Volume 10 Issue 10, October 2013

Editorial

The way you say it

Wording criticism constructively is important before and after publication.

Editorial 27 Sept 2013

Advertisement

Top of page ⤴

This Month

Jeff Dangl

Better surveys of microbial friends and foes.

Vivien Marx
This Month 27 Sept 2013
Error bars

The meaning of error bars is often misinterpreted, as is the statistical significance of their overlap.

Martin Krzywinski
Naomi Altman

Collection:

Statistics for Biologists
This Month 27 Sept 2013

Top of page ⤴

Correspondence

ExpressionBlast: mining large, unstructured expression databases

Guy E Zinman
Shoshana Naiman
Ziv Bar-Joseph
Correspondence 27 Sept 2013
Building an ENCODE-style data compendium on a shoestring

David Ruau
Felicia S L Ng
Berthold Göttgens
Correspondence 27 Sept 2013

Top of page ⤴

Research Highlights

The developing human brain—modeled in a dish

Stem cells grown in three-dimensional cultures self-organize into tissues that resemble the developing human brain.

Erika Pastrana
Research Highlights 27 Sept 2013
A tool belt for GFP

Nanobodies turn any GFP-expressing cells into targets for in vivo functional manipulation.

Tal Nawy
Research Highlights 27 Sept 2013
Antibodies, made to order

Informed by existing molecular recognition motifs, researchers design effective scaffolds for directed evolution of post-translational modification–specific antibodies.

Michael Eisenstein
Research Highlights 27 Sept 2013
Constructing complicated carbohydrates

A stepwise strategy of targeted synthesis enables researchers to reconstruct cellular glycomes in vitro.

Michael Eisenstein
Research Highlights 27 Sept 2013

Top of page ⤴

Methods in Brief

Nanodiamonds to track cells in vivo

Methods in Brief 27 Sept 2013
Binding-site affinities tune promoter output

Methods in Brief 27 Sept 2013
Conditional gene knockouts in worms

Methods in Brief 27 Sept 2013
Allelic effects on translation

Methods in Brief 27 Sept 2013

Top of page ⤴

Tools in Brief

Extracting microbial function from phylogeny

Tools in Brief 27 Sept 2013
The NCI-60 proteomes

Tools in Brief 27 Sept 2013
Anterograde rabies neural tracers

Tools in Brief 27 Sept 2013
Highly multiplexed proteome analysis

Tools in Brief 27 Sept 2013

Top of page ⤴

Research Highlights

Self-destruct sequences

High-throughput sequencing of massive mutant libraries helps researchers catalog determinants of protein stability.

Michael Eisenstein
Research Highlights 27 Sept 2013
Studying function at the genome scale

Genomic position effects are probed in a highly parallel fashion with a clever combination of existing methods.

Natalie de Souza
Research Highlights 27 Sept 2013
Engineering off the beaten pathway

Interfacing synthetic diverters with a native yeast signaling pathway adds a robust layer of cell fate control.

Tal Nawy
Research Highlights 27 Sept 2013

Top of page ⤴

Technology Feature

Genomics in the clouds

Cloud computing can help busy genomics labs. But researchers will want to be cautious shoppers as they scan the skies for the cloud best suited to their needs.

Vivien Marx
Technology Feature 27 Sept 2013

Top of page ⤴

News & Views

hiFRET: some tailwind for FRET resolves weak protein interactions

Use of helper interactions to encourage weak heteromeric interactions between fluorescent protein pairs helps ensure optimal fluorescence resonance energy transfer (FRET) signals and minimizes the impact on target protein interactions.

Kees Jalink
News & Views 27 Sept 2013

Top of page ⤴

Review Article

Recommendations for the design and analysis of epigenome-wide association studies

Fourteen scientists who participated in a recent workshop to identify and address challenges of epigenome-wide association studies summarize their recommendations in this Review.

Karin B Michels
Alexandra M Binder
Rafael A Irizarry
Review Article 27 Sept 2013

Top of page ⤴

Perspective

Cas9 as a versatile tool for engineering biology

This Perspective describes current and prospective advances in genome engineering made possible with the CRISPR-Cas9 system.

Prashant Mali
Kevin M Esvelt
George M Church

Collection:

Nobel Prize in Chemistry 2020
Perspective 27 Sept 2013

Top of page ⤴

Resource

A reversible gene trap collection empowers haploid genetics in human cells

A collection of single-gene-mutant human cells is described. This growing resource is based on gene-trap mutagenesis of a near-haploid human cell line and covers almost 3,500 human genes.

Tilmann Bürckstümmer
Carina Banning
Sebastian M B Nijman
Resource 25 Aug 2013

Top of page ⤴

Brief Communication

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

Synthetic transcription factors based on the RNA-guided CRISPR-Cas9 system are used to activate specific endogenous genes in human cells. Also online, Joung and colleagues report similar developments at two other loci.

Pablo Perez-Pinera
D Dewran Kocak
Charles A Gersbach

Collections:

Department of Biomedical Engineering at Duke University

Synthetic Biology
Brief Communication 25 Jul 2013
CRISPR RNA–guided activation of endogenous human genes

Synthetic transcription factors based on the RNA-guided CRISPR-Cas9 system are used to activate endogenous genes in human cells. Also online, Gersbach and colleagues report similar developments at multiple other loci.

Morgan L Maeder
Samantha J Linder
J Keith Joung
Brief Communication 25 Jul 2013
Site-specific characterization of the Asp- and Glu-ADP-ribosylated proteome

A proteomic method to identify human proteins post-translationally modified by poly(ADP-ribosyl)ation is reported, which will help yield further insights into the biological role of this modification.

Yajie Zhang
Jianqi Wang
Yonghao Yu
Brief Communication 18 Aug 2013
DeNovoGear: de novo indel and point mutation discovery and phasing

The DeNovoGear software detects de novo point mutations and indels with high specificity in familial and somatic tissue sequence data.

Avinash Ramu
Michiel J Noordam
Donald F Conrad
Brief Communication 25 Aug 2013
DMSO enhances electrospray response, boosting sensitivity of proteomic experiments

The addition of a low percentage of DMSO into liquid chromatography solvents strongly enhances peptide electrospray ionization, substantially improving proteome analysis by liquid chromatography–tandem mass spectrometry.

Hannes Hahne
Fiona Pachl
Bernhard Kuster
Brief Communication 25 Aug 2013
Recombinant antibodies to histone post-translational modifications

Renewable affinity reagents with high specificity and affinity for histone modifications perform well in ChIP-seq and other applications in epigenetics research.

Takamitsu Hattori
Joseph M Taft
Shohei Koide
Brief Communication 18 Aug 2013
UPARSE: highly accurate OTU sequences from microbial amplicon reads

To determine microbial community structure, the UPARSE software extracts operational taxonomic unit (OTU) representative sequences with high accuracy on the basis of amplified marker-gene sequences.

Robert C Edgar
Brief Communication 18 Aug 2013
Practical innovations for high-throughput amplicon sequencing

A set of practical improvements and software provide more accurate and less biased metagenomic amplicon sequencing at lower sequencing effort.

Derek S Lundberg
Scott Yourstone
Jeffery L Dangl
Brief Communication 01 Sept 2013
Absolute quantification by droplet digital PCR versus analog real-time PCR

Droplet digital PCR shows greater precision and reproducibility but no consistent gain in sensitivity when compared to real-time PCR.

Christopher M Hindson
John R Chevillet
Muneesh Tewari
Brief Communication 01 Sept 2013

Top of page ⤴

Article

Solid-state NMR spectroscopy structure determination of a lipid-embedded heptahelical membrane protein

A strategy, based on solid-state NMR spectroscopy, for determining the structure of an oligomeric, seven-helix membrane protein (Anabaena sensory rhodopsin) in a lipid environment is described.

Shenlin Wang
Rachel A Munro
Vladimir Ladizhansky
Article 08 Sept 2013
Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light

This work describes wide-field temporal focusing, a two-photon volumetric imaging technique based on light sculpting that enables functional imaging of the majority of neurons in the head ganglia of C. elegans with high temporal and spatial resolution.

Tina Schrödel
Robert Prevedel
Alipasha Vaziri
Article 08 Sept 2013
Engineering of weak helper interactions for high-efficiency FRET probes

Addition of weak helper interactions to fluorescent protein pairs by protein engineering provides a simple method to increase FRET efficiency with little or no background.

Raik Grünberg
Julia V Burnier
Luis Serrano
Article 01 Sept 2013
Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination

CRISPR-Cas9–mediated cleavage is used to stimulate homologous recombination at specific target sites in the C. elegans genome, permitting flexible tagging and sequence modification of endogenous worm genes.

Daniel J Dickinson
Jordan D Ward
Bob Goldstein
Article 01 Sept 2013