Gene regulation

Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana

After constructing two hybrid strains of yeast—a 'sender' strain that expresses and secretes a plant-derived hormone, and a 'receiver' strain that expresses a hybrid signal transduction pathway capable of responding to the hormone—Chen & Weiss demonstrate the engineering of simple, synthetic networks that can model a variety of cell-cell communication processes.

Chen, M.-T. & Weiss, R. Nat. Biotechnol. 23, 1551–1555 (2005).

Proteomics

Quantitative analysis of protein phosphorylation in mouse brain by hypothesis-driven multistage mass spectrometry

The sensitive detection of site-specific in vivo phosphorylation changes for a given target protein can pose a complex problem. Jin et al. offer a promising new solution, in which protein samples from drug-treated animals are subjected to a mass spectrometry strategy that allows simultaneous measurement of phosphorylation at many different residues, even at low levels.

Jin, M. et al. Anal. Chem.; published online 9 November 2005.

Cell biology

Unmodified cadmium telluride quantum dots induce reactive oxygen species formation leading to multiple organelle damage and cell death

It has been known for some time that quantum dots alone are cytototoxic and require modification for in vivo use. Lovrić et al. find that cells treated with 'naked' quantum dots undergo nonclassical apoptosis, exhibiting organelle damage and elevated generation of reactive oxygen species, and they suggest that the gradual loss of surface modifications may lead to in vivo toxicity.

Lovrić, J. et al. Chem. Biol. 12, 1227–1234 (2005).

Bioinformatics

Kernel-based machine learning protocol for predicting DNA-binding proteins

Bhardwaj et al. describe a support vector machine (SVM)-based computational method for the characterization of DNA-binding proteins. After training their system for the analysis of features that distinguish DNA-binding from non–DNA-binding proteins, they are capable of achieving prediction with 85–90% accuracy without relying on homology or motif information.

Bhardwaj, N. et al. Nucleic Acids Res. 33, 6486–6493 (2005).

Imaging and visualization

Light-switching excimer probes for rapid protein monitoring in complex biological fluids

Background signal can be an issue when using fluorescence for quantitative protein analysis. Yang et al. describe a modified aptamer whereby binding of target protein puts the molecule into an 'excimer' conformation that brings two pyrene molecules into close proximity, resulting in a fluorescence shift that is quantitative and can be easily distinguished from background.

Yang, C.J. et al. Proc. Natl. Acad. Sci. USA 102, 17278–17283 (2005).