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Computational methods can frequently identify protein-interaction motifs in otherwise uncharacterized open reading frames. However, the identification of candidate ligands for these motifs (e.g., so that partnering can be determined experimentally in a directed manner) is often beyond the scope of current computational capabilities. One exception is provided by the coiled-coil interaction motif, which consists of two or more α helices that wrap around each other: the ligands for coiled-coil sequences are generally other coiled-coil sequences, thereby greatly simplifying the motif/ligand recognition problem. Here, we describe a two-step approach to identifying protein–protein interactions mediated by two-stranded coiled coils that occur in Saccharomyces cerevisiae . Coiled coils from the yeast genome are first predicted computationally, by using the multicoil program, and associations between coiled coils are then determined experimentally by using the yeast two-hybrid assay. We report 213 unique interactions between 162 putative coiled-coil sequences. We evaluate the resulting interactions, focusing on associations identified between components of the spindle pole body (the yeast centrosome).

Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels. Here, we present a ribosome-profiling strategy that is based on the deep sequencing of ribosome-protected mRNA fragments and enables genome-wide investigation of translation with subcodon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control in both determining absolute protein abundance and responding to environmental stress. We also observed distinct phases during translation that involve a large decrease in ribosome density going from early to late peptide elongation as well as widespread regulated initiation at non–adenine-uracil-guanine (AUG) codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible.

A major goal of biology is to provide a quantitative description of cellular behaviour. This task, however, has been hampered by the difficulty in measuring protein abundances and their variation. Here we present a strategy that pairs high-throughput flow cytometry and a library of GFP-tagged yeast strains to monitor rapidly and precisely protein levels at single-cell resolution. Bulk protein abundance measurements of >2,500 proteins in rich and minimal media provide a detailed view of the cellular response to these conditions, and capture many changes not observed by DNA microarray analyses. Our single-cell data argue that noise in protein expression is dominated by the stochastic production/destruction of messenger RNAs. Beyond this global trend, there are dramatic protein-specific differences in noise that are strongly correlated with a protein's mode of transcription and its function. For example, proteins that respond to environmental changes are noisy whereas those involved in protein synthesis are quiet. Thus, these studies reveal a remarkable structure to biological noise and suggest that protein noise levels have been selected to reflect the costs and potential benefits of this variation.

In eukaryotes, the combinatorial association of sequence-specific DNA binding proteins is essential for transcription. We have used protein arrays to test 49 2 pairings of a nearly complete set of coiled-coil strands from human basic-region leucine zipper (bZIP) transcription factors. We find considerable partnering selectivity despite the bZIPs' homologous sequences. The interaction data are of high quality, as assessed by their reproducibility, reciprocity, and agreement with previous observations. Biophysical studies in solution support the relative binding strengths observed with the arrays. New associations provide insights into the circadian clock and the unfolded protein response.

Cells of the same type can generate diverse sets of physiological traits from a single set of genes. Part of this diversity could stem from 'noise' that arises from variations in the way proteins are expressed.

Previous studies have shown that approximately 80% of patients with X-linked ichthyosis have a total deletion of the steroid sulphatase (STS) locus which lies in Xp22.3-Xpter. We show by Southern analysis that a common core of sequences are absent in 78.6% of our cases, suggesting that the deletion breakpoints may be highly clustered. To characterize the region in more detail a long-range physical map of over 3 megabases (Mb) surrounding the STS locus was constructed using pulse-field gel electrophoresis. The map enabled the order of sequences tel-SI19-GMGXY3-[STS,GMGXY19]-GMGX9-[dic56 ,SIII2]-cen and the localization of the deletion breakpoints to be established. In ten cases the pulse-field evidence supports the clustering of breakpoints and indicates a deletion size of 2 Mb in most patients. Five CpG islands have been positioned around the STS locus and may be associated with other loci in the region involved in mental retardation and Kallman's syndrome. The map will be instrumental in an attempt to isolate and characterize the deletion breakpoints and to access other genes located in the region.

Miller and Liberman [Percept. Psychophys. 25, 457–465 (1979)] demonstrated that listeners use vowel duration information when making the /ba/–/wa/ distinction. They also found that adding a final consonant to the syllables shifted the /ba/–/wa/ boundary. However, they did not examine the effects of changing the final consonant duration. Furthermore, by using stimuli that were voiced throughout, the potential effects of acoustic and auditory similarity between the initial consonant distinction and the succeeding phonemes could not be examined. In this experiment CVC syllables were used to examine the effect of this later‐occurring speaking rate information on an initial /sh/–/ch/ distinction. The syllables ended with /s/, and both vowel and final fricative duration were varied independently. This allowed one to examine the effect of acoustic similarity on the coding of rate information. The relevance of these results to the auditory and/or phonetic coding of speaking rate information will be discussed. [Work supported by NIDCD Grant No. DC00219 to SUNY at Buffalo.]

The purpose of the longitudinal study was to investigate the prediction of children's academic achievement on the basis of cognitive tasks given prior to kindergarten, and academic attitudes on the basis of teachers' and mothers' ratings of the children's general cognitive abilities and actual achievement. Subjects were tested initially before entering kindergarten; from 105 to 154 of the 255 kindergarten children were followed through grades 1, 2, 3, 5, and 10. A subset of cognitive tasks maintained a high relation to high school achievement scores, especially in reading. Tenth-grade self-concept of ability, expectancy for success, value of success, and perception of task difficulty showed effects of sex and academic content area, with boys generally being more favorable toward math and girls more favorable toward reading. Children's attitudes were related both to mothers' earlier ratings of their children's cognitive abilities and actual achievement scores; this was especially the case for girls. There was a negative relation between mothers' ratings and girls' attitudes toward mathematics. Sex differences in all measures throughout the 11-year period are reviewed.