Reviews & Analysis

A method uses single-molecule, real-time DNA sequencing to detect the modified base 5-hydroxymethylcytosine, an epigenetic mark recently suspected of having essential roles in genome regulation.

A brief description of tools for targeted cleavage and tailored modification of genomes is presented.

Microbial rhodopsins convert light into ion flux; in neurons, this can be used to control activity. New work shows that the opposite is also true: rhodopsins can be used to visualize neural activity.

This Review covers recent technological developments to label and manipulate genes in selected populations of cells in Drosophila melanogaster. The Review is intended as a user guide to help with the selection of the best expression systems and clonal analysis techniques for developmental studies in the fly.

Authors present workflows for the analysis of metabolism phenotypes in mice and recommend analysis of covariance to asses body composition effects.

Chromatin immunoprecipitation and yeast one-hybrid systems are complementary approaches to identify protein-DNA interactions. Improvements to these methods now make them more versatile and high-throughput, and should lead to the generation of rich datasets for the study of gene regulation.

A cardiac-specific reporter genetically engineered into human embryonic stem cells allows the optimization of differentiation protocols and the identification of cell-surface markers—a welcome new tool to help isolate and define cardiac cell lineages.

Daisy-chaining light-sensitive ion channels, pumps and fluorescent proteins extends the possibilities for control of neuronal activity.

In this Perspective the authors discuss strategies for the development of improved fluorescent proteins, with a focus on probes at the red end of the spectrum. They synthesize the literature on chromophore photochemistry and protein structure to identify residues for targeted mutagenesis, and consider improvements in molecular evolution methodologies to enable improved screening for desired probes.

A hydrogel microdevice speeds up the investigation of microenvironmental parameters that direct stem-cell differentiation.

Isobaric tagging methods allow multiplexed quantitative analysis of a wide variety of proteome samples but have been severely limited by problems of accuracy. Two groups now explore this issue and provide complementary solutions to address the problem.

In this Review, the authors thoroughly discuss solution-state NMR spectroscopy methods used for characterizing the dynamic structure landscape of RNA molecules, from picosecond to second timescale motions.

A comparison of embryonic stem cells and induced pluripotent stem cells on the proteome level reveals subtle distinctions between these cell types that might explain differences in their ability to differentiate into specific lineages.

Induced pluripotent stem cells have been derived from two endangered wildlife species. There are exciting possibilities, yet formidable challenges, for these cells to contribute to real-life species preservation.

The combination of optogenetics with feedback control counteracts variability in cellular signaling responses to promote a deeper understanding of the biochemical mechanisms involved.

Presented is a Review of the principles and practice of optical sectioning microscopy using planar illumination or structured illumination with descriptions of the advantages and disadvantages of these techniques.

A new collection of Minos transposon insertions will enhance the range and flexibility of genome engineering in Drosophila melanogaster.

In two independent studies, researchers experimentally test the cleavage specificity of zinc-finger nucleases across the genome.

Two fluorescent proteins that emit in the far-red and infrared range for imaging applications in cells and in vivo are described.