Volume 12 Issue 6, June 2015

Editorial

Windows into the ivory tower

Editorial 28 May 2015

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This Month

Stefan Florian

Tracking cell cycles in vivo, and the temptation of science fiction.

Vivien Marx
This Month 28 May 2015
Sampling distributions and the bootstrap

Anthony Kulesa
Martin Krzywinski
Naomi Altman

Collection:

Statistics for Biologists
This Month 28 May 2015

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Correspondence

Off-target mutations are rare in Cas9-modified mice

Vivek Iyer
Bin Shen
William C Skarnes
Correspondence 28 May 2015
ClearVolume: open-source live 3D visualization for light-sheet microscopy

Loic A Royer
Martin Weigert
Eugene W Myers
Correspondence 28 May 2015
BigDataViewer: visualization and processing for large image data sets

Tobias Pietzsch
Stephan Saalfeld
Pavel Tomancak
Correspondence 28 May 2015
MAGI: visualization and collaborative annotation of genomic aberrations

Mark D M Leiserson
Connor C Gramazio
Benjamin J Raphael
Correspondence 28 May 2015

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Research Highlights

Synapses seen at different scales

Synapse morphology and molecular composition can be analyzed in detail with conjugate light-electron array tomography, which combines immunofluorescence imaging with electron microscopy in a precisely aligned fashion.

Nina Vogt
Research Highlights 28 May 2015
A small molecule improves Cas9 specificity

Making Cas9 nuclease activity dependent on the self-cleavage of a ligand-responsive intein decreases Cas9's off-target activity.

Nicole Rusk
Research Highlights 28 May 2015
Highly multiplexed transcriptome imaging

A single-molecule imaging approach allows for error-robust transcriptomic analyses in single cells.

Rita Strack
Research Highlights 28 May 2015
Splice and sequence

A ligation-based sequencing method reveals distant exon connections within long RNA molecules.

Tal Nawy
Research Highlights 28 May 2015

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Methods in Brief

Epigenome editing

Methods in Brief 28 May 2015
Chemical modification of native proteins

Methods in Brief 28 May 2015
Transcripts in space

Methods in Brief 28 May 2015
Engineering the mosquito genome

Methods in Brief 28 May 2015

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Tools in Brief

A red calcium indicator dye for dual-color imaging

Tools in Brief 28 May 2015
Enter the diatom

Tools in Brief 28 May 2015
Bright cyan and orange probes for bioluminescence imaging

Tools in Brief 28 May 2015
Pre- and postsynaptic activity reporters

Tools in Brief 28 May 2015

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Research Highlights

Tinkering with chromatin

Protein trans-splicing is used to study chromatin signaling in the cell nucleus.

Allison Doerr
Research Highlights 28 May 2015
From form to function

DNA building blocks that interact on the basis of shape rather than sequence assemble into highly dynamic and complex structures.

Michael Eisenstein
Research Highlights 28 May 2015

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Commentary

Reproducibility: changing the policies and culture of cell line authentication

Quality control of cell lines used in biomedical research is essential to ensure reproducibility. Although cell line authentication has been widely recommended for many years, misidentification, including cross-contamination, remains a serious problem. We outline a multi-stakeholder, incremental approach and policy-related recommendations to facilitate change in the culture of cell line authentication.

Leonard P Freedman
Mark C Gibson
Yvonne A Reid

Collections:

Challenges in irreproducible research

Best Practices in Method Reporting
Commentary 28 May 2015

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Technology Feature

Visualizing epigenomic data

Vivien Marx

Collection:

NatureTech
Technology Feature 28 May 2015

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Review Article

Correlated light and electron microscopy: ultrastructure lights up!

Correlated light and electron microscopy (CLEM) gives context to biomolecules studied with fluorescence microscopy. This Review discusses recent improvements and guides readers on probes, instrumentation and sample preparation to implement CLEM.

Pascal de Boer
Jacob P Hoogenboom
Ben N G Giepmans

Focus:

PDB 50th Anniversary: celebrating the future of structural biology
Review Article 28 May 2015

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Brief Communication

A fast- and positively photoswitchable fluorescent protein for ultralow-laser-power RESOLFT nanoscopy

Kohinoor is a fast- and positively switching fluorescent protein with high photostability over many photoswitching cycles. Its improved photophysical properties enable nanoscopy with low phototoxicity and allow use of a simplified RESOLFT setup.

Dhermendra K Tiwari
Yoshiyuki Arai
Takeharu Nagai
Brief Communication 20 Apr 2015
G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

G&T-seq offers robust full-length transcript and whole-genome sequencing simultaneously from a single cell.

Iain C Macaulay
Wilfried Haerty
Thierry Voet
Brief Communication 27 Apr 2015
MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

A software tool, MS-DIAL, enables the identification of metabolomes by data independent acquisition–based mass spectrometry.

Hiroshi Tsugawa
Tomas Cajka
Masanori Arita
Brief Communication 04 May 2015
CONSERTING: integrating copy-number analysis with structural-variation detection

CONSERTING detects somatic copy-number alterations from whole-genome sequence data with high accuracy and sensitivity and identifies breakpoints even in heterogeneous or impure tumors.

Xiang Chen
Pankaj Gupta
Jinghui Zhang
Brief Communication 04 May 2015
MIMP: predicting the impact of mutations on kinase-substrate phosphorylation

This machine learning method predicts whether single-nucleotide variants disrupt or create phosphorylation sites.

Omar Wagih
Jüri Reimand
Gary D Bader
Brief Communication 04 May 2015

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Article

Rapid reverse genetic screening using CRISPR in zebrafish

Targeting 48 loci in a pooled CRISPR-Cas9 screen reveals new genes essential for electrical-synapse formation.

Arish N Shah
Crystal F Davey
Cecilia B Moens
Article 13 Apr 2015
High-resolution whole-brain staining for electron microscopic circuit reconstruction

An improved method for preparing mouse brains for electron microscopy allows reliable tracing of neurites and identification of synapses and appears suitable for whole-brain connectomic reconstruction.

Shawn Mikula
Winfried Denk
Article 13 Apr 2015
Multispectral labeling technique to map many neighboring axonal projections in the same tissue

The topography of axonal projections can be deciphered by retrograde labeling with multiple overlapping dye injections, as the dye composition in retrogradely transported vesicles is indicative of axonal projection sites.

Shlomo Tsuriel
Sagi Gudes
Jeff W Lichtman
Article 27 Apr 2015
Rapid, optimized interactomic screening

Extraction conditions can have a substantial effect on protein complexes isolated from within cells. A platform for rapid, systematic screening of these conditions is described, which should enable the identification of biologically relevant complexes.

Zhanna Hakhverdyan
Michal Domanski
John LaCava
Article 04 May 2015
Isotope-targeted glycoproteomics (IsoTaG): a mass-independent platform for intact N- and O-glycopeptide discovery and analysis

Metabolically labeling proteins with glycans that enable attachment of an isotopically encoded tag allows for the identification of N- and O- glycopeptides and their glycan structures.

Christina M Woo
Anthony T Iavarone
Carolyn R Bertozzi

Collection:

Nobel Prize in Chemistry 2022
Article 20 Apr 2015
High-performance probes for light and electron microscopy

'Spaghetti monster' fluorescent proteins combine the power of conventional fluorescent proteins with the benefits of commonly used epitopes. These probes are demonstrated to be extremely versatile in diverse imaging applications.

Sarada Viswanathan
Megan E Williams
Loren L Looger
Article 27 Apr 2015
In vivo cell-cycle profiling in xenograft tumors by quantitative intravital microscopy

Methods for quantitative, automated in vivo cell-cycle profiling are applied to tumor xenografts in the mouse to study the effects of drug treatment.

Deepak R Chittajallu
Stefan Florian
Timothy J Mitchison
Article 13 Apr 2015

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Advertising Feature: Application Note

Rapid screening for protein solubility and expression

Mark Maffitt
Michele Auldridge
Eric Steinmetz
Advertising Feature: Application Note 28 May 2015

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Volume 12 Issue 6, June 2015

Editorial

This Month

Correspondence

Research Highlights

Methods in Brief

Tools in Brief

Research Highlights

Commentary

Technology Feature

Review Article

Brief Communication

Article

Advertising Feature: Application Note

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