Notable

J.S. Andersen et al., "Directed proteomic analysis of the human nucleolus," Current Biology, 12:1-11, Jan. 8, 2002.

"This is a good paper showing the large scale analysis of a very large protein complex, the nucleolus. [Points of interest]: The size of the complex and that it is dynamic. The mass spectrometry methods used here were a combination of high throughput (matrix-assisted laser desorption ionization coupled to time of flight detection) and low throughput (static nanoelectrospray). Both were apparently needed to achieve the 271 protein total that was reported."

W.K. Scott et al., "Complete genomic screen in Parkinson disease: Evidence for multiple genes," Journal of the American Medical Association, 286:2239-44, Nov. 14, 2001.

F1000 Recommendation: Must Read

"I think this is an interesting, but flawed study, suggesting that tau is locus for Parkinson's disease (PD). Flawed because the finding of a tau locus for PD may well reflect contamination of clinical PD cases by either progressive supranuclear palsy or by frontal temporal dementia with parkinsonism, both of which are encoded at the tau locus. However, others, especially Larry Golbe and colleagues, have also reported tau associations with clinically diagnosed PD, so we await the confirmation of this work in pathologically proven cases."

Y.G. Choi et al., "tRNA elements mediate the assembly of an icosahedral RNA virus," Proceedings of the National Academy of Sciences (PNAS), 99:655-60, Jan. 22, 2002.

F1000 Recommendation: Recommended

"This study reveals a novel function for the tRNA-like structure present at the 3'-terminus of a positive sense RNA virus in promoting the assembly of protein complexes during viral RNA packaging. The authors demonstrate that the tRNA-like structure from brome mosaic virus serves as a chaperone that, in a transient association with virion coat protein, initiates assembly of viral RNA into icosahedral virions with T=3 quasi-symmetry. Their observation that even tRNAs can substitute for this chaperone function suggests the possibility that cellular tRNAs might promote the assembly of cellular protein complexes in ways yet to be discovered."

S.W. Stevens et al., "Composition and functional characterization of the yeast spliceosomal penta-snRNP," Molecular Cell, 9:31-44, January 2002.

F1000 Recommendation: Exceptional

"Stevens et al. provide evidence that the core components of the spliceosome exist as a pre-assembled macromolecular machine that binds to pre-mRNA, catalyzes splicing, releases the spliced mRNA and then proceeds on to bind a new pre-mRNA. This is in contrast to the prevailing view, in which the splicing components assemble on a pre-mRNA in a stepwise fashion. This may well be an example of a huge step forward in a field caused by a small change in salt concentration."

K. Morino et al., "Antibody fusions with fluorescent proteins: A versatile reagent for profiling protein expression," Journal of Immunological Methods, 257:175-84, Nov. 1, 2001.

F1000 Recommendation: Recommended

"The paper describes the creation of two vectors that allow for transfer of single chain antibodies into either of two types of fluorescent proteins for creation of fluorescent protein-antibody fusions. This confirms and extends the results of Griep et al. showing that antibodies to different antigens can be used and different fluorescent proteins can be used. The technique is a rapid means for generating rare reagents with the required read-out for high throughput screening, fluorescence sorting, or fluorescent in situ hybridization experiments."

R. Breitling et al., "Structure-based phylogenetic analysis of short-chain alcohol dehydrogenases and reclassification of the 17beta-hydroxysteroid dehydrogenase family," Molecular Biology and Evolution, 18:2154-61, 2001.

F1000 Recommendation: Recommended

"This paper presents novel methods for using structural data in assessing the phylogeny of proteins, which in turn permit hypotheses of function. Structural coordinates are used to create similarity matrices for a set of short-chain alcohol dehydrogenases; these matrices could be used in phylogenetic analysis even though the proteins were highly divergent in primary sequence. Unexpectedly, the results showed that 17 ß-hydroxysteroid dehydrogenase activity arose more than once in evolutionary time."

B.P. Berman et al., "Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome," PNAS, 99:757-62, Jan. 22, 2002.

M. Markstein et al., "Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo," PNAS, 99:763-8, Jan. 22, 2002.

F1000 Recommendation: Recommended

These papers demonstrate that functional cis-regulatory regions can be identified by searching for clustering of known transcription factor binding sites along a DNA sequence. "The most surprising result [in Berman et al.] is that the local density of binding sites itself appears to encode much of the specificity of transcription-factor function. The most surprising result of [Markstein et al.] is that even knowledge of a single binding site motif is sufficient to identify many relevant cis-regulatory modules."