A non-EST-based method for exon-skipping prediction

Efforts to identify alternatively spliced human genes have been hindered by the limitations of EST-based strategies. Sorek et al. have identified a number of genomic sequences and structural elements that are conserved between mice and humans and appear to be indicators for alternatively spliced exons, and apply these parameters toward the design of a computational method for prediction of splice variants.

Sorek, R., et al. Genome Res. 14, 1617–1623 (2004).

Chemical tools

An investigation on the analytical potential of polymerized liposomes bound to lanthanide ions for protein analysis

Lanthanide ions, such as Eu3+, offer a potentially promising solution for protein sensing applications, although their usefulness is limited by their weak luminescence. Santos et al. found that by incorporating 5-aminosalicylic acid–sensitized Eu3+ ions into polymerized liposomes, they could achieve sensitive quantification of protein concentrations in aqueous samples.

Santos, M., et al. J. Am. Chem. Soc. 126, 10738–10745 (2004).


Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics

Blagoev et al. grew individual cell cultures in medium containing one of three different isotope-labeled arginine variants, and then stimulated each with EGF for varying lengths of time. Tyrosine-phosphorylated proteins were affinity purified from the pooled lysates and subjected to mass spectrometry. From the resulting MS profiles, a kinetic time-course of phosphorylation was established.

Blagoev, B., et al. Nat. Biotechnol. 22, 1139–1145 (2004).

Chemical biology

DNA-templated organic synthesis and selection of a library of macrocycles

A collection of DNAs consisting of shuffled oligonucleotide tags, each with a corresponding complementary primer conjugated to a specific chemical functional group, form the basis of a system for the stepwise organic synthesis of small-molecule libraries. As an initial test, Gartner et al. use this technique to generate and screen an array of macrocycle compounds.

Gartner, Z.J., et al. Science, published online 19 August 2004.


Exploring the O-GlcNAc proteome: direct identification of O-GlcNAc-modified proteins from the brain

Khidekel et al. expand on a technique previously developed by their group as a strategy for the global identification and analysis of targets of O-GlcNAc-glycosylation. O-GlcNAc-modified proteins from whole-cell lysates were labeled with a ketone-biotin tag by means of an engineered galactosyltransferase enzyme, enabling affinity purification and identification by mass spectrometry.

Khidekel, N., et al. Proc. Natl. Acad. Sci. USA 101, 13132–13137 (2004).