Trace metal contamination and benthic assemblages in Subaé estuarine system, Brazil.
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Animals↗
Biomedical subjects
F Barros
Publications and source records attributed to F Barros.
Duplication and deletion analysis by fluorescent real-time PCR-based genotyping.
BACKGROUND: Gene dosage determination is an increasingly important field for the study of genome variation and organization. In parallel, the advances in our understanding of the genetic basis of disease have produced an exponential increase in the demand for molecular diagnostic analyses. Although efforts have been spent on increasing both the accuracy and the throughput of the gene dosage analysis, the success has been limited. METHODS: A large number of suitable methods has been proposed; most are based on quantitative real-time PCR or amplification of multiple targets. A new approach exploits the differences between fluorescent signals of SNP alleles in heterozygous samples to assess duplications. The SNP typing-dependent fluorescent signal allelic asymmetry is an intrinsic characteristic of a SNP typing assay and can lead to a simple and cost-effective gene dosage method. This strategy provides sufficient throughput and sensitivity for duplication analysis. CONCLUSIONS: There are advantages and disadvantages of real-time methodology when applying the approach to the molecular diagnostic field.
Fluorescence↗
CARD15/NOD2 analysis in rheumatoid arthritis susceptibility.
OBJECTIVE: To determine if the mutations in the CARD15/NOD2 gene predisposing to Crohn's disease (CD) contribute also to the genetic susceptibility to rheumatoid arthritis (RA). METHODS: The frequencies of the three commonest mutations of CARD15/NOD2 predisposing to CD (2104C > T, 2722G>C and 3020insC) were determined in 210 RA patients and 227 controls. RESULTS: Allelic frequencies of the CARD15/NOD2 mutations in RA patients (2104C>T, 2.8%; 2722G>C, 0.9%; and 3020insC, 2.4%) did not differ significantly from the controls (2104C>T, 5.3%; 2722G>C, 0.7%; and 3020insC, 1.1%). CONCLUSION: There was no evidence of association between the commonest CD CARD15/NOD2 mutations and RA susceptibility.
Arthritis, Rheumatoid↗
The three most common CARD15 mutations associated with Crohn's disease and the chromosome 16 susceptibility locus for systemic lupus erythematosus.
OBJECTIVE: To test if the three most common mutations contributing to Crohn's disease on the CARD15/NOD2 gene could contribute also to genetic susceptibility to systemic lupus erythematosus (SLE), which has been found to be linked to the region of chromosome 16q13 where the CARD15 gene is located. METHODS: We obtained DNA samples from the blood of 189 SLE patients (according to the American College of Rheumatology classification criteria) and 194 controls of Spanish ancestry. Genotypes for the three CARD15 mutations (3020insC, 2722G>C and 2104C>T) were determined by hybridization with fluorescence resonance energy transfer probes on a LightCycler real-time polymerase chain reaction system. RESULTS: CARD15 genotypes were similar in SLE patients and in controls from the general population (allelic frequencies for 3020insC 0.013 in SLE patients vs 0.013 in controls; for 2722G > C 0.011 vs 0.008; and for 2104C > T 0.032 vs 0.051). CONCLUSION: We did not find evidence that the Crohn's disease-associated mutations on CARD15 contributed to SLE susceptibility.
Carrier Proteins↗
Influence of amino-terminal structures on kinetic transitions between several closed and open states in human erg K+ channels.
Gating kinetics of human ether-a-go-go (eag)-related gene (HERG) K+ channel expressed in Xenopus oocytes was studied using non-inactivating channel variants carrying different structural modifications in the amino terminus. A kinetics model was elaborated to describe the behavior of full-length channels, that includes at least three open states besides the three closed states previously proposed. Deletion of the HERG-specific proximal domain (HERG D138-373) accelerated all individual forward transitions between closed states. Whereas relatively large amplitude depolarizations were required to drive full-length HERG channels to more distal open states, these were reached more easily in channels without proximal domain. Alteration of the initial eag/PAS domain by introduction of a short amino-acid sequence at the beginning of the amino terminus did not alter transitions between closed states, but prevented the channels from reaching the farthest open states that determine slower deactivation rates. This indicates that the presence of specific amino-terminal structures can be correlated with the occurrence of distinctive molecular transitions. It also demonstrates that both proximal and eag/PAS domains in the amino terminus contribute to set the gating characteristics of HERG channels.
Amino Acid Sequence↗
Analysis of BRCA1 and BRCA2 in breast and breast/ovarian cancer families shows population substructure in the Iberian peninsula.
An estimated 5-10% of all breast and ovarian cancers are due to an inherited predisposition, representing a rather large number of patients. In Spain 1/13-1/14 women will be diagnosed with breast cancer during their lifetime. Two major breast cancer genes, BRCA1 and BRCA2, have been identified. To date, several hundred pathogenic mutations in these two genes have been published or reported to the Breast Cancer Information Core, BIC database (http://www.nhgri.nih.gov/Intramural_research_Lab transfer/Bic/index.html). In the present study, 30 Spanish breast and breast/ovarian cancer families (29 from Galicia, NW Spain, and 1 from Catalonia, NE Spain) were screened for mutations in the BRCA1 and BRCA2 genes. The analysis of these genes was carried out by SSCP for shorter exons and direct sequencing in the case of longer ones. Mutations were found in 8 of the 30 families studied (26.66%). It is important to note that all mutations were detected within the BRCA1 gene: 330 A>G, 910_913delGTTC, 2121 C>T, 3958_3962delCTCAGinsAGGC, and 5530 T>A. The BRCA1 330 A>G mutation was found in four unrelated families and accounted for 50% of all identified mutations.
Adult↗
Correlation between electrical activity and intracellular Ca2+ oscillations in GH3 rat anterior pituitary cells.
Simultaneous measurements of electrical activity and intracellular Ca(2+) levels were performed in perforated-patch current-clamped individual GH3 cells. Both in cells showing brief (<100 ms) and long action potentials (APs), we found a good correlation between the averaged intracellular Ca2+ concentration ([Ca2+]i) and AP frequency, but not between the mean [Ca2+]i and AP duration. Nevertheless, the magnitude of spontaneous Ca2+ oscillations was highly dependent on the size and duration of the APs. The decay of the Ca2+ transients was not slowed when the size of the oscillations was varied either spontaneously or after elongation of the AP with the K+ channel blocker tetraethyl ammonium. Furthermore, the recovery from Ca2+ loads similar to those induced by the APs was slightly retarded after treatment of the cells with intracellular store Ca2+-ATPase inhibitors. Among previous results showing that caffeine-induced [Ca2+]i increases are secondary to electrical activity enhancements in GH3 cells, these data indicate that the Ca2+ entry triggered via APs is the primary determinant of the [Ca2+]i variations, and that Ca2+-induced Ca2+ release has a minor contribution to Ca2+ oscillations recorded during spontaneous activity. They also point to modulation of electrical activity patterns as a crucial factor regulating spontaneous [Ca2+]i signalling, and hence pituitary cell functions in response to physiological secretagogues.
Action Potentials↗
Rare HRAS1 alleles are a risk factor for the development of brain tumors.
BACKGROUND: The highly polymorphic HRAS1 minisatellite locus, located 1 kilobase downstream from the H-ras1 gene, has been associated with increased susceptibility to a variety of cancers. Microsatellite instability (MI), another molecular abnormality observed in human neoplasms, most likely reflects an increased mutation rate and also is thought to underlie cancer predisposition. The purpose of this study was to investigate the association between rare HRAS1 alleles and brain tumors and to correlate the HRAS1 allelotype with MI and clinicopathologic features. METHODS: Ninety-four patients with primary brain tumors (52 gliomas, 32 meningiomas, and 10 schwannomas) and 109 healthy control individuals were studied. The size of HRAS1 alleles was determined by fluorescent detection in an automated DNA sequencer. The interspersion pattern was assessed by the minisatellite variant repeat-polymerase chain reaction technique. RESULTS: Twenty of 94 (21.28%) patients with brain tumors had at least one rare allele, compared with 13 of 109 (11.92%) in the control population (Fisher exact test; P = 0.0329). The presence of rare alleles was associated with an increased risk of brain tumors (odds ratio, 1.99; 95% confidence interval, 0.93-4.27). The overrepresentation of rare alleles in tumor patients mainly reflects the higher frequency observed in the glioma group (P = 0.0086). The authors did not detect association between the presence of rare HRAS1 alleles and MI in their series. No significant difference in the distribution of these alleles was found when tumors were compared according to other clinicopathologic variables. CONCLUSIONS: The presence of rare HRAS1 alleles is associated with an increased risk for the development of glial neoplasms (OR = 2.72; 95% CI, 1.17-6.32). The lack of association between rare HRAS1 polymorphisms and MI suggests that these two genetic factors are not likely to be expression of the same underlying defect.
Alleles↗
[Microsatellite analysis in the diagnosis of second primary tumor of lung in patient with head neck squamous cell carcinoma].
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Carcinoma, Squamous Cell↗
Mutation analysis of the adenomatous polyposis coli (APC) gene in northwest Spanish patients with familial adenomatous polyposis (FAP) and sporadic colorectal cancer.
Germline mutations in the tumor-suppresor APC gene are associated with hereditary familial adenomatous polyposis (FAP) and somatic mutations are common in sporadic colorectal cancer. In this study, we report the identification of three novel germline mutations: 1682-1683insA, 3252-3253insAT, 3544A>T and a new somatic mutation 4130-4131delTT, all giving rise to truncated APC proteins. The majority of the mutations we found originate a truncated APC protein and cause the FAP phenotype. However, special attention must be given to the missense mutations Asp1822Val and Ser2621Cys since their segregation with the FAP phenotype is questionable. In our FAP families we did not find any genetical alterations at codon 1309, being this mutation the most frequent reported in APC. Differences in the recurrence of pathological mutations in APC could exist among populations. However, epidemiological studies must be performed to confirm this hypothesis.
Adenomatous Polyposis Coli↗
Length variability and interspersion patterns of the HRAS1 minisatellite: a new approach for the reconstruction of human population relationships.
During recent years the HRAS1 minisatellite has been analysed by several authors because of its putative association with cancer susceptibility. The aim of this report is to test the usefulness of this minisatellite in investigating human population relationships. We have studied 370 chromosomes from two well-differentiated populations: Galicia (North-west Iberia) and South-east Africa, as well as available data on allele length gene frequencies. The fragment analysis results show a strong tendency to differentiate between non-African and African populations. In spite of the usefulness of fragment analysis, the minisatellite variant repeat (MVR) approach of the HRAS1 minisatellite appears to be a more powerful method for use in human population studies, due to the high level of diversity of its interspersion pattern structures. In addition, this approach has allowed us to define some new structural characteristics of this minisatellite. Four different major groups of human HRAS1 minisatellite alleles could be distinguished following a structural criterion based on the MVR code. Furthermore, the characterisation of the HRAS1 minisatellite in chimpanzees revealed clear differences when compared to humans, not only with respect to the allele size but also to the internal structure.
Africa, Southern↗
The Asp1822Val variant of the APC gene is a common polymorphism without clinical implications.
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Alleles↗
Analysis of 2 antiapoptotic factors in gliomas: bcl-2 overexpression and p53 mutations.
BACKGROUND: p53 mutations and immunoreactivity have been described in human gliomas. During the past few years, some authors have found bcl-2 overexpression in astrocytomas, although their correlation with histological grade is a matter of disagreement. A relation between bcl-2 overexpression and p53 immunoreactivity has also been suggested. OBJECTIVES: To analyze the frequency of presentation of bcl-2 and p53, their clinicopathologic implications, and their possible coexpression. METHODS: We studied p53 and bcl-2 with immunohistochemical and molecular methods in 61 gliomas (including 21 astrocytomas, 9 anaplastic astrocytomas, 29 glioblastomas, 1 oligodendroglioma, and 1 mixed glioma). RESULTS: We discovered a high level of bcl-2 overexpression (57%). Overexpression of bcl-2 can be an early event in gliomas tumorigenesis, although no correlation was found with any of the clinicopathologic parameters studied. p53 mutations were present in a small proportion of gliomas (17%). p53 immunoreactivity was present in 34 cases (57%), and it was related to histological grade and a supratentorial location. A high percentage of tumors (26 cases, 42%) presented p53 immunoreactivity without p53 mutations. CONCLUSIONS: Since there was no relation between bcl-2 overexpression and p53 mutations or p53 immunoreactivity, both factors may not act together in the genesis and evolution of gliomas.
Adolescent↗
Rapid genotyping of the M129V polymorphism of prion protein using real-time fluorescent PCR.
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Genotype↗
Assessing microsatellite instability with semiautomated fluorescent technology: application to the analysis of primary brain tumors.
The replication error phenotype, revealed by the observation of widespread microsatellite instability (MIN), has been identified as a new mechanism of cancer susceptibility, and the comparison of the allele sizes of polymorphic microsatellite repeats between normal and tumor DNA is now frequently undertaken in colorectal and other human neoplasias. The lack of precise characterization of the electrophoretic profiles of microsatellites is one of the main sources of discord between the rate of MIN reported for the same type of tumor by different investigators. The recent introduction of fluorescent-based semiautomated microsatellite analysis allows a more accurate size comparison, but one or more artificial peaks, generated during polymerase chain reaction (PCR) and/or electrophoresis, are frequently detected along with the true allele peaks. The aim of this study was to characterize the most frequent artificial extra peaks in the short tandem repeats (STRs) used by us to assess MIN in human cancers. We analyzed eight microsatellite loci in 113 primary brain tumors. HumFibra/FGA exhibited the most frequent extra peak formation. For each microsatellite there is a characteristic pattern of artifact formation which must be recognized to avoid a false-positive diagnosis of MIN.
Automation↗
Differential effects of amino-terminal distal and proximal domains in the regulation of human erg K(+) channel gating.
The participation of amino-terminal domains in human ether-a-go-go (eag)-related gene (HERG) K(+) channel gating was studied using deleted channel variants expressed in Xenopus oocytes. Selective deletion of the HERG-specific sequence (HERG Delta138-373) located between the conserved initial amino terminus (the eag or PAS domain) and the first transmembrane helix accelerates channel activation and shifts its voltage dependence to hyperpolarized values. However, deactivation time constants from fully activated states and channel inactivation remain almost unaltered after the deletion. The deletion effects are equally manifested in channel variants lacking inactivation. The characteristics of constructs lacking only about half of the HERG-specific domain (Delta223-373) or a short stretch of 19 residues (Delta355-373) suggest that the role of this domain is not related exclusively to its length, but also to the presence of specific sequences near the channel core. Deletion-induced effects are partially reversed by the additional elimination of the eag domain. Thus the particular combination of HERG-specific and eag domains determines two important HERG features: the slow activation essential for neuronal spike-frequency adaptation and maintenance of the cardiac action potential plateau, and the slow deactivation contributing to HERG inward rectification.
Amino Acid Sequence↗
Low frequency of replication errors in primary nervous system tumours.
OBJECTIVES: Automated DNA technology was used to analyze the incidence of microsatellite instability (MIN) among the most frequent types of adult primary CNS tumours and to determine its relation with clinicopathological characteristics. METHODS: Fifty six gliomas, 32 meningiomas and 11 schwannomas were screened for size changes at eight microsatellite loci using fluorescent polymerase chain reaction (PCR) followed by fragment analysis in an automated sequencer. A tumour was considered as MIN+ when a different electrophoretic pattern between constitutional and tumour DNA was evidenced in one or more microsatellite markers and as replication error positive (RER+) when at least 25% of the markers analyzed (2/8) showed instability. The MIN phenotype was correlated with relevant clinical and pathological parameters. RESULTS: Globally, instability was found in 19/767 analyses (2.47%), with a higher rate among tetranuceotide than dinucleotide repeats (chi(2) test, p=0.018). Ten gliomas (17.9%), two meningiomas (6.3%), and two schwannomas (18.2%) were MIN+, whereas one glioma (1.8%), two meningiomas (6.3%), and one schwannoma (9.1%) were classified as RER+. A possible association between microsatellite instability and a shorter duration of clinical course was found in meningiomas. The MIN+ phenotype was more frequent in spinal than intracranial schwannomas (Fisher's exact test, p=0.018). No other significant association with clinical or histological features was detected. CONCLUSIONS: Although microsatellite instability can be demonstrated at a low rate in some primary CNS tumours, a true replication error phenotype (revealed by widespread microsatellite instability at numerous loci) is uncommon and unlikely to play an important part in the pathogenesis of these neoplasms. This form of instability was more frequent in tetranucleotide than in dinucleotide repeats. To our knowledge, this is the first report of MIN in schwannomas, where it was associated with the spinal localisation of the tumour.
Adult↗
Rapid real-time fluorescent PCR gene dosage test for the diagnosis of DNA duplications and deletions.
BACKGROUND: Current methods to determine gene dosage are time-consuming and labor-intensive. We describe a new and rapid method to assess gene copy number for identification of DNA duplications or deletions occurring in Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP), respectively. METHODS: We studied 16 patients with HNPP, 4 with CMT1A, and 49 control subjects. We used real-time PCR on the LightCycler system with use of a single capillary tube and no post-PCR handling. A polymorphic fragment of the PMP22 gene was amplified to determine gene dosage for heterozygous samples. The presence of two alleles was used to indicate that no deletion was present in HNPP samples. The ratio obtained between the areas under each allele melting curve of heterozygous CMT1A samples was used to determine whether the sequence was duplicated or normal. Homozygous samples required a competitive gene dosage test, where the ratio between the areas under the melting curves of the target DNA of samples and of the competitor molecule was used to determine whether the target sequence was duplicated, deleted, or normal. Samples from HNPP, CMT1A, and controls were analyzed. RESULTS: Area ratios were approximately 0.6, 1.0, and 2.0 for HNPP, control, and CMT1A samples, respectively. The results agreed with those obtained by Southern blotting and microsatellite analysis in the same samples. CONCLUSIONS: Direct and competitive real-time fluorescent PCR can differentiate one, two, or three copies of the target DNA. The method described is sensitive and accurate for detection of CMT1A duplications and HNPP deletions and is faster and easier than current methods.
Charcot-Marie-Tooth Disease↗