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Allele frequencies for twelve STRs included in the AmpFlSTR Profiler Plus kit (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) and GenePrint CTTv kit (VWA, TH01, TPO and CSF1PO) were estimated from a sample of 110 unrelated individuals from Mozambique.
The reference database of highly informative Y-chromosomal short tandem repeat (STR) haplotypes (YHRD), available online at http://ystr.charite.de, represents the largest collection of male-specific genetic profiles currently available for European populations. By September 2000, YHRD contained 4688 9-locus (so-called "minimal") haplotypes, 40% of which have been extended further to include two additional loci. Establishment of YHRD has been facilitated by the joint efforts of 31 forensic and anthropological institutions. All contributing laboratories have agreed to standardize their Y-STR haplotyping protocols and to participate in a quality assurance exercise prior to the inclusion of any data. In view of its collaborative character, and in order to put YHRD to its intended use, viz. the support of forensic caseworkers in their routine decision-making process, the database has been made publicly available via the Internet in February 2000. Online searches for complete or partial Y-STR haplotypes from evidentiary or non-probative material can be performed on a non-commercial basis, and yield observed haplotype counts as well as extrapolated population frequency estimates. In addition, the YHRD website provides information about the quality control test, genotyping protocols, haplotype formats and informativity, population genetic analysis, literature references, and a list of contact addresses of the contributing laboratories.
Allele frequencies for the nine STRs included in the AmpFlSTR Profiler Plus kit (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) were estimated from a sample of 365-427 unrelated individuals born in north Portugal.
We report a simultaneous study of the VWA STR locus by the Perkin-Elmer Profiler Plus kit and the Promega GenePrint CTTv kit in a population sample from North Portugal and in 418 meiosis from family material and paternity cases. PCR amplification and genotyping were performed according to the manufacturer's instructions using ABI 377 or ABI 310 automatic sequencers. Biological kinship in family material and paternity cases was validated by the use of the STR loci D3S1358, D5S818, D7S820, D8S1179, D13S317, D18S51, D21S11, FGA, CSF1PO, TH01 and TPOX. Out of 434 unrelated individuals we found 4 inconsistencies between the genotypes obtained using each kit. No exclusions were found in the meiotic analyses. In all cases, these inconsistencies were due to an annealing failure of the Perkin-Elmer forward primer resulting in false homozygotes. Sequencing analysis revealed an A-to-T substitution at position 1631 (GenBank sequence M25858), 52 bases upstream of the first TCTA motif of the repeat region. An estimate of the null allele frequency (s) in this study is thus obtainable from the expression s = 4/(2 x 434) = 0.46%. The relatively high frequency of these discrepancies in our population demonstrates the need for caution when comparing genotype or gene frequency estimates made from amplicons produced by different primers, when evaluating apparent exclusions in paternity testing and when searching for a match between individual genetic profiles in forensic databases. Our findings are also compared with those previously reported.
Seven Y-chromosome STR loci, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393 have been analysed in population samples of Angolares, Forros and Tongas, three ethnic groups from the African archipelago of São Tomé e Príncipe (Gulf of Guinea). Complete typings were obtained for 103 chromosomes, which belonged to 79 different haplotypes. The mean heterozygosity per locus in the overall São Tomean sample was 0.566, with the highest value found among Forros and the lowest among Angolares. Angolares also showed the lowest level of haplotype diversity. On average, the mean pairwise difference between two random haplotypes from Angolares, Forros and Tongas was 4.69, 6.74 and 6.23 repeats, respectively. The genetic distances were found to be statistically significant between Angolares and Forros or Tongas. In accordance, AMOVA revealed that the percentage of variation attributable to differences among groups was only significant when we distinguished between Angolares and non-Angolares. Globally, these results indicate that, with respect to the pool of male lineages of São Tomé e Príncipe, some genetic sub-structuring does exist, basically determined by the Angolares ethnic group.
In this work we present results on DYS434, DYS437, DYS438 and DYS439 loci studied in three population samples from North Portugal (N: 69), Macao (N: 59) and Mozambique (N: 64). Gene and haplotype diversity values are presented and compared. Gene diversity values ranged from 0.0290 to 0.0620 for DYS434; 0.0615 to 0.5959 for DYS437; 0.4906 to 0.6424 for DYS438; 0.5873 to 0.7038 for DYS439. The highest average gene diversity was found in Macao and the lowest in Mozambique. Haplotype diversity in North Portugal, Macao and Mozambique was calculated to be 0.925, 0.928 and 0.787, respectively. Allele and haplotype frequency distributions for all markers were compared between the three populations. At the haplotype level all the differences between pairs of samples were significant. Sequencing analysis was performed for all alleles found in the four loci. Identical flanking sequences were observed with most of the alleles differing only by the repeat number. However, two variations were found in allele 10 of DYS438: one in a Macao sample presenting a TTTTA before the last TTTTC repetition and one in a Portuguese sample showing a base substitution (A/C) at position 7 downstream from the tandem repeat. A base substitution (C/T) at position 3 upstream from the repeat motif was also found in allele 14 of DYS437 in a sample from Mozambique.
A genomic library of the yeast Zygosaccharomyces bailii ISA 1307 was constructed in pRS316, a shuttle vector for Saccharomyces cerevisiae and Escherichia coli. The library has an average insert size of 6 kb and covers the genome more than 20 times assuming a genome size similar to that of S. cerevisiae. This new tool has been successfully used, by us and others, to isolate Z. bailii genes. One example is the beta-isopropylmalate dehydrogenase gene (ZbLEU2) of Z. bailii, which was cloned by complementation of a leu2 mutation in S. cerevisiae. An open reading frame encoding a protein with a molecular mass of 38.7 kDa was found. The nucleotide sequence of ZbLEU2 and the deduced amino acid sequence showed a significant degree of identity to those of beta-isopropylmalate dehydrogenases from several other yeast species. The sequence of ZbLEU2 has been deposited in the EMBL data library under accession number AJ292544.
To characterize the isoenzyme distribution of creatine kinase (CK) in endothelial cells (ECs) and its functional role during substrate depletion, ECs from aorta (AECs) and microvasculature (MVECs) of pig and rat were studied. In addition, high- energy phosphates were continuously monitored by (31)P NMR spectroscopy in pig AECs attached to microcarrier beads. CK activity per milligram of protein in rat AECs and MVECs (0.08 +/- 0.01 and 0.15 +/- 0.08 U/mg, respectively) was <3% of that of cardiomyocytes (6.46 +/- 1.02 U/mg). Rat and pig AECs and MVECs displayed cytosolic BB-CK, but no MM-CK. Gel electrophoresis of mitochondrial fractions of rat and pig ECs indicated the presence of mitochondrial Mi-CK, mostly in dimeric form. The presence of Mi(a)-CK was demonstrated by indirect immunofluorescence staining using Mi(a)-CK antibodies. When perifused with creatine-supplemented medium, phosphocreatine (PCr) continuously increased with time (1.2 +/- 0.6 nmol x h(-1) x mg x protein(-1)), indicating creatine uptake and CK activity. Glucose withdrawal from the medium induced a rapid decrease in PCr, which was fully reversible on glucose addition, demonstrating temporal buffering of an energy deficit. Because both cytosolic and mitochondrial CK isoforms are present in ECs, the CK system may also contribute to energy transduction ("shuttle hypothesis").
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The introduction of highly active antiretroviral therapy with protease inhibitors in 1996 has changed the morbidity and mortality of acquired immune deficiency syndrome patients. Therefore, the aetiologies and prognostic factors of human immunodeficiency virus (HIV)-infected patients with life-threatening respiratory failure requiring intensive care unit (ICU) admission need to be reassessed. From 1993 to 1998, we prospectively evaluated 57 HIV patients (mean+/-SEM age 36.5+/-1.3 yrs) admitted to the ICU showing pulmonary infiltrates and acute respiratory failure. A total of 21 and 30 patients were diagnosed as having Pneumocystis carinii and bacterial pneumonia, respectively, of whom 13 and eight died during their ICU stay (p=0.01). Both groups of patients had similar age, Acute Physiology and Chronic Health Evaluation (APACHE) II score, and severity in respiratory failure. The number of cases with bacterial pneumonia admitted to ICU decreased after 1996 (p=0.05). Logistic regression analysis showed that (APACHE) II score >17, serum albumin level <25 g.(-1), and diagnosis of P. carinii pneumonia were the only factors at entry associated with ICU mortality (p=0.02). Patients with bacterial pneumonia are less frequently admitted to the intensive care unit after the introduction of highly active antiretroviral therapy with protease inhibitors in 1996. Compared to the previous series, it was observed that the few Pneumocystis carinii pneumonia patients that need intensive care still have a bad prognosis.
The genotyping of two population samples from Galicia and northern Portugal was performed for nine STR loci using a single multiplex reaction with the AmpF/STR Profiler Plus PCR amplification kit which co-amplifies the systems D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820 and the XY homologous gene amelogenin. Allele frequencies for these nine tetranucleotide repeat markers were calculated and no significant differences were observed when comparing these two populations. Conformity with Hardy-Weinberg equilibrium proportions was good for all systems in both samples. The combined power of exclusion was 99.981% and 99.980% in Galicia and northern Portugal, respectively and the combined power of discrimination was greater than 99.999%. Segregation analysis of all loci detected two incompatibilities, one in D3S1358 (out of 112 meioses) and another in D7S820 (out of 104 meioses). Both could be explained by single-step mutations. In general co-amplification was good except for some relatively degraded samples in which poor amplification was observed for the largest STRs. Nevertheless the system is technically robust even when small amounts of template DNA are used and in the addition is highly informative and time-saving. However, caution should be taken in the interpretation of profiles in degraded samples and the apparently high mutation rate of D3S1358 and D7S820 should also be kept in mind.
The promoter region of the human GSTP1 gene contains a polymorphic short tandem repeat (STR) locus consisting of pentanucleotide repeat units (ATAAA). In this work we report the existence of a total of 26 alleles in a Caucasian population. While differences in size (ranging from one to five base pairs) were responsible for the major variation, in five size-defined classes, two alternative sequences were found. Automatic fragment sizing and sequencing analysis revealed that this polymorphism is of a highly complex nature in contrast with previous reports. A genetic population study was carried out on a random sample from Portugal showing no deviation from Hardy-Weinberg equilibrium. Somatic instability studies were also performed on gastric and thyroid tumours using this STR: no instability was detected in thyroid tumour tissues when compared with their normal counterpart but in gastric tumour tissues microsatellite instability (MSI) was detected in 9.6% of the cases and loss of heterozygosity (LOH) also in 9.6% of the cases studied. The results obtained with GSTP1 in gastric cancer were compared with previously reported data on MSI using BAT-26 and several dinucleotide repeat markers.
BACKGROUND: Hereditary spastic paraplegias (HSPs) are a heterogeneous group of neurodegenerative disorders characterized by progressive and predominant spasticity of the lower limbs, in which dominant, recessive, and X-linked forms have been described. While autosomal dominant HSP has been extensively studied, autosomal recessive HSP is less well known and is considered a rare condition. OBJECTIVE: To analyze the clinical presentation in a large group of patients with autosomal recessive HSP from Portugal and Algeria to define homogeneous groups that could serve as a guide for future molecular studies. RESULTS: Clinical features in 106 patients belonging to 46 Portuguese and Algerian families with autosomal recessive HSP are presented, as well as the results of molecular studies in 23 of these families. Five phenotypes are defined: (1) pure early-onset families, (2) pure lateonset families, (3) complex families with mental retardation, (4) complex families with mental retardation and peripheral neuropathy, and (5) complex families with cerebellar ataxia. Six additional families have specific complex presentations, each of which is unique in the present series. Pyramidal signs in the upper limbs and pes cavus are frequent findings, while pseudobulbar signs, including dysarthria, dysphagia, and brisk jaw jerks, are more frequent in the complex forms. The complex forms have a poorer prognosis, while pure forms, particularly those with early onset, are more benign. One Algerian pure early-onset kindred was linked to the locus on chromosome 8, previously reported in 4 Tunisian families. Two of the Portuguese kindreds with complex forms (one with mental retardation and the other associated with hypoplasia of the corpus callosum) showed linkage to the locus recently identified on chromosome 16. CONCLUSIONS: Although autosomal recessive HSP represents a heterogeneous group of diseases, some phenotypes can be defined by analyzing a large group of patients. The fact that only one Algerian family was linked to chromosome 8 suggests that this is a rare localization even in kindreds with the same ethnic background. Linkage to chromosome 16 was found in 2 clinically diverse Portuguese kindreds, illustrating that this locus is also rare and may correspond to different phenotypes.
The association between genetic instability in repetitive DNA domains and cancer has been reported in different types of malignancies. In this work we perform a comparative study of 29 gastric tumors with paired normal tissue using seven tetra-(FES/FPS, VWA31/A, HTPO, TH01, MBPB) and pentanucleotide (CD4, TP53) STR polymorphic markers regarding loss of heterozygosity and replication error status. Furthermore, we compare the gene frequencies obtained in normal tissue from patients with those of a normal control population from the same area, looking for allele associations between any of these polymorphic loci and gastric cancer risk. The results have shown that FES/FPS and TP53 present the higher rates of somatic instability. The observed results for TP53 are in accordance with those previously reported in gastric carcinogenesis, while instability of FES/FPS is for the first time reported in this tumor type. Our data suggest that different loci show different rates of instability and/or loss of heterozygosity and do not seem to consist of a result of an RER+ phenotype affecting several genomic repetitive domains. Furthermore, the instability in markers TH01, MBPB, TP53, and FES was generally detected in genotypes involving alleles with a high number of repeats. Comparing gene frequencies in patients and normal controls, no significant differences were found, although longer alleles are consistently more frequent in patients for the markers MBPB, TH01, and CD4.
Sodium flux rate and energy consumption of the Na(+)-K+ pump in vascular endothelial cells of porcine aorta grown on micro-carrier beads were studied using a combination of nuclear magnetic resonance spectroscopy of intracellular 23Na and microcalorimetry. The Na+ flux into the cells was determined in the presence of the shift reagent Dy(P3O10)2(7-), while the Na(+)-K+ pump was inhibited with ouabain. Basal Na+ influx was 17 +/- 3 nmol.min-1.mg protein-1, and intracellular Na+ concentration was 23.5 +/- 3.8 mM, resulting in a complete exchange of intracellular Na+ within 5-6 min. Spin-lattice relaxation time (T1) measurements of intracellular Na+ showed a T1 of 19 +/- 1 ms under basal conditions and a T1 of 26.2 +/- 1.6 ms after pump inhibition with 50 microM ouabain. Such an increase is typical for a system in which the total amount of Na+ increases but where the amount of bound Na+ remains constant. The Na+ ionophore nystatin maximally increased the Na(+)-K+ pump rate about twofold, whereas the amount of intracellular Na+ only increased 14%. With microcalorimetry a cellular heat flux of 183 +/- 18 microW per mg endothelial protein was determined, which relates to 7.6 microW/mg endothelial protein generated by the Na(+)-K(+)-adenosinetriphosphatase. Our data demonstrate that small intracellular changes of Na+ can stimulate the endothelial Na(+)-K+ pump activity. The contribution of the Na(+)-K+ pump to total endothelial energy expenditure is approximately 4-5%.
23Na(+)-NMR was used to determine the intracellular mobility and cell membrane permeability of Na+ in porcine vascular endothelial cells. The cells were grown as monolayers onto microcarrier beads and perfused with a medium containing Dy(P3O10)2(7-) to shift the extracellular from the intracellular Na+ resonance. Using triple quantum coherence filtered NMR experiments and spin echoes, it was shown that not all intracellular Na+ ions are in the extreme narrowing limit. The triple quantum coherence filtered experiments resulted in an observed R2f = 2022 +/- 302 s-1 and R2s = 200 +/- 28 s-1. From spin-echo experiments we obtained R2f = 2200 +/- 355 s-1 and a R2s = 145 +/- 15 s-1. These values are similar to those found in other cell systems and indicate water-Na(+)-protein interactions. Using single quantum NMR, the Na+ permeability of the endothelial membrane was determined. To obtain the Na+ transcellular permeability coefficient the cells were treated with 50 microM ouabain in the perfusion medium. Ouabain inhibits the Na-K pump and caused the intracellular Na+ concentration to increase in time. The permeability coefficient was obtained from the time dependence of the intracellular Na+ concentration. Assuming a monolayer of rectangularly shaped cells, we obtained a value of P = 0.02.10-5 cm s-1.
Transport and phosphorylation of 2-fluoroadenosine (F-AR) were studied in human erythrocytes and porcine aortic endothelial cells by 19F-nuclear magnetic resonance (NMR) spectroscopy. F-AR (590 microM) added to a human erythrocyte suspension (15% hematocrit) was rapidly incorporated into adenine nucleotides at a rate of 38 nmol.min-1.ml red blood cells-1. Intracellular F-AR could be distinguished from extracellular F-AR due to a chemical shift difference of 0.43 +/- 0.03 ppm (n = 5 experiments). Compared with F-AR, fluoro-ATP purified by high-performance liquid chromatography (HPLC) exhibited a chemical shift of -0.052 ppm, which was too small to differentiate intracellular F-AR and fluoro-ATP in vivo. F-AR uptake was decreased by inhibition of membrane transport with dipyridamole (25 microM) or blockade of adenosine kinase by iodotubercidin (10 microM). The time course of F-AR uptake suggested that the rate-limiting step was not membrane transport but the intracellular phosphorylation by adenosine kinase. In porcine aortic endothelial cells grown on microcarrier beads and perfused within the magnet, there was a linear relation between the F-AR concentration applied (2, 4, 8, or 32 microM) and net uptake measured (27-827 pmol.min-1.mg-1). Intra- and extracellular fluoroadenine compounds were separated by 0.12 ppm, and HPLC analysis confirmed F-AR conversion to fluoroadenine nucleotides. Our findings demonstrate that cellular transport and metabolism of F-AR can be noninvasively studied and analyzed by 19F-NMR.
Leprechaunism (Donohue syndrome) is an autosomal recessive disorder characterized by hyperglycemia, extreme insulin resistance, dysmorphic features, failure to thrive, and early death. In this study, recombinant IGF-I, which has both insulin-like and anabolic effects, was administered to two infants with leprechaunism in an attempt to reduce hyperglycemia and improve nutritional status. IGF-I was infused for 66 h in patient FL-1 and 62 h in patient NC-2, with maximal infusion rates of 110 and 40 micrograms/kg/h, respectively. Although supraphysiologic concentrations of IGF-I were achieved (459 and 1583 micrograms/L in FL-1 and NC-2, respectively), there were no apparent glucose-lowering or nitrogen-sparing effects. Insulin concentrations decreased from extremely high values (16804 and 10224 pmol/L) but remained elevated (611 pmol/L in FL-1 and 5869 pmol/L in NC-2). No changes in serum and urinary urea nitrogen or electrolytes occurred. IGF binding protein-2, which was the predominant IGF binding protein in serum by ligand blot and immunoblot, did not change with IGF-I infusion. IGF binding protein-3 levels were low at baseline and increased slightly during the infusion. We hypothesize that the lack of significant glucose-lowering and anabolic responses to IGF-I could be secondary to a postreceptor defect in IGF-I signaling resulting from the absence of functional insulin receptors.