Volume 9 Issue 10, October 2012

Tugging at single molecules shows how they shake hands.

Two-dimensional visualizations of multivariate data are most effective when combined.

New research explores in vivo protein function in the worm—at the genome scale.

Two studies of tumor ancestry reveal evidence for discrete populations of cancer stem cells.

Looking for agreement between Watson and Crick strands weeds out sequencing artifacts.

Widely used dyes for conventional microscopy of subcellular structures can also be used for super-resolution imaging.

A map of the male worm's posterior nervous system offers some surprises.

Single-molecule imaging helps researchers to begin a biography for clathrin-coated vesicles.

Parallel reaction monitoring (PRM)-based targeted mass spectrometry is comparable in performance to selected reaction monitoring (SRM) but requires much less investment in assay development for targeted proteomics applications.

In vivo imaging scientists broadcast from inside the brains of moving animals.

Two studies plant a signpost on the road toward a robust and detailed chromatin interaction map.

A new high-throughput method for monitoring G protein–coupled receptor activation is highly suited to assaying Gα_12/13-coupled receptors and is used to deorphanize a group of receptors activated by lysophosphatidylserine.

A high-resolution 4C-seq protocol involving two restriction digests and a revised analysis pipeline allows robust detection of physical interactions between regulatory DNA elements.

Coexpression of DNA end–processing enzymes with targeted nucleases improves the efficiency of gene disruption in mammalian cells.

An integrated system composed of a microfluidic device, computer-vision tools and statistical methods for automatically handling, imaging, classifying and sorting C. elegans organisms is presented. The system performs automated screens of subcellular phenotypes and is used here to identify genes involved in synaptogenesis.

Removing phosphopantetheine-tagged labels from acyl carrier proteins (ACPs) and ACP fusion proteins contributes to a versatile labeling method in which tags can be iteratively swapped.

A method for single-molecule imaging at high protein concentrations is presented and demonstrated in the context of DNA replication in cell extracts.

This paper reports genetic manipulation of the malaria parasite Plasmodium falciparum with zinc-finger nucleases. It demonstrates gene disruption as well as replacement and site-specific editing of both an integrated reporter and an endogenous gene.

ICE (iterative correction and eigenvector decomposition) provides insight into inter- and intrachromosome interaction patterns.

Development of the bright green and red fluorescent proteins, Clover and mRuby2, creates a fluorescence resonance energy transfer (FRET) pair with the highest Förster radius among existing ratiometric FRET pairs. Substitution of this pair for current FRET pairs in several existing sensors reliably and substantially improves sensor performance.

A dual-trap force-clamp configuration is used to apply a constant load between a binding protein and a single intermittently interacting biological polymer. This allows high-resolution measurements of short-lived molecular complexes and reveals previously undetected complex regulation of the myosin working stroke.

A G protein–coupled receptor (GPCR) signaling assay based on ectodomain shedding of a membrane-bound proform of alkaline phosphatase-tagged TGFα provides a platform for studying poorly characterized Gα_12/13-coupled GPCRs. The assay allowed identification of three orphan GPCRs as Gα_12/13-coupled lysophosphatidylserine receptors.