Imaging and fluorescence

Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light

The market for photoactivatable fluorescent proteins is crowded, but Dendra offers a useful twist: sensitivity to visible blue light. Gurskaya et al. show that their engineered, monomeric variant of a coral-derived protein can undergo 1,000–4,500-fold photoconversion from green to red after exposure to 488-nm laser light, a less cytotoxic alternative to ultraviolet light.

Gurskaya, N.G. et al. Nat. Biotechnol. 24, 461–465 (2006).

Bioinformatics

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

Advances in computing power have finally allowed researchers to complete the first all-atom molecular dynamics simulation of an entire organism. Although the subject is a relatively simple RNA virus, this is a major computational achievement, and Freddolino et al. use their detailed simulation to explore important questions about the structure and assembly of the virus.

Freddolino, P.L. et al. Structure 14, 437–449 (2006).

Genomics

Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray

Working with a high-density yeast tiling array, Gresham et al. trained their SNPscanner algorithm to sensitively detect single-base mutations throughout the genome with high resolution. With a single array experiment they were able to pinpoint individual mutations in both reference and nonreference strains, and even identify larger genomic alterations.

Gresham, D. et al. Science 311, 1932–1936 (2006).

Microbiology

Robust Salmonella metabolism limits possibilities for new antimicrobials

Hoping to identify new genes affecting Salmonella enterica virulence, Becker et al. pooled data from previously published mouse studies, comparative genomic analyses of different S. enterica serovars, and in vivo proteomic profiling. This strategy allowed them to assemble a metabolic network map that suggests that most of the best potential drug targets may already be known.

Becker, D. et al. Nature 440, 303–307 (2006).

RNA interference

A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen

Moffat et al. describe ongoing efforts to build a valuable research resource: a library of lentiviral constructs capable of targeting every human and mouse gene for downregulation via RNA interference. The authors test the potential of their still incomplete library in an array-based, high-content imaging screen to identify genes associated with mitotic regulation in human cancer cells.

Moffat, J. et al. Cell 124, 1283–1298 (2006).