Public Databanks Research Articles

Reliable quality-control methods for protein crystal structures.

The emergence of structure-determination initiatives that employ high-throughput protein crystallography emphasizes the need to establish quality-control methods for screening the resulting models prior to deposition with the public data banks. An in-house database of 26 new protein structures, associated diffraction data and high-quality experimentally determined electron-density maps have been used to develop (i) a set of minimal global quality criteria that a structure must meet before the refinement may be considered completed and (ii) a reliable set of indicators for detecting local errors in protein structures. These criteria have been applied to detecting local errors to a set of structures recently deposited in the Protein Data Bank and it is estimated that about 3% of amino acids are incorrectly modeled.

Differential expression of multiple genes during articular chondrocyte redifferentiation.

Articular chondrocytes undergo a rapid change in phenotype and gene expression, termed dedifferentiation, when isolated from cartilage tissue and cultured on tissue culture plastic. On the other hand, "redifferentiation" of articular chondrocytes in suspension culture is characterized by decreased cellular proliferation and the reinitiation of synthesis of hyaline articular cartilage extracellular matrix molecules. The molecular triggers for these events have yet to be defined. Subtracted cDNA libraries representing genes involved in the early events of adult human articular chondrocyte redifferentiation were generated from human articular chondrocytes that were first cultured in monolayer, and subsequently transferred to suspension culture at 10(6) cells/ml for redifferentiation. Differential regulation of genes involved in cellular organization, nuclear structure, cellular growth regulation, and extracellular matrix deposition and remodeling were observed within 48 hr of this transfer. Many of these genes had not been previously identified in the chondrocyte differentiation pathway and a number of the isolated cDNAs did not have homologies to sequences in the public data banks. Genes involved in IL-6 signal transduction including acute phase response factor (APRF), Mn superoxide dismutase, and IL-6 itself were up-regulated in suspension culture. Membrane glycoprotein gp130, a component of the IL-6 receptor, was down-regulated. Other genes involved in cell polarity, cell adherence, apoptosis, and possibly TGF-beta signaling were differentially regulated. The differential regulation of the cytokine connective tissue growth factor (CTGF) during the early stages of articular chondrocyte redifferentiation, decreasing within 48 hours of transfer to suspension culture, was particularly interesting given its reported role in the stimulation of cellular proliferation. CTGF was highly expressed in proliferative monolayer culture, and then greatly reduced by redifferentiation in standard high-density suspension culture. When articular chondrocytes were seeded in suspension at low-density (10(4) cells/ml), however, high levels of CTGF were observed along with increased levels of mature articular cartilage extracellular matrix protein RNAs, such as type II collagen and aggrecan. Although the role of CTGF in articular cartilage biology remains to be elucidated, the results described here demonstrate the potential utility of subtractive hybridization in understanding the process of articular chondrocyte redifferentiation.

Changing the rules? The agreement between Celera and Science magazine concerning Celera's publication of its human genome sequence is upsetting many researchers in bioinformatics.

Science writers have for some years been moving away from their historically awestruck ‘ain't‐science‐grand’ reporting of research developments. Instead, they are more often inspecting science with a critical eye, particularly policy matters. While they are at it, they are filling an information gap, performing a job that the scientific press cannot—or will not—do. The result, however, is that disputes which might in the past have been kept in the scientific family are now broadcast much more widely. The larger world has begun to learn that the rules of science are being revised in ways that some find unsettling, and that science is at something of a loss about what to do. > The larger world has begun to learn that the rules of science are being revised in ways that some find unsettling, and that science is at something of a loss about what to do The latest episode in the discord between science and commerce spilled into public view in the Los Angeles Times in early December, 2000. The case in point is the decision by the journal Science to allow special—unprecedented, some charge—rules governing the data underlying a paper that it wanted very much: Celera Genomics's account of its once‐derided but highly successful shotgun sequencing of the human genome. The agreement between the company and the journal will let Celera keep the sequence data on the company's own computers, rather than deposit it in one of the public databanks as is usual. In practice, this has been GenBank at the National Institutes of Health, the European Bioinformatics Institute in Hinxton, UK and the DNA Data Bank of Japan, designated as official and cost‐free repositories at a 1995 meeting where the NIH and the Wellcome Trust drafted principles for the Human Genome Project. The three databanks have melded so seamlessly …

Analysis of the SOS Response in Salmonella enterica Serovar Typhimurium Using RNA Fingerprinting by Arbitrarily Primed PCR

We report an analysis of a sample of the SOS response of Salmonella enterica serovar Typhimurium using the differential display of RNA fingerprinting gels of arbitrarily primed PCR products. The SOS response was induced by the addition of mitomycin C to an exponentially growing culture of serovar Typhimurium, and the RNA population was sampled during the following 2 h. These experiments revealed 21 differentially expressed PCR fragments representing mRNA transcripts. These 21 fragments correspond to 20 distinct genes. All of these transcripts were positively regulated, with the observed induction starting 10 to 120 min after addition of mitomycin C. Fifteen of the 21 transcripts have no homologue in the public sequence data banks and are therefore classified as novel. The remaining six transcripts corresponded to the recE, stpA, sulA, and umuC genes, and to a gene encoding a hypothetical protein in the Escherichia coli lysU-cadA intergenic region; the recE gene was represented twice by nonoverlapping fragments. In order to determine if the induction of these 20 transcripts constitutes part of a classical SOS regulon, we assessed the induction of these genes in a recA mutant. With one exception, the increased expression of these genes in response to mitomycin C was dependent on the presence of a functional recA allele. The exception was fivefold induced in the absence of a functional RecA protein, suggesting another layer of regulation in response to mitomycin C, in addition to the RecA-LexA pathway of SOS induction. Our data reveal several genes belonging to operons known to be directly involved in pathogenesis. In addition, we have found several phage-like sequences, some of which may be landmarks of pathogenicity determinants. On the basis of these observations, we propose that the general use of DNA-damaging agents coupled with differential gene expression analysis may be a useful and easy method for identifying pathogenicity determinants in diverse organisms.

The sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes.

We report the sequence of a 30,469 bp long DNA fragment on the left arm of chromosome XV of Saccharomyces cerevisiae. The fragment contains 15 open reading frames (ORFs) of at least 300 bp. Five previously sequenced yeast genes, PHO80, TIR2, SLG1, the gene encoding the subtilisin-like protease III precursor and the gene coding for ATP-dependent permease, are found among these ORFs. By DNA sequence comparison, two ORFs identified previously reported expressed sequence tags from yeast. Of the proteins encoded by the remaining eight ORFs, six show similarities to proteins from different organisms and two lack detectable similarity with any amino acid sequence described in public data banks.

The angiogenins.

The angiogenic and other biological functions of the angiogenins, members of the pancreatic RNase superfamily of proteins, are reviewed in the context of their primary and tertiary structures. The ribonucleolytic activity and interactions with the placental ribonuclease inhibitor have seen much study in the last few years. The mechanism of the angiogenic activity of angiogenin has recently been postulated as involving multiple interactions with other proteins through specific regions on the molecular surface of angiogenin. These molecular partners include heparin, plasminogen, elastase, angiostatin, actin and most importantly a 170-kilodalton receptor on subconfluent endothelial cells. The existence of the latter receptor was established in conjunction with a mitogenic activity of angiogenin on subconfluent cells. The levels of angiogenin in various physiological and disease states are summarized, including various studies on pregnancy and angiogenin. Correlations are seen between states of enhanced angiogenesis and angiogenin levels. An overview of the relationship of angiogenin and the other RNases of the superfamily showed that their genes all are in relative close proximity on human chromosome 14. Examination of the many expressed sequence tags published in the public databanks, for angiogenin and the other RNases, revealed that angiogenin and RNase-4 (the most evolutionarily conserved RNase), share various identical 5'-untranslated regions on their sets of messenger RNAs, suggesting that their genes are in very close proximity on chromosome 14 and that they are products of differential splicing. This in turn suggests that, in both humans and mice, expression of these two proteins is under identical control, with obvious implications for their biological activities. The evolutionary history of the angiogenins is examined briefly on the basis of the protein sequences of the human, rabbit, pig, two bovine and four mouse angiogenins, and two mouse angiogenin pseudogene sequences. The discrepancy between the conventional requirement for conservatism in structure to allow multimolecule interactions, and the actual fast-changing sequence of the angiogenins, in concert with the wide-ranging activity even in birds, of human angiogenin, is discussed.

Cementum attachment protein/protein-tyrosine phosphotase-like member A is not expressed in teeth

Cementum is a highly specialized connective tissue that covers tooth roots. The only cementum-specific protein described to date is the cementum attachment protein (CAP). A putative sequence for CAP was established from a cDNA clone isolated from a human cementifying fibroma cDNA library. This sequence overlaps with a phosphatase-like protein in muscle termed the protein-tyrosine phosphatase-like member A (PTPLA). To clarify the nature of CAP/PTPLA, we cloned the homologous rat protein and determined its sequence. The rat protein shared 94% sequence identity with the human protein. On Northern blots containing RNA from various rat tissues of different developmental stages, the cDNA hybridized to an mRNA expressed in heart and skeletal muscle but not in teeth. These results were confirmed by real-time PCR. Thus, the sequence deposited in public databanks under the name 'cementum attachment protein' does not represent genuine CAP.

The Sequence of a 30 kb Fragment on the Left Arm of Chromosome XV from Saccharomyces cerevisiae Reveals 15 Open Reading Frames, Five of which Correspond to Previously Identified Genes

We report the sequence of a 30 469 bp long DNA fragment on the left arm of chromosome XV of Saccharomyces cerevisiae. The fragment contains 15 open reading frames (ORFs) of at least 300 bp. Five previously sequenced yeast genes, PHO80, TIR2, SLG1, the gene encoding the subtilisin-like protease III precursor and the gene coding for ATP-dependent permease, are found among these ORFs. By DNA sequence comparison, two ORFs identified previously reported expressed sequence tags from yeast. Of the proteins encoded by the remaining eight ORFs, six show similarities to proteins from different organisms and two lack detectable similarity with any amino acid sequence described in public data banks. The DNA sequence has been deposited in GenBank under Accession Number U43491.

The sequence of a 30 kb fragment on the left arm of chromosome XV fromSaccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes

We report the sequence of a 30 469 bp long DNA fragment on the left arm of chromosome XV of Saccharomyces cerevisiae. The fragment contains 15 open reading frames (ORFs) of at least 300 bp. Five previously sequenced yeast genes, PHO80, TIR2, SLG1, the gene encoding the subtilisin-like protease III precursor and the gene coding for ATP-dependent permease, are found among these ORFs. By DNA sequence comparison, two ORFs identified previously reported expressed sequence tags from yeast. Of the proteins encoded by the remaining eight ORFs, six show similarities to proteins from different organisms and two lack detectable similarity with any amino acid sequence described in public data banks. The DNA sequence has been deposited in GenBank under Accession Number U43491.

Molecular Cloning of a Highly Conserved Mouse and Human Integral Membrane Protein (Itm1) and Genetic Mapping to Mouse Chromosome 9

We have isolated and characterized a novel cDNA coding for a highly hydrophobic protein (B5) from a fetal mouse mandibular condyle cDNA library. The full-length mouse B5 cDNA is 3095 nucleotides long and contains a potential open reading frame coding for a protein of 705 amino acids with a calculated molecular weight of 80.5 kDa. The B5 mRNA is differentially polyadenylated, with the most abundant transcript having a length of 2.7 kb. The human homolog of B5 was isolated from a cDNA testis library. The predicted amino acid sequence of the human B5 is 98.5% identical to that of mouse. The most striking feature of the B5 protein is the presence of numerous (10–14) potential transmembrane domains, characteristic of an integral membrane protein. Similarity searches in public databanks reveal that B5 is 58% similar to the T12A2.2 gene ofCaenorhabditis elegansand 60% similar to the STT3 gene ofSaccharomyces cerevisiae.Furthermore, the report of an EST sequence (Accession No. Z13858) related to the human B5, but identical to the STT3 gene, indicates that B5 belongs to a larger gene family coding for novel putative transmembrane proteins. This family exhibits a remarkable degree of conservation in different species. The gene for B5, designatedItm1(Integral membrane protein 1), is located on mouse chromosome 9.

Databases on Measures to Prevent Occupational Exposure to Toxic Substances

Abstract In various countries databanks have been set up to collect and stimulate transfer of information on practical experience to prevent occupational exposure to health-threatening factors. This article presents the results of a study of existing databanks. The selection, storage, and retrieval of relevant records was studied along with the effectiveness of existing databanks in transferring information between companies and industries. The databanks provide descriptive and condensed information, two to four pages long, including graphic presentations of the solution, and are primarily focused on an audience with marginal training in occupational safety and health. The main function of existing databanks is to stimulate creativity among user-groups rather than providing clear-cut solutions to be implemented immediately. It is yet unproven whether current public databanks fill a need, and the effectiveness of the databank in transferring information is not yet clear. Databanks within large companies seem to meet a demand when incorporated in a broader health and safety company policy. The generalizability of preventive measures is not guaranteed in the present databanks, due to the lack of a classification of solutions and processes that would allow the user to find relevant solutions across industry boundaries. None have any built-in guidance to help users navigate from their defined problem to the most useful solutions. These issues are the starting point for a discussion on “solution databases.” Swuste, P.; Hale, A.: Databases on Measures to Prevent Occupational Exposure to Toxic Substances. Appl. Occup. Environ. Hyg. 9(1):57–61; 1994.

Statistical information for businesses from Eurostat

Eurostat is one of the directorates‐general of the Commission of the European Communities. Its aim is to create a European statistical system which will produce comparable statistics, by developing common classifications for products, industries, activities and regions, by surveys and questionnaires prepared by Eurostat in collaboration with the national statistical offices of the Member States and also by detailed methodologies giving common concepts and definitions for such areas as national accounts, agriculture and foreign trade. Eurostat publishes macro economic statistics for the twelve Member States covering national accounts, finance, balance of payments, social, agriculture, foreign trade, industry, energy and developing countries. An effort is made to have comparable information for the Communities, main trading partners, the United States of America and Japan, especially where the short‐term economic indicators are concerned. Three public databanks have been developed. CRONOS contains over a million chronological time series covering all the above subjects in very great detail. COMEXT is the foreign trade databank for the trade between the Member States and over 200 partner countries using the Combined Nomenclature, a goods classification with approximately 10,000 products. REGIO has the macroeconomic regional data for the Member States using the NUTS classification to breakdown the countries into three interrelated levels. A wide range of publications, microfiches, floppy discs and CD‐ROMs are also available. Eurostat's products reflect the economic and social policies of the Commission, especially where agriculture and national accounts are concerned. The information Eurostat requests from the Member States is directed by the needs of the Commission services.