Volume 9 Issue 4, April 2012

Building a better sequence alignment program

Different analytical tasks require different visual representations.

Researchers in three independent laboratories develop nanoscale devices for network-level electrophysiology.

Voltage-driven and enzyme-regulated control allows precise ratcheting of a DNA strand in and out of a nanopore.

Massively parallel reporter assays enable the functional dissection of enhancer sequences in cells and in vivo.

Statistical methods vary widely in the power to predict which rare genetic sequence variants are functional.

New nanostructure delivers potent dose of short interfering RNA

A small chemical probe allows detailed spatial imaging of the temperature in single cells.

Manipulating either culture conditions or genes can precipitate iron particles in yeast cells and render them magnetic.

As more genomes are assembled from scratch, scientists are struggling to assess and improve their quality.

Single-molecule DNA sequencing takes an important step in a surprising new direction with a sequence-detection method based on magnetic tweezers.

Deletion of a genomic locus may affect the function of neighboring loci, creating genetic uncertainty. Researchers now present a computational algorithm for identifying such neighboring-gene effects and improving the quality of functional annotations.

Presented is an update on the status and current practices of the International Molecular Exchange (IMEx) consortium and on its efforts to create a single nonredundant set of protein interactions curated from the scientific literature.

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.

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.

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.

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.

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.

Comprehensive mutation libraries are an invaluable resource for screens in yeast, but anecdotal cases link phenotypes to the neighbor of a mutated gene rather than the mutant itself. The authors show that the neighboring gene effect is widespread and present software that uses protein-protein interaction networks to predict it.

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.

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.

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.

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.

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.

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.