News & Views in 2011

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.

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.

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.

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.

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.

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.

The two-color traffic light reporter reads out what pathway is used to repair a DNA break and will increase insights into genome engineering.

An absolute quantification approach combined with differential affinity capture provides a means by which to accurately measure distinct pools of ubiquitin in cells or tissues.

Automated methods can now extract brain-image coordinates appearing in hundreds of publications in targeted topic areas and then integrate these data to form computational models that classify new brain-image data.

A technique that combines the speed of pyrosequencing with the sensitivity of fluorescent detection may lead to faster sequencing with smaller quantities of DNA.

A method for clustering billions of unidentified tandem mass spectra from shotgun proteomics experiments offers new ways of storing, organizing and analyzing proteomics data, with potential benefits to the entire proteomics community.

A large-scale, multifaceted screening and validation strategy combining traditional and recombinant antibody technologies yielded a broad spectrum of validated protein binders with high binding affinity and specificity applicable to many fields in proteome research.

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.