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At least 1,387 records · Page 77Linked to original sources
PubMed1993

VMA13 encodes a 54-kDa vacuolar H(+)-ATPase subunit required for activity but not assembly of the enzyme complex in Saccharomyces cerevisiae.

Previous purifications and characterizations of the Saccharomyces cerevisiae vacuolar proton-translocating ATPase (V-ATPase) have indicated that this enzyme is a multisubunit complex composed of at least eight subunits of 100-, 69-, 60-, 42-, 36-, 32-, 27-, and 17-kDa (Kane, P. M., Yamashiro, C. T., and Stevens, T. H. (1989) J. Biol. Chem. 264, 19236-19244). We report the cloning and characterization of an additional V-ATPase subunit, the 54-kDa subunit, which is encoded by the VMA13 gene. VMA13 was isolated by complementation of the growth phenotypes associated with the vma13 mutation, which was originally described as cls11 (Ohya, Y., Umemoto, N., Tanida, I., Ohta, A., Iida, H., and Anraku, Y. (1991) J. Biol. Chem. 266, 13971-13977). The nucleotide sequence of the VMA13 gene predicted a hydrophilic polypeptide with a calculated molecular mass of 54,415 daltons. The VMA13 54-kDa gene product resides on the vacuolar membrane and co-purified with the active V-ATPase complex. Characterization of a null vma13 mutant (delta vma13) revealed that the Vma13 polypeptide is essential for V-ATPase activity. However, the Vma13 polypeptide is not required for targeting of the other V-ATPase subunits (100-, 69-, 60-, 42-, 27-, or 17-kDa subunits) to the vacuolar membrane as shown by the association of these subunits with vacuolar membranes isolated from delta vma13 cells. The nature of the V-ATPase "complex" in delta vma13 mutant is, nevertheless, fundamentally different from the wild-type enzyme. This is evidenced by the fact that the inactive V-ATPase complex from delta vma13 cells is less stable than the wild-type enzyme. Taken together, these results indicate that VMA13 encodes the 54-kDa subunit of the V-ATPase and that this subunit is essential for activity, but not assembly, of the enzyme complex.

Amino Acid Sequence↗
PubMed1993

[Use of the in vitro enzymatic amplification method for the detection of Mycobacterium paratuberculosis in feces].

A polymerase chain reaction was developed, using as target sequence an insertion element of 1,451 base pairs (IS 900), specific for Mycobacterium paratuberculosis (15-20 copies per genome). The test was performed in three stages: (1) extraction of bacterial deoxyribonucleic acid (DNA), from faeces stored at +4 degrees C, -20 degrees C, in 70% ethanol or in a buffer solution; (2) amplification of the target DNA by means of thermostable DNA polymerase; (3) detection of the amplified DNA by electrophoresis, confirmed by dot blot assay after hybridisation with an internal labelled oligonucleotide of digoxigenin. Reproducible results were obtained with DNA extracted from faeces stored at -20 degrees C or in 70% ethanol. The sensitivity and specificity of the method used, particularly double amplification and hybridisation, are discussed by comparing the results obtained by bacterial culture from faeces.

Animals↗
PubMed1996

Five novel mutations of the protein S active gene (PROS 1) in 8 Norman families.

To further elucidate the molecular basis for hereditary thrombophilia, we screened the protein S active gene in 11 families with type I deficiency, using a strategy based on denaturing gradient gel electrophoresis (DGGE) of all the coding sequences. Fragments with an abnormal DGGE pattern were sequenced, and 5 novel mutations were identified in 8 families. The mutations were a 7-nucleotide deletion in exon II, a 4-nucleotide deletion in exon III, a T insertion in exon VII, a C to T transition transforming Leu 259 into Pro and a T to C transition transforming Cys 625 into Arg in 4 families. These mutations were the only sequence variations found in the propositus' gene exons and co-segregated with the plasma phenotype. A total of 28 members of these 8 families were heterozygous for one of the 5 mutations. Twenty-four (58,5%) of the 41 deficient subjects over 18 years of age had clinical thrombophilia, whereas the 13 subjects under 18 were asymptomatic. Of the 28 subjects, 6 (21,5%) were also found to bear the factor V Arg 506 Gln mutation.

Adolescent↗
PubMed1996

[Hemorrhagic colitis caused by verotoxigenic Escherichia coli. Presentation of 9 cases].

OBJECTIVE: To describe the clinical and epidemiological characteristics of nine patients with enteritis caused by verocytotoxin-producing E. coli O157. PATIENTS AND METHODS: Clinical data of patients was collected retrospectively, the isolated strains were tested for verotoxin production (VT) using Vero cell culture line, and presence of VT1 and VT2 gene sequences was detected using amplification techniques (PCR), biotype was also determined using twelve biochemical tests, and genomic macrorestriction profile (PFGE). RESULTS: The patients' age ranged from 11 months to 70 years. The mean duration of diarrhea was 4.7 days. All patients but one had abdominal cramps, seven of nine reported hemorrhagic stools and six had fever. Three patients were affected of haematologycal neoplasia and two of them developed hemolytic-uremic syndrome as a complication. All strains produced VT2 and two of them also produced VT1. Epidemiological link between patients has not been established. Three different biotypes had been distinguished between the nine isolated strains. All but two had different macrorestriction profiles. DISCUSSION: The results obtained showed that clinical manifestations are rather inespecific, including fever (6/9 patients) and there is high association of severe complications. The heterogeneity in PFGE results obtained confirms that the cases are not related.

Adult↗
PubMed1996

A locus for Fanconi anemia on 16q determined by homozygosity mapping.

We report the results of a genomewide scan using homozygosity mapping to identify genes causing Fanconi anemia, a genetically heterogeneous recessive disorder. By studying 23 inbred families, we detected linkage to a locus causing Fanconi anemia near marker D16S520 (16q24.3). Although -65% of our families displayed clear linkage to D16S520, we found strong evidence (P = .0013) of genetic heterogeneity. This result independently confirms the recent mapping of the FAA gene to chromosome 16 by Pronk et al. Family ascertainment was biased against a previously identified FAC gene on chromosome 9, and no linkage was observed to this locus. Simultaneous search analysis suggested several additional chromosomal regions that could account for a small fraction of Fanconi anemia in our families, but the sample size is insufficient to provide statistical significance. We also demonstrate the strong effect of marker allele frequencies on LOD scores obtained in homozygosity mapping and discuss ways to avoid false positives arising from this effect.

Chromosome Mapping↗
PubMed1997

Cytochrome P-4502E1-dependent formation of trifluoroacetyl adducts from halothane by transduced HepG2 cells.

E-9 cells, a HepG2 cell line that has the alcohol-inducible human cytochrome P-4502E1 (CYP2E1) cloned into its genome, was tested for its ability to produce trifluoroacetyl (TFA) adducts from the metabolism of halothane. The metabolism of halothane results in the production of TFA halide that can readily react with cellular proteins to form TFA adducts, which can be detected by antibodies directed against them. E-9 cells formed TFA adducts when incubated with halothane. The major consistent bands that were detected were of molecular weights of approximately 50, 78, and 100 kDa. The formation of these adducts was dependent on halothane concentration and time of incubation with halothane. MV-5 cells, the control cell line that has the viral vector without the P-450, did not produce any adducts. Inhibitors of CYP2E1 function, such as 4-methylpyrazole, inhibited adduct formation. Furthermore, phorbol esters, which have been shown to increase the CYP2E1 level in this cell line, increased TFA adduct formation. This HepG2 cell line may be of value in studying the metabolism and toxicity of halothane in a human cell culture model.

Animals↗
PubMed1998

Presence of two plasminogen alleles in normal populations.

When we compared nucleotide sequences of the 5'-flanking regions for plasminogen genes from 11 individuals, six substitutions were identified even among normal subjects. A new haplotype (termed allele II) was screened by PCR-RFLP analysis among 54 Japanese and 58 Caucasian normal subjects. The frequency of allele II was 0.787 in the Japanese and 0.560 in the Caucasians, indicating that the ratio of alleles differs between populations. Examination of 118 cases with dysplasminogenemia revealed that the Ala601-Thr mutation was present on allele I in most cases. This mutation was also associated with allele II in one-fourth of all cases, suggesting possible recombination within the plasminogen gene. Interestingly, we previously demonstrated that the expression activity of allele II was about 1.8 fold that of allele I in vitro.

Alanine↗
PubMed1998

Maternal disomy and Prader-Willi syndrome consistent with gamete complementation in a case of familial translocation (3;15) (p25;q11.2).

Maternal uniparental disomy (UPD) for chromosome 15 is responsible for an estimated 30% of cases of Prader-Willi syndrome (PWS). We report on an unusual case of maternal disomy 15 in PWS that is most consistent with adjacent-1 segregation of a paternal t(3;15)(p25;q11.2) with simultaneous maternal meiotic nondisjunction for chromosome 15. The patient (J.B.), a 17-year-old white male with PWS, was found to have 47 chromosomes with a supernumerary, paternal der(15) consisting of the short arm and the proximal long arm of chromosome 15, and distal chromosome arm 3p. The t(3;15) was present in the balanced state in the patient's father and a sister. Fluorescent in situ hybridization analysis demonstrated that the PWS critical region resided on the derivative chromosome 3 and that there was no deletion of the PWS region on the normal pair of 15s present in J.B. Methylation analysis at exon alpha of the small nuclear ribonucleoprotein-associated polypeptide N (SNRPN) gene showed a pattern characteristic of only the maternal chromosome 15 in J.B. Maternal disomy was confirmed by polymerase chain reaction analysis of microsatellite repeats at the gamma-aminobutyric acid receptor beta3 subunit (GABRB3) locus. A niece (B.B.) with 45 chromosomes and the derivative 3 but without the der(15) demonstrated a phenotype consistent with that reported for haploinsufficiency of distal 3 p. Uniparental disomy associated with unbalanced segregation of non-Robertsonian translocations has been reported previously but has not, to our knowledge, been observed in a case of PWS. Furthermore, our findings are best interpreted as true gamete complementation resulting in maternal UPD 15 and PWS.

Adolescent↗
PubMed1995

Mapping segmental imbalances using comparative genomic hybridization and eigenanalysis.

We have tested a new approach to comparative genomic hybridization (CGH) analysis using digital ratio images and eigenanalysis, which allows the recognition of consistent patterns along the chromosomes and discards random (background noise) patterns. We have performed test experiments using genomic DNAs from a patient with a duplication, another with a deletion of a chromosome segment, and a prostate cancer biopsy. Image ratio analysis was performed, and ratio images of the relevant chromosome were subjected to eigenanalysis. The results showed a high-contrast enhancement of the regions corresponding to the unbalanced genomic segment, with clearly defined limits between normal and abnormal fluorescence ratios. The combination of digital ratio images and eigenanalysis allowed the precise mapping of unbalanced regions consistent with other methods of analysis. Because there is no limit to the number of chromosomes that can be analyzed at any one time, the method has the potential of increasing the sensitivity of CGH by reducing the noise component.

Cell Line↗
PubMedDate not supplied

Attitudes toward genetic testing: gender, role, and discipline.

As a result of the Human Genome Project, genetic testing could result in the availability of detailed genetic information (presence of disease, genetic risk or predisposition to disease, and characteristics or traits) that can ultimately be used for healthcare-related decisions. This study explored whether gender, role, and professional discipline would influence attitudes toward genetic testing when making reproductive decisions, as interpreted by 2 roles--as a parent making decisions or as a professional giving advice. An original research instrument was administered to masters and doctoral genetics students, pediatric residents, and masters-level ministry students. Statistical analyses revealed that discipline strongly influenced decision making while gender rarely did. In addition, differences in attitudes were also found based on parental and professional roles.

Adult↗
PubMed2006

Genome comparison using Gene Ontology (GO) with statistical testing.

BACKGROUND: Automated comparison of complete sets of genes encoded in two genomes can provide insight on the genetic basis of differences in biological traits between species. Gene ontology (GO) is used as a common vocabulary to annotate genes for comparison. Current approaches calculate the fold of unweighted or weighted differences between two species at the high-level GO functional categories. However, to ensure the reliability of the differences detected, it is important to evaluate their statistical significance. It is also useful to search for differences at all levels of GO. RESULTS: We propose a statistical approach to find reliable differences between the complete sets of genes encoded in two genomes at all levels of GO. The genes are first assigned GO terms from BLAST searches against genes with known GO assignments, and for each GO term the abundance of genes in the two genomes is compared using a chi-squared test followed by false discovery rate (FDR) correction. We applied this method to find statistically significant differences between two cyanobacteria, Synechocystis sp. PCC6803 and Anabaena sp. PCC7120. We then studied how the set of identified differences vary when different BLAST cutoffs are used. We also studied how the results vary when only subsets of the genes were used in the comparison of human vs. mouse and that of Saccharomyces cerevisiae vs. Schizosaccharomyces pombe. CONCLUSION: There is a surprising lack of statistical approaches for comparing complete genomes at all levels of GO. With the rapid increase of the number of sequenced genomes, we hope that the approach we proposed and tested can make valuable contribution to comparative genomics.

Anabaena↗
PubMed1997

Comprehensive method for the typing of HLA-A, B, and C alleles by direct sequencing of PCR products obtained from genomic DNA.

Molecular testing is gradually replacing standard typing techniques in the field of HLA because it allows higher resolution, which has significant functional implications. Although several techniques have been so far described for this purpose, the definitive means to determine which alleles are present in a particular sample is to identify their sequence. We describe a simplified method for typing HLA-A, B, and C alleles by direct sequencing of polymerase chain reaction (PCR) products amplified from genomic DNA that could allow large-scale handling of samples for clinical use. The template is the product of a nested PCR. A first round of PCR amplifications from genomic DNA is performed with three different sets of primers, one pair specific for each locus. The PCR products encompass exons 2 and 3, the regions of interest to determine the allele present. These fragments are a mixture of both alleles present in one locus. In a second round of PCRs using the first fragment as template, exons 2 and 3 are separately amplified and simultaneously tailed with sequences corresponding to fluorescent-labeled commercial primers. The sense and antisense sequence of each exon is obtained and compared with a database of all known HLA-A, B, or C alleles. Heterozygous positions are determined and the most probable alleles assigned. This simplified procedure has the practical advantage of allowing high-resolution typing of clinical material by utilizing the same genomic DNA used for standard molecular typing of HLA class I.

Alleles↗
PubMed2006

Testing for genetic heterogeneity in the genome search meta-analysis method.

The Genome Search Meta-Analysis (GSMA) method is widely used to detect linkage by pooling results of previously published genome-wide linkage studies. The GSMA uses a non-parametric summed rank statistic in 30 cM bins of the genome. Zintzaras and Ioannidis ([2005] Genet. Epidemiol. 28:123-137) developed a method of testing for heterogeneity of evidence for linkage in the GSMA, with three heterogeneity statistics (Q, Ha, B). They implement two testing procedures, restricted versus unrestricted for the summed rank within the bin. We show here that the rank-unrestricted test provides a conservative test for high heterogeneity and liberal test for low heterogeneity in linked regions. The rank-restricted test should therefore be used, despite the extensive simulations needed. In a simulation study, we show that the power to detect heterogeneity is low. For 20 studies of affected sib pairs, simulated assuming linkage in all studies to a gene with sibling relative risk of 1.3, the power to detect low heterogeneity using the Q statistic was 14%. With linkage present in 50% of the studies (to a gene with sibling relative risk of 1.4), the Q heterogeneity statistic had power of 29% to detect high heterogeneity. The power to detect linkage using the summed rank was high in both of these situations, at 98% and 79%, respectively. Although testing for heterogeneity in the GSMA is of interest, the currently available method provides little additional information to that provided by the summed rank statistic.

Genetic Heterogeneity↗
PubMed2001

Genome scan for linkage to asthma using a linkage disequilibrium-lod score test.

We report a genome-wide linkage study of asthma on the German and Collaborative Study on the Genetics of Asthma (CSGA) data. Using a combined linkage and linkage disequilibrium test and the nonparametric linkage score, we identified 13 markers from the German data, 1 marker from the African American (CSGA) data, and 7 markers from the Caucasian (CSGA) data in which the p-values ranged between 0.0001 and 0.0100. From our analysis and taking into account previous published linkage studies of asthma, we suggest that three regions in chromosome 5 (around D5S418, D5S644, and D5S422), one region in chromosome 6 (around three neighboring markers D6S1281, D6S291, and D6S1019), one region in chromosome 11 (around D11S2362), and two regions in chromosome 12 (around D12S351 and D12S324) especially merit further investigation.

Adult↗
PubMed2000

Induced genome instability as a potential screening test for cancer susceptibility?

The variety of mutations associated with carcinogenesis, along with variations in penetrance and environmental factors, complicate the genetic screening for cancer predisposition. It is proposed here that the detection of inherent genome instability as determined by increased mutagen susceptibility may enhance the identification of populations at risk for cancer. In support for this hypothesis, our analysis reveals a strong association between mutagen-induced chromosomal instability in peripheral blood lymphocytes and the propensity for cancers of oral cavity, pharynx, larynx, and lung. DNA instability in response to a variety of mutagens identifies patients with gastrointestinal, brain, endocrine, breast, skin, and hematologic tumors as well as individuals with cancer family syndromes. Induced genome instability therefore appears to be strongly linked to cancer predisposition, and prospective studies may yield a screening test utilizing a panel of mutagens to better identify populations at risk.

Chromosomes, Human↗