Research articles

Automated cell segmentation in time-lapse confocal images of growing Arabidopsis combined with ratiometric imaging of fluorescent gene expression reporters permits the correlation of cellular properties with gene expression in the growing plant.

The combination of a genetically encoded aldehyde tag and optimized labeling method allows high-efficiency, site-specific labeling of tagged proteins after purification or in cell extracts. The authors use the high labeling efficiency for single-molecule measurements of the dynamic interactions between two DNA polymerases and polymerase processivity factor bound to DNA.

Mouse cells are reprogrammed to induced pluripotency in suspension culture and can be further differentiated into cardiac cells, also in suspension. Also in this issue, Shafa et al. report suspension-culture reprogramming of mouse cells.

Segway, a method using dynamic Bayesian network techniques, segments a genome and produces functional labels defined by histone modifications, transcription-factor binding, locations of open chromatin and other genome-wide functional data.

Protein localization changes in cells are monitored at high-throughput applying pulse-shape analysis to flow-cytometry data. The authors use the technique in combination with tetracysteine-based oligomer sensors to monitor toxic protein aggregation in a cellular model of Huntington's disease.

ClusterONE detects overlapping protein complexes from large-scale weighted and unweighted protein-interaction networks.

The temporal resolution of current signals from solid-state nanopores is improved by integrating a complementary metal-oxide-semiconductor preamplifier with the nanopores in thin silicon nitride membranes.

The binary 'Q system' for controlling gene expression in Caenorhabditis elegans is reported. The system affords reversible activation of either extrachromosomal or single-copy integrated transgenes; a complementation-based 'split Q' system also permits specific expression in desired cell types.

In this proof of principle the authors use magnetic tweezers to unzip a DNA hairpin and then measure the molecule extension during rezipping in the presence of oligomers that transiently block the rezipping process. The extent of these blockages allows them to determine the DNA sequence.

The biotin-reversible interaction between a 'hook' protein localized to a particular cellular compartment and a reporter protein of interest is exploited in a simple system to synchronize protein traffic through the secretory pathway.

The Bowtie 2 software achieves fast, sensitive, accurate and memory-efficient gapped alignment of sequencing reads using the full-text minute index and hardware-accelerated dynamic programming algorithms.

Light-inducible dimerization tags are engineered to rapidly recruit proteins to precise points in living yeast and mammalian cells. The affinities and response time of the interactions are tunable, and the authors used the system to activate cell signaling and to direct cell polarization in yeast.

We describe software, MiceProfiler, for automatic tracking of two interacting mice and analysis of their social interactions without the need of animal tagging. The program allows the identification of key elements that trigger social contact in different mouse strains.

Tough decoy microRNA inhibitor, shown to be the most effective of several designs, is packaged in recombinant adeno-associated virus and used for prolonged microRNA inhibition in living mice. A single injection effectively reduces miR-122 in the liver and serum cholesterol for at least 25 weeks.

Reported is the unexpected release of polymorphonuclear neutrophilic granulocytes into the blood as a side effect of diphtheria toxin receptor–mediated dendritic cell depletion in two widely used transgenic mouse lines. The authors present a bacterial artificial chromosome transgenic mouse line that circumvents this problem.

A photoisomerizable molecule, quaternary ammonium–azobenzene–quaternary ammonium (QAQ) enables reversible optical silencing of nociceptive neurons. The selective entry of QAQ into active nociceptive neurons allows spatially and temporally precise regulation of nociceptor activity in vitro and in vivo.

Reported is a method, genome-wide enrichment of seed sequence (GESS), to analyze primary data from siRNA screens to identify major off-targeted transcripts. Using GESS the authors identify off-targeted transcripts in several screens.

The systematic functional dissection of long non-coding RNA (lncRNA) is simplified using a combined knockdown and localization approach based on endoribonuclease-prepared siRNA (esiRNA). A pilot screen reveals lncRNAs involved in the maintenance of pluripotency.

Algorithms that integrate genome-wide copy number and gene expression data offer a promising way to uncover genes that drive the progression of cancers. The performance of ten software tools on simulated and real cancer datasets of different sizes is directly compared in this Analysis.

A light-inducible dimerization domain is used to create a genetically encoded, light-switchable transactivator of gene expression. The system allows rapid blue light–mediated activation of transgenes containing an appropriate activation sequence with low background and high induction.