Volume 9 Issue 8, August 2012

Boosting accuracy by building consensus.

Data structure informs choice of color maps.

Recruiting chromatin modifiers to a specific locus allows the regulation of heterochromatin formation in living cells.

Researchers continue to improve the performance of the atomic force microscope.

Codifferentiating human pluripotent stem cells along neural and endothelial lineages provides cues to efficiently generate blood-brain barrier endothelial cells.

Tracking single molecules in real time reveals the hidden dynamics of translational initiation.

Tandem fluorescent protein timers allow measurements of both protein turnover and trafficking in the cell.

Lifespan in nematodes is markedly extended when an unusual combination of aging components is engineered into their genome.

Rapidly maturing techniques reveal messengers within cells.

A precomputed database of lineage-restricted reference genes yields a fast and accurate tool that uses sequence similarity alone to compute clade abundances from shotgun metagenomic data sets.

An experimental infrastructure consisting of environmentally controlled and spatially linked habitat patches permits studies on terrestrial animal dispersal at an unprecedented scale for an experiment with such strict control.

This analysis comprehensively compares methods for gene regulatory network inference submitted through the DREAM5 challenge. It demonstrates that integration of predictions from multiple methods shows the most robust performance across data sets.

Due to an unexpected cell-penetrating property, zinc-finger nucleases (ZFNs) can be delivered to several mammalian cell types as proteins. Dose-dependent disruption of an endogenous gene was achieved with reduced activity at known off-target sites.

Genotyping based on restriction site7ndash;associated (RAD) sequencing around type IIB enzyme recognition sites is reported. The streamlined reduced-representation approach features even and tunable genome coverage and enables large-scale genotyping studies by maximizing the amount of genotypic information that can be obtained from individuals for a given amount of sequencing.

MetaPhlAn (metagenomic phylogenetic analysis) allows the rapid and accurate identification of microbial species and higher clades from shotgun sequencing data.

This method achieves simultaneous and spatially colocalized excitation of three fluorophores with distinct spectra, doing so via two-photon microscopy using a femtosecond laser and an optical parametric oscillator and by temporally overlapping the beams. Imaging of 'Brainbow'-labeled mouse and chicken nervous tissue and of developing fly embryos is shown.

A machine learning–based structural-variant discovery approach that incorporates prior knowledge shows high sensitivity and specificity even on single genomes.

A rare cutting protease that creates large peptides is well suited for differentiating protein isoforms and detecting combinations of post-translational modifications by tandem mass spectrometry.

This paper reports a fluorescence imaging method based on interference contrast in which the incidence angle of the excitation light is actively scanned. The high axial precision and temporal resolution are used for dynamic nanoscale imaging of cytoskeleton and adhesion proteins in living cells.

A flexible, environmentally controlled experimental setup for the study of terrestrial animal dispersal is reported. Its unprecedented scale should enable studies in spatial ecology and permit tests of conservation strategies in the face of environmental change.

The combination of cell-free protein expression and combinatorial dual labeling–aided NMR analysis allows for the rapid backbone structure assessment of human membrane proteins.

Two large-scale resources for studying microRNA function are presented: one is a library of fluorescent sensors with a corresponding assay for global profiling of microRNA activity in different cell types; the other is a decoy library for suppressing microRNA activity individually or in pooled loss-of-function screens.