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PubMed2002

Partial sequencing of env gene of bovine leukaemia virus from Brazilian samples and phylogenetic analysis.

Analysis of the partial bovine leukaemia virus (BLV) env gp51 gene sequences obtained from three BLV strains isolated in three different regions of Brazil was carried out. The Brazilian BLV env gp51 sequences were compared with seven other corresponding sequences of BLV strains isolated in different countries and with consensus sequence as well. The obtained data point on qualitative and quantitative differences among the analysed strains as far as the occurrence of single point mutations is concerned. Two Brazilian strains show significantly higher mutation rate than other analysed strains. Amino acid analysis did not show, however, any substantial changes of the primary protein structure coded by well conserved region of BLV env gp51 gene. Based on the obtained data, the putative dendogram image of possible phylogenetic relations among the studied BLV strains is presented as well.

Amino Acid Sequence↗
PubMed1995

A Chinese hamster mutant cell line with a defect in the integral membrane protein CII-3 of complex II of the mitochondrial electron transport chain.

In this study, a respiration-deficient Chinese hamster cell line with a defect in succinate dehydrogenase activity is shown to result from a single base change in a codon in the coding sequence for the membrane anchor protein CII-3 (also referred to as QPs-1). A premature translation stop results in the truncation of 33 amino acids from the C terminus. Bovine cDNA encoding this peptide complements the mutation. There is about 82% identity between these two mammalian proteins. The gene for CII-3 was mapped on human chromosome 1, and because it is also found on minichromosomes characterized by our laboratory, we can localize it on the short arm within 1-2 megabases from the centromere.

Amino Acid Sequence↗
PubMedDate not supplied

Statistical vector field analysis applied to mixed cross-sectional and longitudinal data.

Combined cross-sectional and longitudinal data often present complex patterns of change. Growth functions representing the change in some measure as a function of chronological age can be a function of initial values of the measurement. Individual differences in developmental age with respect to chronological age tend to distort attempts to fit a single growth curve through combined cross-sectional and longitudinal data. We present a method by which these data can be visualized along with several examples from a data set comprising measurements of intellectual abilities with respect to aging. We call this new method a statistical vector field (svf) plot. An svf plot simultaneously allows the visualization of cross-sectional information summarizing sampling densities and longitudinal information summarizing how individuals at each particular age and ability are likely to change over time. The C source code for the svf software described in this paper may be obtained free from the University of Virginia anonymous ftp archive server (ftp. Virginia.EDU), or from the authors.

Adult↗
PubMed1996

Isolation and sequence determination of cDNA encoding mouse rab 4 and candidate approach for the beige mutation in mice.

The Chediak-Higashi syndrome is characterized by partial albinism and recurrent infections with giant granules in granulocytes. This syndrome has been proposed to have a defect in vesicular transport. Rab 4 is a member of a family of Ras-related small GTP-binding proteins, which has been mapped in the locus of the Chediak-Higashi syndrome. We isolated a full length cDNA of rab 4 from a cDNA library of mouse liver. The clone is 1428 base pairs (bp) in length and contains a 639 bp open reading frame encoding a polypeptide of 213 residues. The deduced amino acid sequence is highly homologous to rab 4 from rat and human. We analyzed rab 4 as a candidate gene of the beige mouse, but we could not find any change in the sequence of the coding region of rab 4 mRNA.

Amino Acid Sequence↗
PubMed1988

A single amino acid substitution in the human histocompatibility leukocyte antigen DR3 beta chain selectively alters antigen presentation.

Activation of T lymphocytes by immunogenic peptides bound to HLA molecules is a central event in the generation of an immune response. To determine the sites on HLA molecules involved in this process, we isolated mutant EBV-transformed B cell clones that express altered HLA-DR3 molecules. One mutant has lost the ability to stimulate a T cell clone specific for a mycobacterial protein, but retains the ability to stimulate other antigen-specific T cells. The DNA sequence of the complete DR alpha and beta coding regions revealed a single nucleotide change resulting in a glutamic acid to lysine substitution at amino acid 9 in the first hypervariable region of the DR beta chain. These results are discussed in relation to a recently proposed model of class II molecule structure.

Amino Acid Sequence↗
PubMed1998

Phenotype-genotype relationships in complementation group 3 of the peroxisome-biogenesis disorders.

The peroxisome-biogenesis disorders (PBDs) are a set of often lethal genetic diseases characterized by mental retardation and defective peroxisomal matrix protein import. Mutations in PEX12 are known to underlie the disease in two patients from complementation group 3 of the PBDs. Here we show that all patients from this group carry mutations on both alleles of PEX12. A comparison between PEX12 genotypes and the clinical and cellular phenotypes of the corresponding PBD patients suggests a relatively straightforward relationship between genotype and phenotype in this group of the PBDs, such that the loss of PEX12 function leads to more-severe cellular and clinical phenotypes. However, one patient who presented relatively mild clinical and cellular phenotypes was a compound heterozygote for two seemingly severe mutations on each PEX12 allele. PEX12 mRNA present in the patient's cells was derived from only one allele, the one that carried a 2-bp deletion early in the PEX12 coding region, c.26,27Delta. The deduced protein product of this mRNA would contain only the first eight amino acids of the protein, and yet this mutant PEX12 cDNA displayed significant PEX12 activity in a functional complementation assay. Surprisingly, the PEX12/c.26, 27Delta cDNA directed the synthesis of a 29-kD PEX12 protein in vitro, a result that is consistent with translation initiation at a downstream AUG codon. Transfection studies confirmed the expression of similarly sized PEX12 proteins from the PEX12/c.26,27Delta allele. Thus, it appears that translation initiation at internal AUG codons may modulate disease phenotypes and should be considered whenever unexpectedly mild phenotypes result from severe mutations early in the coding region.

Amino Acid Sequence↗
PubMed1989

Issues in reproducibility and validity of dietary studies.

Numerous factors affect the reproducibility and validity of dietary assessment questionnaires. Although the respondents' abilities to respond accurately are most frequently discussed as the cause of apparently poor reproducibility and validity, many other factors are as important and perhaps more important. Most of these other factors are under the control of the investigator, and thus are amenable to improvement. Factors which may affect reproducibility included the degree of variability permitted by the instrument, the error-proneness of the response format, quality control of coding and keying and real dietary change in the time between the two administrations of the questionnaire. Factors affecting real or apparent validity include respondent characteristics, questionnaire design and quantification, quality control, and the adequacy of the reference data. The implications of inadequate reference data are illustrated and discussed.

Humans↗
PubMed2005

Eliminating diagnostic drift in the validation of acute in-hospital myocardial infarction--implication for documenting trends across 25 years: the Minnesota Heart Survey.

Long-term trends in epidemiologic studies of acute myocardial infarction (AMI) require application of a consistent diagnostic algorithm. Typically an algorithm includes chest pain, cardiac enzymes, electrocardiographic findings, and autopsy results. The Minnesota Heart Survey (MHS) has determined trends for incident AMI and for in-hospital and long-term outcomes over a 25-year period (1970-1995). However, dramatic changes have occurred that seriously challenge the ability of the MHS and other epidemiologic studies to use a consistent diagnostic algorithm. These include newer and more sensitive cardiac biomarkers, introduction of diagnosis-related groups, and change in International Classification of Diseases coding. In the MHS, the electrocardiogram is the only diagnostic element consistently available and consistently classified over this 25-year period. The authors identified eight dichotomous Minnesota Code criteria that provided a consistent diagnostic method from 1970 to 1995 as documented by extensive cross-validation. These criteria were combined into a logistic score and used to define incident, recurrent, and attack AMI rates over this 25-year period. For both men and women, AMI rates determined by electrocardiogram are parallel to rates based on the International Classification of Diseases and parallel over adjacent survey periods to the standard MHS algorithm. The electrocardiogram classified by Minnesota Code provides the only consistent long-term diagnostic tool for AMI trends over this 25-year period.

Adult↗
PubMed1998

Improving influenza vaccination coverage among high-risk patients: a role for computer-supported prevention strategy?

BACKGROUND: Worldwide, population-based influenza vaccination strategies are being developed to trace, immunize and monitor high-risk persons efficiently. Computerized prevention modules may facilitate such a strategy in general practice. OBJECTIVES: We established the applicability of a computerized influenza prevention module and specifically addressed improvement of immunization coverage in high-risk patients during two consecutive influenza vaccination rounds after introduction of the module. METHODS: In this descriptive study, four computerized practices of the Utrecht General Practices Network, covering about 36000 patients, participated. In 1995, all patients with high-risk diseases were traced by relevant tags, ICPC- and ATC-codes, using the module. According to changed Dutch immunization guidelines in 1996, healthy elderly people over 65 years were also traced. Demographical and medical data included age, high-risk disease and vaccine uptake. RESULTS: In October 1995, 3871 high-risk patients were identified (11% of population); overall vaccination coverage was 68%. Over one-third of these patients had not been indicated before. In between the two vaccination rounds, 1104 previously unknown patients with high-risk disease <65 years were found by means of the module's on-line status. In October 1996, 6889 persons, including 2308 healthy elderly, were indicated (19%), and vaccination coverage was 62%. Of 3477 patients whose high-risk diseases were documented in both vaccination rounds, an overall improvement of vaccination coverage from 71 % in 1995 to 76% in 1996 was observed (P < 0.05). Main improvements were found in elderly patients. Immunization rates were highest in those with more than one risk factor, lung or cardiac disease, and lowest in healthy elderly and patients under 65 years with lung, renal or other diseases. CONCLUSION: Computerized prevention modules and CMRs may facilitate population-based prevention of influenza and the use should be further encouraged.

Adult↗
PubMed1994

Identification of a gene from Xp21 with similarity to the tctex-1 gene of the murine t complex.

Long range physical mapping within the p21 region of the X chromosome identified a CpG rich island approximately 180 kb centromeric to the chronic granulomatous disease (CGD) locus. The segments adjacent to the CpG island hybridized to discrete bands in DNAs of several species and when used to screen retinal cDNA libraries led to the identification of cDNAs that detected a mRNA of 2.1 kb in many tissues. Molecular characterization of corresponding genomic clones of this novel human gene confirmed the origin of the cDNA clones and indicated a genomic structure with five exons spanning a total of 9 kb. The complete cDNA sequence revealed that this gene contained a putative open reading frame of 116 amino acids with a 3' untranslated region of 1.74 kb. The amino acid sequence shows a high degree of similarity to the predicted product of the tctex-1 gene of the mouse t complex. As linkage studies and patients with deletions have implicated the Xp21 region as containing the retinitis pigmentosa defect (RP3), the gene was assessed as a candidate disease gene in RP3 families. A single base pair polymorphism was identified within the coding region but no disease associated changes were found by single strand conformational polymorphism and sequencing analysis of amplified exons of 20 RP patients. Analysis of a dinucleotide repeat polymorphism within this gene in families affected with RP3 suggested refinement of the RP3 region.

Amino Acid Sequence↗
PubMed1998

Position effect in human genetic disease.

The spatially, temporally and quantitatively correct expression of a gene requires the presence not only of intact coding sequence, free of adverse nucleotide changes, but also correctly functioning regulatory control. With the identification of an increasing number of disease-related genes, the molecular defect in many cases has been defined. It is becoming clear that it is not always the transcription unit that bears the defect: there are a number of cases where the regulation of gene expression has been compromised. Cases associated with chromosomal rearrangement outside the transcription and promoter regions are categorized as position effects. A number of different mechanisms may explain their aetiology. Here, we examine the human disorders where such position effects are implicated. Further study of such cases may lead to important insights into mechanisms of gene regulation and transcriptional control.

Animals↗
PubMed1995

United States mortality from ill-defined causes, 1968-1988: potential effects on heart disease mortality trends.

BACKGROUND: Deaths are coded to the International Classification of Diseases (ICD) category, 'Symptoms, Signs, and ill-defined Conditions' when there is insufficient information for cause of death determination. Due to difficulties of diagnosis of coronary heart disease (CHD) death and since CHD is the leading cause of death among US adults, CHD is the most likely cause of ill-defined deaths. METHODS: Vital statistics and census data were used to create annual age-adjusted ill-defined rates, unrevised CHD rates, and CHD rates revised to include ill-defined deaths for US African Americans and whites, ages 35-74 years, during 1968-1988. Ill-defined and CHD mortality trend analyses were conducted. RESULTS: In 1968, African American/white ratios of ill-defined mortality were 5 among men and 7 among women; following steep declines in ill-defined mortality among African Americans, ratios were 3 among men and 2 among women in 1988. In 1968, approximately 3% and 1% of all deaths among African Americans and whites, respectively, were certified to ill-defined causes; in 1988, approximately 1.5% of deaths among African Americans were coded ill-defined, with no change among whites. Revised CHD rates showed substantially higher excess CHD mortality among African Americans than whites compared to unrevised CHD rates. Declines in revised CHD mortality steepened throughout the study period among men, and among women began to decelerate after 1978. CONCLUSIONS: Ill-defined mortality was of sufficient magnitude to potentially contribute to substantial underestimation of racial disparities in CHD mortality. Also, temporal changes in ill-defined mortality may have affected CHD trends which are used to evaluate the efficacy of public health interventions.

Adult↗
PubMed1990

Effect of dietary restriction on the age-dependent changes in the expression of antioxidant enzymes in rat liver.

The effects of aging and dietary restriction on the expression of several enzymes (superoxide dismutase, catalase and glutathione peroxidase) that are involved in free radical detoxification were studied in liver tissue from male Fischer F344 rats. The expression (i.e., activities and mRNA levels) of superoxide dismutase (Cu-Zn) and catalase decreased with age in liver. Dietary restriction (40% restriction of energy intake) increased the activities of superoxide dismutase (24 to 38%) and catalase (64 to 75%) in liver at 21 and 28 mo of age. Glutathione peroxidase activity in liver of diet-restricted rats was significantly higher (37%) at 28 mo of age than that of rats fed ad libitum. The age-related changes in the relative levels of mRNA for superoxide dismutase, catalase and glutathione peroxidase paralleled the changes in the activities of these enzymes in rats fed ad libitum or rats fed the restricted diet. Thus, the changes in the activities of superoxide dismutase, catalase and glutathione peroxidase with age and dietary restriction appear to arise from changes in the levels of mRNAs coding for these enzymes. Free radical damage, as measured by thiobarbituric acid-reactive material and lipofuscin accumulation, was lower in diet-restricted rats than in rats fed ad libitum.

Aging↗
PubMed2003

Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects.

A number of studies indicated that lineages of animals with high rates of mitochondrial (mt) gene rearrangement might have high rates of mt nucleotide substitution. We chose the hemipteroid assemblage and the Insecta to test the idea that rates of mt gene rearrangement and mt nucleotide substitution are correlated. For this purpose, we sequenced the mt genome of a lepidopsocid from the Psocoptera, the only order of hemipteroid insects for which an entire mtDNA sequence is not available. The mt genome of this lepidopsocid is circular, 16,924 bp long, and contains 37 genes and a putative control region; seven tRNA genes and a protein-coding gene in this genome have changed positions relative to the ancestral arrangement of mt genes of insects. We then compared the relative rates of nucleotide substitution among species from each of the four orders of hemipteroid insects and among the 20 insects whose mt genomes have been sequenced entirely. All comparisons among the hemipteroid insects showed that species with higher rates of gene rearrangement also had significantly higher rates of nucleotide substitution statistically than did species with lower rates of gene rearrangement. In comparisons among the 20 insects, where the mt genomes of the two species differed by more than five breakpoints, the more rearranged species always had a significantly higher rate of nucleotide substitution than the less rearranged species. However, in comparisons where the mt genomes of two species differed by five or less breakpoints, the more rearranged species did not always have a significantly higher rate of nucleotide substitution than the less rearranged species. We tested the statistical significance of the correlation between the rates of mt gene rearrangement and mt nucleotide substitution with nine pairs of insects that were phylogenetically independent from one another. We found that the correlation was positive and statistically significant (R2 = 0.73, P = 0.01; Rs = 0.67, P < 0.05). We propose that increased rates of nucleotide substitution may lead to increased rates of gene rearrangement in the mt genomes of insects.

Animals↗
PubMed1987

Pneumonia--the quality of medical records data.

The quality of medical records data for patients who were hospitalized with community-acquired pneumonia was assessed by comparing medical records data with data obtained in a prospective study of pneumonia for the period April 1, 1984, to December 31, 1984. One hundred five patients fulfilled the case definition of pneumonia for entry into the prospective study. One hundred twenty-seven patients were identified by medical records data. Seventy-three of the patients appeared in both studies. The positive predictive accuracy of the medical records data was 57%. When the etiologic diagnoses for the 73 patients identified by both studies were compared, there was agreement only 52.6% of the time. Streptococcus pneumoniae was overdiagnosed, and Mycoplasma, specific viral causes, and Haemophilus influenzae were not recorded by the medical records data. The quality of medical records data regarding pneumonia can be improved by changing the current ICD-9-CM coding system for pneumonia and by providing instruction and an algorithm for abstractors to follow in assigning a diagnosis of pneumonia.

Humans↗
PubMed1990

Nucleotide sequence of feline panleukopenia virus: comparison with canine parvovirus identifies host-specific differences.

The nucleotide sequence of feline panleukopenia virus (FPV) strain 193 was determined and compared with the sequence of canine parvovirus (CPV) strain N and partial sequences of FPV strain Carl and CPV strain b. Base differences were identified at 115 positions in these 5.1 kb genomes and predicted amino acid differences occurred at 40 positions. The two overlapping capsid protein genes contained almost twice as many base differences as the single non-structural protein gene (49 compared to 26) and about the same ratio was calculated for predicted amino acid differences (27 compared to 13). The 27 variant amino acids in the capsid proteins were clustered at three sites in the primary sequence, whereas 10 of the 13 variant amino acids in the non-structural protein occurred in the 130 C-terminal amino acids. The two FPV strains differed consistently from the two CPV strains at 31 bases: 12 base changes in the capsid protein genes resulted in six amino acid changes, six base changes in the non-structural protein gene resulted in three amino acid changes, and 13 base changes occurred in the non-coding sequence.

Amino Acid Sequence↗
PubMed2006

Combined transcript and metabolite profiling of Arabidopsis leaves reveals fundamental effects of the thiol-disulfide status on plant metabolism.

In this study, we used gas chromatography-mass spectrometry analysis in combination with flux analysis and the Affymetrix ATH1 GeneChip to survey the metabolome and transcriptome of Arabidopsis (Arabidopsis thaliana) leaves in response to manipulation of the thiol-disulfide status. Feeding low concentrations of the sulfhydryl reagent dithiothreitol for 1 h at the end of the dark period led to posttranslational redox activation of ADP-glucose pyrophosphorylase and major alterations in leaf carbon partitioning, including an increased flux into major respiratory pathways, starch, cell wall, and amino acid synthesis, and a reduced flux to sucrose. This was accompanied by a decrease in the levels of hexose phosphates, while metabolites in the second half of the tricarboxylic acid cycle and various amino acids increased, indicating a stimulation of anaplerotic fluxes reliant on alpha-ketoglutarate. There was also an increase in shikimate as a precursor of secondary plant products and marked changes in the levels of the minor sugars involved in ascorbate synthesis and cell wall metabolism. Transcript profiling revealed a relatively small number of changes in the levels of transcripts coding for components of redox regulation, transport processes, and cell wall, protein, and amino acid metabolism, while there were no major alterations in transcript levels coding for enzymes involved in central metabolic pathways. These results provide a global picture of the effect of redox and reveal the utility of transcript and metabolite profiling as systemic strategies to uncover the occurrence of redox modulation in vivo.

Arabidopsis↗
PubMed1991

The soybean 94-kilodalton vegetative storage protein is a lipoxygenase that is localized in paraveinal mesophyll cell vacuoles.

Soybean leaves contain three proteins (the vegetative storage proteins or VSPs) that respond to nitrogen status and are believed to be involved in the temporary storage of nitrogen. One of these proteins, with a molecular mass of 94 kD and termed vsp94, was microsequenced. Partial amino acid sequence indicated that vsp94 was highly homologous to the lipoxygenase protein family. Further evidence that vsp94 is a lipoxygenase was obtained by demonstrating that vsp94 cross-reacted with a lipoxygenase antibody. Also, a lipoxygenase cDNA coding region was able to detect changes in an mRNA that closely parallel changes in vsp94 protein levels resulting from alteration of nitrogen sinks. Extensive immunocytochemical data indicate that this vsp94/lipoxygenase is primarily expressed in the paraveinal mesophyll cells and is subcellularly localized in the vacuole. These observations are significant in that they suggest that plant lipoxygenases may be bifunctional proteins able to function enzymatically in the hydroperoxidation of lipids and also to serve a role in the temporary storage of nitrogen during vegetative growth.

Amino Acid Sequence↗