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At least 703 records · Page 39Linked to original sources
PubMed2000

Validation of death certificate diagnosis of out-of-hospital coronary heart disease deaths in Olmsted County, Minnesota.

OBJECTIVE: To evaluate the validity of death certificate diagnosis of out-of-hospital (OOH) coronary heart disease (CHD) and sudden cardiac death (SCD) in Olmsted County, Minnesota, between 1981 and 1994. METHODS: In this review of the medical records, autopsy reports, and coroner's files, OOH deaths with heart disease as the underlying cause of death on the death certificate were classified into CHD (International Classification of Diseases, 9th Revision, Clinical Modification [ICD-9-CM] codes 410-414) and non-CHD (other ICD-9-CM heart disease codes) deaths. A 10% random sample (n = 174) of these death certificates was reviewed by physicians, and published validation criteria were applied to classify these deaths into validated CHD or non-CHD categories. Sudden cardiac death was defined as validated CHD that occurred at an OOH location with less than 24 hours between symptom onset and death. RESULTS: The death certificate definition of OOH CHD death (ICD-9-CM codes 410-414) had high sensitivity and positive predictive value of 91% and 96%, respectively. The specificity and the negative predictive value were slightly lower at 86% and 72%, respectively. The sensitivity of death certificate diagnosis of CHD for validated SCD was 89%, and the positive predictive value was 77%. Using a more restrictive definition of SCD, that is, less than 1 hour between the onset of symptoms and death, the positive predictive value of CHD codes for SCD was lower at 52%. CONCLUSIONS: In Olmsted County, the positive predictive values of death certificate diagnosis for OOH CHD and SCD are high. Relying on death certificate diagnoses results in about 5% underestimation of the true CHD rates, whereas their use as a surrogate for SCD yields a 16% overestimation of the true SCD rates.

Autopsy↗
PubMed2004

Mining single nucleotide polymorphisms from EST data of silkworm, Bombyx mori, inbred strain Dazao.

We made use of 81,635 expressed sequence tags (ESTs) derived from 12 different cDNA libraries of the silkworm, Bombyx mori, inbred strain Dazao (P50), to identify high-quality candidate single nucleotide polymorphisms (SNPs). By PHRAP assembling, 12,980 contigs containing 11,537 contigs assembled by more than one read were obtained, and 101 candidate SNPs and 27 single base insertions/deletions were identified from 117 contigs assembled from 1576 high-quality reads base-called with PHRED and screened on the basis of the neighborhood quality standard (NQS). Simultaneously, we also predicted 40 SNPs in coding regions (cSNPs), of which 26 were predicted to lead to amino acid non-synonymous variations and 14 synonymous substitutions. Also, the 1.66:1 ratio of transition/transversion is different from that of other insects. As the first SNP analysis of a Lepidoptera, B. mori, the single nucleotide polymorphic density is estimated to be 1.3 x 10(-3) by sequence diversity. This analysis shows that expressed sequences from multiple libraries may provide an abundant source of comparative reads to mine for cSNPs from the silkworm genome.

Amino Acid Substitution↗
PubMed2002

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).

Streptomyces coelicolor is a representative of the group of soil-dwelling, filamentous bacteria responsible for producing most natural antibiotics used in human and veterinary medicine. Here we report the 8,667,507 base pair linear chromosome of this organism, containing the largest number of genes so far discovered in a bacterium. The 7,825 predicted genes include more than 20 clusters coding for known or predicted secondary metabolites. The genome contains an unprecedented proportion of regulatory genes, predominantly those likely to be involved in responses to external stimuli and stresses, and many duplicated gene sets that may represent 'tissue-specific' isoforms operating in different phases of colonial development, a unique situation for a bacterium. An ancient synteny was revealed between the central 'core' of the chromosome and the whole chromosome of pathogens Mycobacterium tuberculosis and Corynebacterium diphtheriae. The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering.

Bacterial Proteins↗
PubMed2006

Establishment of a pipeline to analyse non-synonymous SNPs in Bos taurus.

BACKGROUND: Single nucleotide polymorphisms (SNPs) are an abundant form of genetic variation in the genome of every species and are useful for gene mapping and association studies. Of particular interest are non-synonymous SNPs, which may alter protein function and phenotype. We therefore examined bovine expressed sequences for non-synonymous SNPs and validated and tested selected SNPs for their association with measured traits. RESULTS: Over 500,000 public bovine expressed sequence tagged (EST) sequences were used to search for coding SNPs (cSNPs). A total of 15,353 SNPs were detected in the transcribed sequences studied, of which 6,325 were predicted to be coding SNPs with the remaining 9,028 SNPs presumed to be in untranslated regions. Of the cSNPs detected, 2,868 were predicted to result in a change in the amino acid encoded. In order to determine the actual number of non-synonymous polymorphic SNPs we designed assays for 920 of the putative SNPs. These SNPs were then genotyped through a panel of cattle DNA pools using chip-based MALDI-TOF mass spectrometry. Of the SNPs tested, 29% were found to be polymorphic with a minor allele frequency >10%. A subset of the SNPs was genotyped through animal resources in order to look for association with age of puberty, facial eczema resistance or meat yield. Three SNPs were nominally associated with resistance to the disease facial eczema (P < 0.01). CONCLUSION: We have identified 15,353 putative SNPs in or close to bovine genes and 2,868 of these SNPs were predicted to be non-synonymous. Approximately 29% of the non-synonymous SNPs were polymorphic and common with a minor allele frequency >10%. Of the SNPs detected in this study, 99% have not been previously reported. These novel SNPs will be useful for association studies or gene mapping.

Amino Acid Substitution↗
PubMed1998

Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes.

The Caenorhabditis elegans genome contains more than 60 cytochrome P450 (CYP) genes. The exon-intron organizations of all of the available and potentially active C. elegans CYP genes were inferred by a newly developed program for predicting protein-coding exons based on the alignment of a genomic DNA sequence and a protein profile. From the predicted amino acid sequences, all of the C. elegans CYP genes except one were classified into three groups, which were closely related to the mammalian drug-metabolizing P450 gene families CYP2, CYP3, and CYP4. The gene structures were strikingly divergent within each group; 20, 10, and 5 unique gene organizations were identified among 40, 18, and 5 genes in the CYP2-, CYP3-, and CYP4-related groups, respectively. The degrees of divergence in gene organization were strongly correlated with those in the amino acid sequences of encoding proteins, and the minimum rate of change in an intron insertion site was estimated to be about 90 times less frequent than amino acid substitutions. Parsimonious analyses suggested that frequent loss and gain of introns has occurred during the evolution of CYP genes in each group after the divergence of nematodes, arthropods, and deuterostomia. Few, if any, incidents of intron sliding were evident, and a model that did not allow intron insertions was highly inconsistent with the observations. All of these findings are explained better by the intron-late view than by the intron-early view.

Amino Acid Sequence↗
PubMed1999

The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum.

Analysis of Plasmodium falciparum chromosome 3, and comparison with chromosome 2, highlights novel features of chromosome organization and gene structure. The sub-telomeric regions of chromosome 3 show a conserved order of features, including repetitive DNA sequences, members of multigene families involved in pathogenesis and antigenic variation, a number of conserved pseudogenes, and several genes of unknown function. A putative centromere has been identified that has a core region of about 2 kilobases with an extremely high (adenine + thymidine) composition and arrays of tandem repeats. We have predicted 215 protein-coding genes and two transfer RNA genes in the 1,060,106-base-pair chromosome sequence. The predicted protein-coding genes can be divided into three main classes: 52.6% are not spliced, 45.1% have a large exon with short additional 5' or 3' exons, and 2.3% have a multiple exon structure more typical of higher eukaryotes.

Animals↗
PubMed2006

Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate.

Archaea have been shown to produce isoprenoids from mevalonate; however, genome analysis has failed to identify several genes in the mevalonate pathway on the basis of sequence similarity. A predicted archaeal kinase, coded for by the MJ0044 gene, was associated with other mevalonate pathway genes in the archaea and was predicted to be the "missing" phosphomevalonate kinase. The MJ0044-derived protein was tested for phosphomevalonate kinase activity and was found not to catalyze this reaction. The MJ0044 gene product was found to phosphorylate isopentenyl phosphate, generating isopentenyl diphosphate. Unlike other known kinases associated with isoprene biosynthesis, Methanocaldococcus jannaschii isopentenyl phosphate kinase is predicted to be a member of the aspartokinase superfamily.

Archaeal Proteins↗
PubMed1991

The human gene for vascular endothelial growth factor. Multiple protein forms are encoded through alternative exon splicing.

Vascular endothelial growth factor (VEGF) is an apparently endothelial cell-specific mitogen that is structurally related to platelet-derived growth factor. By Northern blot and protein analyses, we show that VEGF is produced by cultured vascular smooth muscle cells. Analysis of VEGF transcripts in these cells by polymerase chain reaction and cDNA cloning revealed three different forms of the VEGF coding region, as had been reported in HL60 cells. The three forms of the human VEGF protein chain predicted from these coding regions are 189, 165, and 121 amino acids in length. Comparison of cDNA nucleotide sequences with sequences derived from human VEGF genomic clones indicates that the VEGF gene is split among eight exons and that the various VEGF coding region forms arise from this gene by alternative splicing: the 165-amino-acid form of the protein is missing the residues encoded by exon 6, whereas the 121-amino-acid form is missing the residues encoded by exons 6 and 7. Analysis of the VEGF gene promoter region revealed a single major transcription start, which lies near a cluster of potential Sp1 factor binding sites. The promoter region also contains several potential binding sites for the transcription factors AP-1 and AP-2; consistent with the presence of these sites, Northern blot analysis demonstrated that the level of VEGF transcripts is elevated in cultured vascular smooth muscle cells after treatment with the phorbol ester 12-O-tetradecanoyl-phorbol-13-acetate.

Amino Acid Sequence↗
PubMed1993

Molecular analysis of two genes between let-653 and let-56 in the unc-22(IV) region of Caenorhabditis elegans.

A previous study of genomic organization described the identification of nine potential coding regions in 150 kb of genomic DNA from the unc-22(IV) region of Caenorhabditis elegans. In this study, we focus on the genomic organization of a small interval of 0.1 map unit bordered on the right by unc-22 and on the left by the left-hand breakpoints of the deficiencies sDf9, sDf19 and sDf65. This small interval at present contains a single mutagenically defined locus, the essential gene let-56. The cosmid C11F2 has previously been used to rescue let-56. Therefore, at least some of C11F2 must reside in the interval. In this paper, we report the characterization of two coding elements that reside on C11F2. Analysis of nucleotide sequence data obtained from cDNAs and cosmid subclones revealed that one of the coding elements closely resembles aromatic amino acid decarboxylases from several species. The other of these coding elements was found to closely resemble a human growth factor activatable Na+/H+ antiporter. Paris of oligonucleotide primers, predicted from both coding elements, have been used in PCR experiments to position these coding elements between the left breakpoint of sDf19 and the left breakpoint of sDf65, between the essential genes let-653 and let-56.

Amino Acid Sequence↗
PubMed2003

An Arabidopsis homologue of bacterial RecA that complements an E. coli recA deletion is targeted to plant mitochondria.

Homologous recombination results in the exchange and rearrangement of DNA, and thus generates genetic variation in living organisms. RecA is known to function in all bacteria as the central enzyme catalyzing strand transfer and has functional homologues in eukaryotes. Most of our knowledge of homologous recombination in eukaryotes is limited to processes in the nucleus. The mitochondrial genomes of higher plants contain repeated sequences that are known to undergo frequent rearrangements and recombination events. However, very little is known about the proteins involved or the biochemical mechanisms of DNA recombination in plant mitochondria. We provide here the first report of an Arabidopsis thaliana homologue of Escherichia coli RecA that is targeted to mitochondria. The mt recA gene has a putative mitochondrial presequence identified from the A. thaliana genome database. This nuclear gene encodes a predicted product that shows highest sequence homology to chloroplast RecA and RecA proteins from proteobacteria. When fused to the GFP coding sequence, the predicted presequence was able to target the fusion protein to isolated mitochondria but not to chloroplasts. The mitochondrion-specific localization of the mt recA gene product was confirmed by Western analysis using polyclonal antibodies raised against a synthetic peptide from a unique region of the mature mtRecA. The Arabidopsis mt recA gene partially complemented a recA deletion in E. coli, enhancing survival after exposure to DNA-damaging agents. These results suggest a possible role for mt recA in homologous recombination and/or repair in Arabidopsis mitochondria.

Amino Acid Sequence↗
PubMed1989

The nucleotide sequence of a soybean mosaic virus coat protein-coding region and its expression in Escherichia coli, Agrobacterium tumefaciens and tobacco callus.

A DNA complementary to the 3'-terminal 1168 nucleotides of the genome of the N strain of soybean mosaic virus (SMV) has been cloned and sequenced. cDNA sequence and coat protein analyses indicate that the SMV coat protein-coding region is at the 3' end of the genome, and that the coat protein is processed from a larger protein. The coat protein-coding sequence is predicted to be 795 nucleotides in length, encoding a protein of 265 amino acids with a calculated Mr of 29,857. The 3' untranslated region is 259 nucleotides in length and is followed by a polyadenylate tract. The SMV coat protein-coding region, along with a small amount of upstream sequence, has been expressed in Escherichia coli as a beta-galactosidase fusion protein. The size of the protein was less than predicted for the fusion protein, suggesting processing in E. coli. The coat protein-coding region has also been expressed in Agrobacterium tumefaciens and transgenic tobacco callus as an unfused protein under the control of the cauliflower mosaic virus 35S promoter. The coat protein produced in transgenic tobacco callus had an electrophoretic mobility identical to that of SMV coat protein and constituted approximately 0.05% (w/w) of the total extracted protein.

Amino Acid Sequence↗
PubMed1991

cDNA cloning of the B cell membrane protein CD22: a mediator of B-B cell interactions.

We have cloned a full-length cDNA for the B cell membrane protein CD22, which is referred to as B lymphocyte cell adhesion molecule (BL-CAM). Using subtractive hybridization techniques, several B lymphocyte-specific cDNAs were isolated. Northern blot analysis with one of the clones, clone 66, revealed expression in normal activated B cells and a variety of B cell lines, but not in normal activated T cells, T cell lines, Hela cells, or several tissues, including brain and placenta. One major transcript of approximately 3.3 kb was found in B cells although several smaller transcripts were also present in low amounts (approximately 2.6, 2.3, and 1.6 kb). Sequence analysis of a full-length cDNA clone revealed an open reading frame of 2,541 bases coding for a predicted protein of 847 amino acids with a molecular mass of 95 kD. The BL-CAM cDNA is nearly identical to a recently isolated cDNA clone for CD22, with the exception of an additional 531 bases in the coding region of BL-CAM. BL-CAM has a predicted transmembrane spanning region and a 140-amino acid intracytoplasmic domain. Search of the National Biological Research Foundation protein database revealed that this protein is a member of the immunoglobulin super family and that it had significant homology with three homotypic cell adhesion proteins: carcinoembryonic antigen (29% identity over 460 amino acids), myelin-associated glycoprotein (27% identity over 425 amino acids), and neural cell adhesion molecule (21.5% over 274 amino acids). Northern blot analysis revealed low-level BL-CAM mRNA expression in unactivated tonsillar B cells, which was rapidly increased after B cell activation with Staphylococcus aureus Cowan strain 1 and phorbol myristate acetate, but not by various cytokines, including interleukin 4 (IL-4), IL-6, and gamma interferon. In situ hybridization with an antisense BL-CAM RNA probe revealed expression in B cell-rich areas in tonsil and lymph node, although the most striking hybridization was in the germinal centers. COS cells transfected with a BL-CAM expression vector were immunofluorescently stained positively with two different CD22 antibodies, each of which recognizes a different epitope. Additionally, both normal tonsil B cells and a B cell line were found to adhere to COS transfected with BL-CAM in the sense but not the antisense direction.(ABSTRACT TRUNCATED AT 400 WORDS)

Adolescent↗
PubMed2003

Striking complexity of lipopolysaccharide defects in a collection of Sinorhizobium meliloti mutants.

Although the role that lipopolysaccharide (LPS) plays in the symbiosis between Sinorhizobium meliloti and alfalfa has been studied for over a decade, its function in this process remains controversial and poorly understood. This is largely due to a lack of mutants affected by its synthesis. In one of the definitive studies concerning this issue, Clover et al. (R. H. Clover, J. Kieber, and E. R. Signer, J. Bacteriol. 171:3961-3967, 1989) identified a series of mutants with putative LPS defects, judged them to be symbiotically proficient on Medicago sativa, and concluded that LPS might not have a symbiotic function in S. meliloti. The mutations in these strains were never characterized at the molecular level nor was the LPS from most of them analyzed. We have transduced these mutations from the Rm2011 background from which they were originally isolated into the sequenced strain Rm1021 and have characterized the resulting strains in greater detail. We found the LPS from these mutants to display a striking complexity of phenotypes on polyacrylamide electrophoresis gels, including additional rough LPS bands and alterations in the molecular weight distribution of the smooth LPS. We found that some of the mutants contain insertions in genes that are predicted to be involved in the synthesis of carbohydrate components of LPS, including ddhB, lpsB, lpsC, and lpsE. The majority, however, code for proteins predicted to be involved in a wide variety of functions not previously recognized to play a role in LPS synthesis, including a possible transcription elongation factor (GreA), a possible queuine synthesis protein, and a possible chemotaxis protein. Furthermore, using more extensive assays, we have found that most of these strains have symbiotic deficiencies. These results support more recent findings that alterations in LPS structure can affect the ability of S. meliloti to form an effective symbiosis.

Acetylene↗
PubMed2005

CFD simulation of aggregation and breakage processes in laminar Taylor-Couette flow.

An experimental and computational investigation of the effects of local fluid shear rate on the aggregation and breakage of approximately 10 microm latex spheres suspended in an aqueous solution undergoing laminar Taylor-Couette flow was carried out according to the following program. First, computational fluid dynamics (CFD) simulations were performed and the flow field predictions were validated with data from particle image velocimetry experiments. Subsequently, the quadrature method of moments (QMOM) was implemented into the CFD code to obtain predictions for mean particle size that account for the effects of local shear rate on the aggregation and breakage. These predictions were then compared with experimental data for latex sphere aggregates (using an in situ optical imaging method) and with predictions using spatial average shear rates. The mean particle size evolution predicted by CFD and QMOM using appropriate kinetic expressions that incorporate information concerning the particle morphology (fractal dimension) and the local fluid viscous effects on aggregation collision efficiency match well with the experimental data.

Biophysics↗
PubMed2005

CFD simulation of shear-induced aggregation and breakage in turbulent Taylor-Couette flow.

An experimental and computational investigation of the effects of local fluid shear rate on the aggregation and breakage of approximately 10 microm latex spheres suspended in an aqueous solution undergoing turbulent Taylor-Couette flow was carried out. First, computational fluid dynamics (CFD) simulations were performed and the flow field predictions were validated with data from particle image velocimetry experiments. Subsequently, the quadrature method of moments (QMOM) was implemented into the CFD code to obtain predictions for mean particle size that account for the effects of local shear rate on the aggregation and breakage. These predictions were then compared with experimental data for latex sphere aggregates (using an in situ optical imaging method). Excellent agreement between the CFD-QMOM and experimental results was observed for two Reynolds numbers in the turbulent-flow regime.

Journal Article↗
PubMed2000

The accuracy of diagnosis and procedural codes for patients with upper GI hemorrhage.

BACKGROUND: Little is known about the accuracy of diagnostic and procedural codes for common gastrointestinal (GI) conditions and endoscopic procedures. METHODS: Eight hundred eighty-two patients with upper GI hemorrhage admitted in 1994 to 1 of 13 regional hospitals were studied. Based on endoscopy reports, the source of hemorrhage, performance of upper endoscopy and use of endoscopic therapy were determined, and we assessed the sensitivity and positive predictive value of discharge codes for measuring the source of hemorrhage and use of upper endoscopy. RESULTS: The sensitivity and positive predictive value of principal diagnosis coding for source of hemorrhage were typically 85% to 95%. The sensitivity and predictive value of coding for upper endoscopy were 97.7% and 99.9%, respectively, and were 72.3% and 99.4%, respectively, for endoscopic therapy. Accuracy did not differ between the 4 major teaching and 9 other hospitals. CONCLUSIONS: Hospital-based diagnostic and procedural codes are a reasonably accurate source of data for clinical and outcomes analyses of upper GI hemorrhage. In particular, it is possible to discern from these data the source of hemorrhage and the overall use of upper endoscopy.

Cohort Studies↗
PubMed1986

A DNA fragment hybridizing to a nif probe in Rhodobacter capsulatus is homologous to a 16S rRNA gene.

We have sequenced the Rhodobacter capsulatus nifH and nifD genes. The nifH gene, which codes for the dinitrogenase reductase protein, is 894 bp long and codes for a polypeptide of predicted Mr 32,412. The nifD gene, which codes for the alpha subunit of dinitrogenase, is 1,500 bp long and codes for a protein of predicted Mr 56,113. A 776-bp BglII-XhoI fragment containing only nif sequences was used as a hybridization probe against R. capsulatus genomic DNA. Two HindIII fragments, 11.8 kb and 4.7 kb in length, hybridize to this probe. Both fragments have been cloned from a cosmid library. The 11.8-kb fragment contains the nifH, D and K genes, as previously demonstrated (Scolnik and Haselkorn, 1984). In this paper we present evidence that suggests that the 4.7-kb HindIII fragment contains a gene coding for 16S rRNA, and that although homology between nif and this fragment can be observed in filter hybridization experiments, a second copy of the nif structural genes seems not to be present in this region.

Base Sequence↗
PubMed2003

MMPI-2 short form proposal: CAUTION.

The Minnesota Multiphasic Personality Inventory-2 (MMPI-2) is widely used in neuropsychology, though its length (567 items) is sometimes prohibitive. This study investigated some psychometric characteristics of the 180-item version of the MMPI-2 () in order to delineate its strengths, limitations, and appropriate scope of clinical application. Limited reliability and poor predictive accuracy were recently reported for many of the MMPI-2 short-form scales in a study that used 205 brain-injured patients. In the present investigation, we used a psychiatric sample (N=186) with normal neurological findings to examine short-form accuracy in predicting basic scale scores, profile code types, identifying high-point scales, and classifying scores as pathological (T>/=65) or normal-range. The results suggest that, even as applied to neurologically normal individuals, the proposed short form of the MMPI-2 is unreliable for predicting clinical code types, identifying the high-point scale, or predicting the scores on most of the basic scales. In contrast, this short form can be used to predict whether the full-scale scores fall within the pathological range (T>/=65). These findings suggest that clinicians might be able to salvage a small amount of information from the shortened (180-item) version of the MMPI-2 when MMPI-2 protocols are incomplete. However, clinicians should not use a standard interpretive approach with this test, and routine clinical application is unwarranted. Future evaluations of short-form validity should provide a more detailed examination of individual protocols, including an analysis of the frequency of accurate prediction of full-form scores.

Adult↗