Gene regulation

Mutagenesis screens in human cells

The classical mutagenesis approach is a powerful method to determine the genes induced in various biological processes. However, the diploid nature of the human and other mammalian genomes has limited large-scale mutagenesis studies. Now, Carette et al. describe an insertional mutagenesis screening approach for human cells that uses a chronic myeloid leukemia cell line with a haploid karyotype, for all but chromosome 8. They used this approach to identify genes required for the lethal effects of bacterial toxins and for infection with influenza virus.

Carette, J.E. et al. Science 326, 1231–1235 (2009).

Protein biochemistry

Structures of transient complexes

Proteins carry out most of their functions by interacting with other proteins. Often these interactions are short-lived and are therefore difficult to isolate and study structurally. Schug et al. describe an approach to obtain structural models for these transient protein complexes. They combine existing structures for the individual proteins with an analysis of mutational patterns to identify interacting surface amino acids and then use molecular dynamics simulations to resolve structural models of the transient complexes.

Schug, A. et al. Proc. Natl. Acad. Sci. USA 106, 22142–22129 (2009).

Microarrays

DNA stiffness as a microarray readout

Gene expression analysis via microarrays usually involves fluorescence labeling. Husale et al. describe an alternative, label-free readout, based on the unique nanomechanical response of hybridized versus single-stranded DNA. They use an atomic force microscope to scan the surface of the array and create a stiffness map; hybridized DNA molecules are less stiff than flat-lying single-stranded DNA probes. This nanomechanical readout offers attomolar sensitivity and a large dynamic range.

Husale, S. et al. Nature 462, 1075–1078 (2009).

Imaging and visualization

Cell cycle imaging in fish

Cell cycle–dependent protein ubiquitination has been previously used by Miyawaki et al. as the basis for genetically encoded fluorescent reporters for the cell cycle in mammalian systems. Using the fish orthologs of these proteins, the researchers now extend this 'Fucci' approach to zebrafish. The transparency of the fish embryo permits the imaging of cell-cycle transitions during development.

Sugiyama, M. et al. Proc. Natl. Acad. Sci. USA 106, 20812–20817 (2009).

Biosensors

Multiplexed biomarker detection

Making the detection of clinical biomarkers routine requires inexpensive, highly sensitive and reliable methods that can be multiplexed. Washburn et al. demonstrate that the relatively new technology of silicon photonic microring resonators can fulfill these requirements. These optical sensors are very sensitive to changes in the refractive index upon binding of an antigen to an antibody, for example. Washburn et al. used this technology for the multiplexed detection of five protein biomarkers in complex solutions.

Washburn, A.L. et al. Anal. Chem. 82, 69–72 (2009).