Volume 8 Issue 6, June 2011

A physicist pushed microscopes beyond theoretical limits to provide a better look inside living cells.

Two new reports describe variants of channelrhodopsin 2 with improved properties.

A normally undesirable property of chromophores is used in the creation of a genetically encoded tag for correlated light and electron microscopy.

Combining proteome analysis with genome sequencing improves gene annotation and yields evidence that some genes presumed to be noncoding are actually expressed.

Phage-assisted continuous evolution of proteins automates and accelerates selection, allowing hundreds of rounds of evolution to occur in a single week.

A paleoenzymology approach yields a thermostable thioredoxin enzyme that is functional at acidic pH; the underlying method could prove effective for generating other enzymes with such properties.

Complex, curved three-dimensional DNA nanostructures can be created using new DNA origami folding techniques.

Microarrays are not just for analyzing gene expression.

Software for fast and accurate alignment of brain images is used to generate a partial brain atlas for Drosophila melanogaster and should enable circuit mapping.

With vast increases in biological data generation, mechanisms for data storage and analysis have become limiting. A data structure, semantically typed data hypercubes (SDCubes), that combines hierarchical data format version 5 (HDF5) and extensible markup language (XML) file formats, now permits the flexible storage, annotation and retrieval of large and heterogenous datasets.

A transposon-insertion method can trap and mutate genes while simultaneously revealing their spatiotemporal expression pattern, all in a conditional manner in the live, transparent zebrafish.

A combination of PCR stitching with next-generation sequencing results in Stitch-seq, a massively parallel method for interactome mapping. The approach is applied to human protein-protein interactions assayed in yeast two-hybrid screens.

An algorithm to combine the results of different quantitative proteomics data processing workflows is presented. The method substantially increases the number of proteins that can be quantified in a proteomics experiment.

The combination of in situ hybridization of fluorescent probes onto chromosomes in solution and flow cytometry allows the quantitative identification of repeat sequences in individual chromosomes.

Semantically typed data hypercubes (SDCubes) are described for the flexible management and organization of stored experimental data and are applied to high-content imaging data using the software package ImageRail.

Software for the automated and accurate registration of multiple images of Drosophila melanogaster brain is reported. It is used to build a preliminary atlas of gene expression in the fly brain.

Judicious choice of probes and imaging conditions allows two-dimensional super-resolution imaging of live cells at speeds up to 2 Hz with ~25-nm resolution and three-dimensional super-resolution imaging at ~1 Hz with ~30 nm x-y and ~50 nm z dimension resolution using stochastic optical reconstruction microscopy (STORM).

A protein-trap mutagenesis system efficiently disrupts expression and reports endogenous expression patterns of genes in the zebrafish. The authors used it to generate an initial collection of 350 freely available fish lines.

Three-dimensional structural RNA modules, defined as ensembles of stacked arrays of ordered non-Watson-Crick base pairs, are found in many RNAs and play important functional roles. The presented computational tool, RMDetect, allows the identification of common RNA modules from sequence alone.