The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information.

The Yeast Proteome Database (YPDtrade mark) has been for several years a resource for organized and accessible information about the proteins of Saccharomyces cerevisiae. We have now extended the YPD format to create a database containing complete proteome information about the model organism Caenorhabditis elegans (WormPDtrade mark). YPD and WormPD are designed for use not only by their respective research communities but also by the broader scientific community. In both databases, information gleaned from the literature is presented in a consistent, user-friendly Protein Report format: a single Web page presenting all available knowledge about a particular protein. Each Protein Report begins with a Title Line, a concise description of the function of that protein that is continually updated as curators review new literature. Properties and functions of the protein are presented in tabular form in the upper part of the Report, and free-text annotations organized by topic are presented in the lower part. Each Protein Report ends with a comprehensive reference list whose entries are linked to their MEDLINE s. YPD and WormPD are seamlessly integrated, with extensive links between the species. They are freely accessible to academic users on the WWW at http://www. proteome.com/databases/index.html, and are available by subscription to corporate users.

The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data.

The Yeast Proteome Database (YPD) is a model for the organization and presentation of comprehensive protein information. Based on the detailed curation of the scientific literature for the yeast Saccharomyces cerevisiae, YPD contains more than 50 000 annotations lines derived from the review of 8500 research publications. The information concerning each of the approximately 6100 yeast proteins is structured around a convenient one-page format, the Yeast Protein Report, with additional information provided as pop-up windows. Protein classification schema have been revised this year, defining each protein's cellular role, function and pathway, and adding a Functional to the Yeast Protein Report. These changes provide the user with a succinct summary of the protein's function and its place in the biology of the cell, and they enhance the power of YPD Search functions. Precalculated sequence alignments have been added, to provide a crossover point for comparative genomics. The first transcript profiling data has been integrated into the YPD Protein Reports, providing the framework for the presentation of genome-wide functional data. The Yeast Proteome Database can be accessed on the Web at http://www.proteome.com/YPDhome.html

The Yeast Protein Database (YPD): a curated proteome database for Saccharomyces cerevisiae.

The Yeast Protein Database (YPD) is a curated database for the proteome of Saccharomyces cerevisiae . It consists of approximately 6000 Yeast Protein Reports, one for each of the known or predicted yeast proteins. Each Yeast Protein Report is a one-page presentation of protein properties, annotation lines that summarize findings from the literature, and references. In the past year, the number of annotation lines has grown from 25 000 to approximately 35 000, and the number of articles curated has grown from approximately 3500 to >5000. Recently, new data types have been included in YPD: protein-protein interactions, genetic interactions, and regulators of gene expression. Finally, a new layer of information, the YPD Protein Minireviews, has recently been introduced. The Yeast Protein Database can be found on the Web at http://www.proteome.com/YPDhome. html

Perinatal vitamin A (retinol) status of northern Canadian mothers and their infants.

Vitamin A (retinol) status was determined in two groups living in the northern part of Canada: native (Indian and Inuit) and non-native (Caucasian). The dietary intake of vitamin A and its plasma concentration were measured prenatally, at delivery and postnatally in mothers. Plasma concentrations were also measured at birth and postnatally in their infants. The mean vitamin A intake of native mothers was significantly lower than that of non-native mothers, 661 +/- 485 versus 1,377 +/- 1,418 retinol equivalents (p < 0.00005), with a higher risk of deficiency without supplementation, 35% versus 8%. Plasma retinol concentrations, although not in the deficient range, were significantly lower in native than non-native mothers prenatally and postnatally. Infant mean plasma retinol concentrations at birth averaged only 52% of those of their mothers and were significantly lower among native than non-native infants although no clinical evidence of vitamin A deficiency was noted. We speculate that vitamin A supplementation in native Northern Canadian mothers during pregnancy and in their neonates during infancy may have a role to play in the prevention of vitamin A deficiency. We also postulate that plasma retinol concentrations of 50-60% of maternal levels and between 0.7 and 2.5 mumol/l represent a 'normal' range for newborn infants.

The mouse 14-3-3 epsilon isoform, a kinase regulator whose expression pattern is modulated in mesenchyme and neuronal differentiation.

Kidney development is a complex, little understood process based on inductive interactions and intricate epithelial and mesenchymal morphogenesis. Here, we report the use of subtractive hybridization to clone cDNAs expressed in early nephrogenesis. cDNA made from E14.5 mouse kidney was hybridized with adult mouse liver mRNA employing a technique based on labeling the driver mRNA with photoactivatable biotin and using streptavidin to remove RNA:cDNA complexes. An aliquot of the unhybridized cDNA identified several clones including three isolates that proved to be the epsilon isoform of the 14-3-3 gene family that is, among other functions, implicated in protein kinase C regulation. Northern blot analysis showed a 2.0-kb transcript widely present in mouse embryos from E7.5 onward, but, as expected from the subtractive strategy, absent in adult liver. In situ hybridization was carried out on mouse embryos aged E8.5 to E15.5. These showed that, in the E8.5 embryo, the 14-3-3 epsilon gene was expressed throughout the embryo, but that, within a day, expression was more marked in mesenchyme than elsewhere (e.g., epithelial tissue, where it was generally low), although levels in neural tissue rose again by about E12.5. This difference was maintained until E15.5 when expression levels started to drop in most tissues, with those of the nervous system, tooth, and kidney being exceptions. Perhaps the most intriguing feature of the expression pattern, however, was that, while the gene was strongly expressed in early mesenchyme, the level of expression decreased as the mesenchyme differentiated. This change was particularly noted in mesenchymal condensations that would become cartilage, bone, and myotome-derived muscle, in the presumptive muscle layer of the gut, and in the kidney. In this last case, the gene was strongly expressed in stem cells and mesenchyme, but expression levels dropped markedly as early nephrogenic condensates epithelialized. The results as a whole thus argue for the 14-3-3 epsilon isoform playing roles in neural development and in early mesenchyme, with this latter function being lost or replaced as the tissue differentiates.

RNA splicing. U2 fulfils a commitment.

Genetic and biochemical studies of pre-mRNA splicing have recently converged to elucidate an early step in the process: the targeting of the U2 small nuclear ribonucleoprotein particle to the pre-mRNA.

The alternative 5'-end of the Drosophila melanogaster epidermal growth factor receptor cDNA (DER) is part of the D14-3-3 cDNA.

A portion of the cDNA reported as a novel cDNA encoding the Drosophila melanogaster homolog of the bovine 14-3-3 protein by Swanson and Ganguly [Gene 113 (1992) 183-190] already exists in the database. It was originally reported as an alternative 5' end of the D. melanogaster homolog of the epidermal growth factor receptor (DER). Schejter and Shilo [Cell 56 (1989) 1093-1164] later reported that this finding was due to a cloning artifact that joined the 14-3-3 cDNA onto the DER cDNA.

Iron status and pregnancy in a northern Canadian population: relationship to diet and iron supplementation.

To determine the extent of iron deficiency, the prognostic value of prenatal ferritin levels and the desirability of prenatal iron supplementation in the western Canadian arctic, dietary iron intake was determined in 171 women and ferritin levels determined in 121 women during pregnancy, 79 at delivery and 77 postnatally, as well as in 65 of their infants at birth and 74 postnatally. Iron deficiency (ferritin < 15 ng/ml) was present in 34% of women during the first two trimesters, 25% (20/79) at delivery and in 51.7% (15/29) of mothers and 31% (9/29) of infants beyond four months after delivery. Maternal follow-up ferritin levels correlated poorly with dietary iron intake but well with prenatal ferritin levels, which appeared to be good predictors of the effectiveness of supplementation. Mean infant follow-up ferritin levels were 105.6 +/- 115.2 ng/ml with, and 46.7 +/- 63.5 without maternal prenatal supplementation (p = 0.03); maternal, 45.5 +/- 40.9 ng/ml with, and 12.8 +/- 9.2 without (p < 0.001). Measurement of prenatal ferritin levels to determine risk of iron deficiency and routine prenatal iron supplementation are recommended.

Smoking and caffeine and alcohol intake during pregnancy in a northern population: effect on fetal growth.

OBJECTIVES: To assess the prevalence of smoking and of caffeine and alcohol intake during pregnancy in a northern population and to determine the relation of these factors to birth weight, length and head circumference. DESIGN: Questionnaire survey and collection of maternal and newborn measurements. SETTING: Ten communities in the Inuvik Zone, NWT. PATIENTS: A total of 162 women (56 Inuit, 38 Indian, 37 white and 31 mixed race) who presented for prenatal care in their community and gave birth in Inuvik between September 1987 and January 1990 and their newborns. RESULTS: In all, 64% (101/159) of the women smoked, 57% (88/154) ingested more than 300 mg of caffeine daily, and 34% (50/145) drank alcohol during their pregnancy. Smoking, caffeine intake and binge drinking were most frequent among the Inuit and Indian mothers. Smoking was significantly associated with decreased birth weight (p less than 0.001) and length (p less than 0.05). Alcohol intake, especially binge drinking, was significantly associated with decreased head circumference (p less than 0.05). Caffeine was found not to be related to any of the outcome variables after smoking was controlled for through stepwise multiple regression. CONCLUSIONS: The marked prevalence of smoking and alcohol intake during pregnancy and their effects on the newborn are public health concerns in the Northwest Territories and warrant intensive countermeasures.

Site-specific creation of uridine from cytidine in apolipoprotein B mRNA editing.

Human apolipoprotein (apo) B mRNA is edited in a tissue specific reaction, to convert glutamine codon 2153 (CAA) to a stop translation codon. The RNA editing product templates and hybridises as uridine, but the chemical nature of this reaction and the physical identity of the product are unknown. After editing in vitro of [32P] labelled RNA, we are able to demonstrate the production of uridine from cytidine; [alpha 32P] cytidine triphosphate incorporated into RNA gave rise to [32P] uridine monophosphate after editing in vitro, hydrolysis with nuclease P1 and thin layer chromatography using two separation systems. By cleaving the RNA into ribonuclease T1 fragments, we show that uridine is produced only at the authentic editing site and is produced in quantities that parallel an independent primer extension assay for editing. We conclude that apo B mRNA editing specifically creates a uridine from a cytidine. These observations are inconsistent with the incorporation of a uridine nucleotide by any polymerase, which would replace the alpha-phosphate and so rule out a model of endonucleolytic excision and repair as the mechanism for the production of uridine. Although transamination and transglycosylation remain to be formally excluded as reaction mechanisms our results argue strongly in favour of the apo B mRNA editing enzyme as a site-specific cytidine deaminase.

The spfash mouse: a missense mutation in the ornithine transcarbamylase gene also causes aberrant mRNA splicing.

Ornithine transcarbamylase (ornithine carbamoyltransferase; carbamoyl-phosphate:L-ornithine carbamoyltransferase, EC 2.1.3.3) is a mitochondrial matrix enzyme of the mammalian urea cycle. The X chromosome-linked spfash mutation in the mouse causes partial ornithine transcarbamylase deficiency and has served as a model for the human disease. We show here that the spfash mutation is a guanine to adenine transition of the last nucleotide of the fourth exon of the ornithine transcarbamylase gene. This nucleotide change produces two remarkably different effects. First, this transition causes ornithine transcarbamylase mRNA deficiency because the involved exon nucleotide plays a part in the recognition of the adjacent splice donor site. As a result of the mutation, ornithine transcarbamylase pre-mRNA is spliced inefficiently both at this site and at a cryptic splice donor site 48 bases into the adjacent intron. Second, two mutant proteins are translated from these mRNAs. From the correctly spliced mRNA, the transition results in a change of amino acid 129 from arginine to histidine. This missense substitution has no discernable effect on mitochondrial import, subunit assembly, or enzyme activity. On the other hand, the elongated mRNA resulting from mis-splicing is translated into a dysfunctional ornithine transcarbamylase subunit elongated by the insertion of 16 amino acid residues.

Survey of amino-terminal proteolytic cleavage sites in mitochondrial precursor proteins: leader peptides cleaved by two matrix proteases share a three-amino acid motif.

We have compiled sequences of precursor proteins for 50 mitochondrial proteins for which the mature amino terminus has been determined by amino acid sequence analysis. Included in this set are 8 precursors that have leader peptides that are cleaved in two places by mitochondrial matrix proteases. When these eight leader peptides are aligned and compared, a highly conserved three-amino acid motif is identified as being common to this class of leader peptides. This motif includes an arginine at position -10, a hydrophobic residue at position -8, and serine, threonine, or glycine at position -5 relative to the mature amino terminus. The initial cleavage of these peptides by matrix processing protease occurs within the motif, between residues at -9 and -8, such that arginine at position -10 is at position -2 relative to the cleaved bond. The rest of the motif is within the octapeptide removed by subsequent cleavage catalyzed by intermediate-specific protease. An additional 14 leader peptides in this collection (all of those that contain an arginine at -10) conform to this motif. Assuming that these 14 precursors are matured in two steps, we compared the internal cleavage sites at position -8 with the ends of the other 30 leader peptides in the collection. We find that 74% of matrix processing protease cleavage sites follow an arginine at position -2 relative to cleavage.

A cDNA clone for the precursor of rat mitochondrial ornithine transcarbamylase: comparison of rat and human leader sequences and conservation of catalytic sites.

We have cloned a DNA complementary to the messenger RNA encoding the precursor of ornithine transcarbamylase from rat liver. This complementary DNA contains the entire protein coding region of 1062 nucleotides and 86 nucleotides of 5'- and 298 nucleotides of 3'-untranslated sequences. The predicted amino acid sequence has been confirmed by extensive protein sequence data. The mature rat enzyme contains the same number of amino acid residues (322) as the human enzyme and their amino acid sequences are 93% homologous. The rat and human amino-terminal leader sequences of 32 amino acids, on the other hand, are only 69% homologous. The rat leader contains no acidic and seven basic residues compared to four basic residues found in the human leader. There is complete sequence homology (residues 58-62) among the ornithine and aspartate transcarbamylases from E. coli and the rat and human ornithine transcarbamylases at the carbamyl phosphate binding site. Finally, a cysteine containing hexapeptide (residues 268-273), the putative ornithine binding site in Streptococcus faecalis, Streptococcus faecium, and bovine transcarbamylases, is completely conserved among the two E. coli and the two mammalian transcarbamylases.