Genomics

Finding noisy promoters

Genetically identical populations of unicellular organisms often show a surprising amount of phenotypic variation. Freed et al. developed a fluorescence-activated cell sorting method to identify 'noisy' promoters in Salmonella enterica ssp. I serovar Typhimurium. They created a GFP-tagged genomic plasmid library and subjected populations to fluctuating selection for GFP expression, thus enriching for promoters exhibiting high noise; the noisiest promoters were involved in flagella synthesis.

Freed, N.E. et al. PLoS Genet. 4, e1000307 (2008).

Molecular libraries

Libraries against libraries

The selection of antigen-specific antibodies is slow because antibodies are typically selected against one antigen at a time. Bowley et al. now present a co-selection method for identifying antibody-antigen pairs from libraries displayed in distinct platforms: yeast and phage. This selection method, in tandem with high-throughput antibody-antigen pair validation, should allow simultaneous identification of all antibody-antigen pairs in the mix and, theoretically, should saturate the proteome.

Bowley, D.R. et al. Proc. Natl. Acad. Sci. USA 106, 1380–1385 (2009).

Proteomics

Predicting high-responding peptides

In targeted proteomics and biomarker discovery applications, it is most effective to set the mass spectrometer to selectively detect specific peptides in multiple reaction monitoring (MRM) mode. Fusaro et al. present a computational predictor to help identify signature peptides that are unique to one protein (proteotypic) as well as most likely to produce a high ion current response in the mass spectrometer, based on their physicochemical properties.

Fusaro, V.A. et al. Nat. Biotechnol. 27, 190–198 (2009).

BioPhysics

Single-molecule filament disassembly

RAD51 plays a central role in homologous recombination. The protein polymerizes around a single-stranded DNA to form a duplex-invading nucleoprotein filament, which then disassembles after strand exchange. van Mameren et al. used a powerful single-molecule approach, combining optical tweezers with fluorescence microscopy and microfluidics, to investigate the molecular mechanism of nucleoprotein filament disassembly.

van Mameren, J. et al. Nature 457, 745–748 (2009).

Stem cells

Distinguishing human embryonic stem cells

Aggressive cancers express human embryonic stem (hES) cell–associated genes, suggesting that hES cells are vulnerable to transformation. Partially transformed cells with cancer cell characteristics should be avoided in clinical applications. Towards developing an approach to identifying such cells, Werbowetski-Ogilvie et al. characterized two hES cell lines expressing pluripotency markers at high levels and show that although they are not malignant, they show signs of neoplastic progression.

Werbowetski-Ogilvie, T.E. et al. Nat. Biotechnol. 27, 91–97 (2009).