samples requires different approaches to the t-test.


Top

Correspondence

Acquisition frame rate affects microtubule plus-end tracking analysis pp219 - 220

Philip R Nicovich & Feng-Quan Zhou

doi:10.1038/nmeth.2846

See also: Correspondence by Danuser



Protein digestion priority is independent of protein abundances pp220 - 222

Mingliang Ye, Yanbo Pan, Kai Cheng & Hanfa Zou

doi:10.1038/nmeth.2850


A Drosophila RNAi collection is subject to dominant phenotypic effects pp222 - 223

Edward W Green, Giorgio Fedele, Flaviano Giorgini & Charalambos P Kyriacou

doi:10.1038/nmeth.2856


Top

Research Highlights

What doesn't kill you may reprogram you p225

Somatic cells in the mouse can be converted to a pluripotent state merely through exposure to a physical stimulus.

Elusive vibrations pp226 - 227

At last, a method to measure long-range vibrations in proteins may provide clues to the functional relevance of these motions.

Nanopores sense protein modifications pp226 - 227

Protein nanopores can detect post-translational modifications in proteins.

Taming the image background beast p228

Background removal greatly improves localization microscopy performance.

Capturing promoter-enhancer interactions in high throughput p231

Capturing the interaction of promoters with their regulatory elements allows a high-resolution view into the regulatory landscape of chromatin.

Knocking down Goliath p232

A small peptide–based method knocks down native proteins in vitro and in vivo.

Methods in Brief

Tools in Brief

Top

Commentary

Art and artifacts in single-molecule localization microscopy: beyond attractive images pp235 - 238

Ulrike Endesfelder & Mike Heilemann

doi:10.1038/nmeth.2852

Single-molecule super-resolution techniques emerged only several years ago but have revolutionized fluorescence microscopy of cellular structures. We discuss some key principles of these techniques, point out pitfalls, highlight recent developments and identify opportunities for the future.


Top

Technology Feature

PCR: paths to sensitivity pp241 - 245

Vivien Marx

doi:10.1038/nmeth.2849

Careful strategizing helps make PCR sensitive enough for the most challenging experiments.


Top

News and Views

A particle tracking meet pp247 - 248

Michael J Saxton

doi:10.1038/nmeth.2851

A first community experiment comparing the performance of analysis methods for single-particle tracking data declares no winner but reveals valuable information for users and developers.

See also: Analysis by Chenouard et al.


Genome editing 101: let's go digital pp248 - 249

Ryan Forster & Dirk Hockemeyer

doi:10.1038/nmeth.2859

An approach is described that simplifies the isolation of rare human pluripotent stem cells engineered to carry precise disease-relevant mutations.

See also: Brief Communication by Miyaoka et al.


ADVERTISEMENT



Top

Reviews

Precisely and accurately localizing single emitters in fluorescence microscopy pp253 - 266

Hendrik Deschout, Francesca Cella Zanacchi, Michael Mlodzianoski, Alberto Diaspro, Joerg Bewersdorf, Samuel T Hess & Kevin Braeckmans

doi:10.1038/nmeth.2843

This first of two review articles provides an overview and practical introduction to the precise and accurate localization of single emitters for single-particle tracking and super-resolution localization microscopy.


Fluorophore localization algorithms for super-resolution microscopy pp267 - 279

Alex Small & Shane Stahlheber

doi:10.1038/nmeth.2844

This second Review introduces readers to the many algorithms used to localize fluorophores in localization-based super-resolution imaging and offers practical advice to guide their choice and usage.


Top

Analysis

Objective comparison of particle tracking methods Open pp281 - 289

Nicolas Chenouard, Ihor Smal, Fabrice de Chaumont, Martin Maška, Ivo F Sbalzarini, Yuanhao Gong, Janick Cardinale, Craig Carthel, Stefano Coraluppi, Mark Winter, Andrew R Cohen, William J Godinez, Karl Rohr, Yannis Kalaidzidis, Liang Liang, James Duncan, Hongying Shen, Yingke Xu, Klas E G Magnusson, Joakim Jaldén, Helen M Blau, Perrine Paul-Gilloteaux, Philippe Roudot, Charles Kervrann, François Waharte, Jean-Yves Tinevez, Spencer L Shorte, Joost Willemse, Katherine Celler, Gilles P van Wezel, Han-Wei Dan, Yuh-Show Tsai, Carlos Ortiz de Solórzano, Jean-Christophe Olivo-Marin & Erik Meijering

doi:10.1038/nmeth.2808

The first community competition designed to objectively compare the performance of particle tracking algorithms provides valuable practical information for both users and developers.

See also: News and Views by Saxton


Top

Brief Communications

Isolation of single-base genome-edited human iPS cells without antibiotic selection pp291 - 293

Yuichiro Miyaoka, Amanda H Chan, Luke M Judge, Jennie Yoo, Miller Huang, Trieu D Nguyen, Paweena P Lizarraga, Po-Lin So & Bruce R Conklin

doi:10.1038/nmeth.2840

This paper describes a method based on sib-selection to isolate rare human pluripotent stem cell clones with a precise engineered mutation.

See also: News and Views by Forster & Hockemeyer


Functional annotation of noncoding sequence variants pp294 - 296

Graham R S Ritchie, Ian Dunham, Eleftheria Zeggini & Paul Flicek

doi:10.1038/nmeth.2832

The genome-wide annotation of variants (GWAVA) software predicts whether noncoding variants are likely to be functional using a classifier trained on a range of genomic and epigenomic annotations.


Continuous throughput and long-term observation of single-molecule FRET without immobilization pp297 - 300

Swati Tyagi, Virginia VanDelinder, Niccolò Banterle, Gustavo Fuertes, Sigrid Milles, Morgane Agez & Edward A Lemke

doi:10.1038/nmeth.2809

A microfluidic platform creates nanochannels from collapsed microchannels for multisecond single-molecule FRET measurements of untethered biomolecules by total-internal-reflection fluorescence microscopy.


Targeted protein quantification using sparse reference labeling pp301 - 304

Ching-Yun Chang, Eduard Sabidó, Ruedi Aebersold & Olga Vitek

doi:10.1038/nmeth.2806

A statistical method, label-sparse quantification, and software tool, SparseQuant, allows targeted proteins to be quantified by selected reaction monitoring mass spectrometry without requiring a full set of isotope-labeled reference peptides.


Correlative super-resolution fluorescence and metal-replica transmission electron microscopy pp305 - 308

Kem A Sochacki, Gleb Shtengel, Schuyler B van Engelenburg, Harald F Hess & Justin W Taraska

doi:10.1038/nmeth.2816

A method for accurate correlative fluorescence and electron microscopy at nanometer resolution is reported for imaging structures at the cell surface.


Epigenome-wide association studies without the need for cell-type composition pp309 - 311

James Zou, Christoph Lippert, David Heckerman, Martin Aryee & Jennifer Listgarten

doi:10.1038/nmeth.2815

A statistical approach using a linear mixed model and principal-component analysis discovers phenotype-specific changes in epigenomes without requiring information on cell type composition.


Top

Articles

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT pp313 - 318

Ralf Jungmann, Maier S Avendaño, Johannes B Woehrstein, Mingjie Dai, William M Shih & Peng Yin

doi:10.1038/nmeth.2835

Variations on point accumulation for imaging in nanoscale topography (PAINT) for super-resolution imaging extend the technology to allow simple imaging of cellular proteins as well as synthetic DNA nanostructures and provide a high level of multiplexing.


Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells pp319 - 324

Nils A Kulak, Garwin Pichler, Igor Paron, Nagarjuna Nagaraj & Matthias Mann

doi:10.1038/nmeth.2834

A streamlined, robust sample-preparation method for mass spectrometry–based proteome analysis is reported. All sample preparation steps are carried out in a single enclosed reactor, reducing the potential for contamination and losses, and enabling comprehensive proteome coverage.


Optogenetic control of Drosophila using a red-shifted channelrhodopsin reveals experience-dependent influences on courtship pp325 - 332

Hidehiko K Inagaki, Yonil Jung, Eric D Hoopfer, Allan M Wong, Neeli Mishra, John Y Lin, Roger Y Tsien & David J Anderson

doi:10.1038/nmeth.2765

A recently described red-shifted channelrhodopsin permits control of complex behaviors in freely moving adult flies and reveals the functional modulation of courtship behavior by social experience.


Similarity network fusion for aggregating data types on a genomic scale pp333 - 337

Bo Wang, Aziz M Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains & Anna Goldenberg

doi:10.1038/nmeth.2810

Similarity network fusion (SNF) is an approach to integrate multiple data types on the basis of similarity between biological samples rather than individual measurements. The authors demonstrate SNF by constructing patient networks to identify disease subtypes with differential survival profiles.


Independent optical excitation of distinct neural populations pp338 - 346

Nathan C Klapoetke, Yasunobu Murata, Sung Soo Kim, Stefan R Pulver, Amanda Birdsey-Benson, Yong Ku Cho, Tania K Morimoto, Amy S Chuong, Eric J Carpenter, Zhijian Tian, Jun Wang, Yinlong Xie, Zhixiang Yan, Yong Zhang, Brian Y Chow, Barbara Surek, Michael Melkonian, Vivek Jayaraman, Martha Constantine-Paton, Gane Ka-Shu Wong & Edward S Boyden

doi:10.1038/nmeth.2836

Sequencing the transcriptomes of more than 100 species of alga yields new channelrhodopsins with promising properties for optogenetics. A far red–shifted channelrhodopsin, Chrimson, opens up new behavioral capabilities in Drosophila, and alongside a fast yet light-sensitive blue channelrhodopsin, Chronos, enables independent excitation of two neuronal populations in brain slices.


ADVERTISEMENT



Top

Addendum

Addendum: Digestion and depletion of abundant proteins improves proteomic coverage pp347 - 348

Bryan R Fonslow, Benjamin D Stein, Kristofor J Webb, Tao Xu, Jeong Choi, Sung Kyu Park & John R Yates III

doi:10.1038/nmeth0314-347


Top

Errata

Erratum: Pouring over liquid handling p349

Vivien Marx

doi:10.1038/nmeth0314-349a


Erratum: Dissecting genomic diversity, one cell at a time p349

Paul C Blainey & Stephen R Quake

doi:10.1038/nmeth0314-349b


Erratum: Singled out for sequencing p349

Kelly Rae Chi

doi:10.1038/nmeth0314-349e


Top

Corrigenda

Corrigendum: Using networks to measure similarity between genes: association index selection p349

Juan I Fuxman Bass, Alos Diallo, Justin Nelson, Juan M Soto, Chad L Myers & Albertha J M Walhout

doi:10.1038/nmeth0314-349c


Corrigendum: Quantifying cell-generated mechanical forces within living embryonic tissues p349

Otger Campàs, Tadanori Mammoto, Sean Hasso, Ralph A Sperling, Daniel O'Connell, Ashley G Bischof, Richard Maas, David A Weitz, L Mahadevan & Donald E Ingber

doi:10.1038/nmeth0314-349d


Top