Imaging and visualization

Nonblinking quantum dots

Single-molecule fluorophore emission intensities fluctuate between bright and dark states, a phenomenon known as blinking. This can make the interpretation of single-molecule data very difficult. Mahler et al. now present a method to synthesize CdSe-CdS core-shell quantum dots in which blinking is suppressed owing to a thick crystalline CdS shell. The researchers hope the nonblinking quantum dots will find application in single-particle tracking experiments.

Mahler, B. et al. Nat. Mater., published online 22 June 2008.

Stem cells

Transcription factor binding in stem cells

Although it is clear that several transcription factors are important for maintaining pluripotency in embryonic stem cells (ESCs), the targets and downstream effectors of these transcriptional programs are far from fully understood. Chen et al. now use chromatin immunoprecipitation followed by sequencing, ChIP-Seq, to map the binding locations of 13 transcription factors and two co-regulators in mouse ESCs. This resource will be useful for studying the regulatory networks underlying ESC identity.

Chen, X. et al. Cell 133, 1106–1117 (2008).

Genomics

Managing sequencing data with EagleView

Next-generation DNA sequencing technologies are facilitating rapid and low-cost sequencing of whole genomes. The enormous volume of sequencing data, however, has presented a huge data management challenge, especially in terms of data visualization. Huang and Marth now present EagleView, a data-integration and visualization tool that supports viewing of millions of reads and is capable of integrating genome annotations. The software is freely available.

Huang, W. & Marth, G. Genome Res., published online 11 June 2008.

Imaging and visualization

A new fluorophore for super-resolution imaging

Super-resolution imaging methods can be used to image single molecules beyond the diffraction limit in cells. Photoswitchable fluorescent proteins that have typically been used for this application are subject to photobleaching. Small organic fluorophores are more resistant to photobleaching and cause less perturbation than large fluorescent proteins but few have been developed for super-resolution imaging. Lord et al. now introduce a bright, photostable, photoactivatable, organic azide-based fluorophore for super-resolution imaging in living cells.

Lord, S.J. et al. J. Am. Chem. Soc. 130, 9204–9205 (2008).

Microbiology

A transposon library for Vibrio cholerae

Vibrio cholerae is the water-borne microorganism responsible for cholera. To facilitate genome-wide screening of gene function in this pathogen, Cameron et al. report the creation of a near-saturation transposon insertion library in V. cholerae strain C6706. They used the library to identify genes involved in chemotactic mobility, a move that may lead to new cholera vaccines.

Cameron, D.E. et al. Proc. Natl. Acad. Sci. USA 105, 8736–8741 (2008).