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C Alves

Publications and source records attributed to C Alves.

At least 19 recordsLinked to original sources
PubMed2024

Oceanic islands act as drivers for the genetic diversity of marine species: Cardita calyculata (Linnaeus, 1758) in the NE Atlantic as a case-study.

Geographic distribution, as well as evolutionary and biogeographic processes and patterns of marine invertebrate benthic species are strongly shaped by dispersal ability during the life cycle. Remote oceanic islands lie at the brink of complex biotic and abiotic interactions which have significantly influenced the biodiversity patterns we see today. The interaction between geological environmental change and taxon-specific dispersal modes can influence species evolutionary patterns, eventually delimiting species-specific biogeographic regions. In this study, we compare the population genetic patterns of the marine bivalve Cardita calyculata in the northeast Atlantic, discussing the role of Macaronesian islands during past climatic cycles. The genetic structure and diversity patterns were outlined based on SSR-GBAS loci of 165 individuals and on the mitochondrial COI marker of 22 individuals from the Canary Islands, Madeira, Azores and the Mediterranean. The highly structured genetic pattern found among regions and within archipelagos suggests the central role of oceanic islands in promoting the divergence of the species in both the NE Atlantic and the Mediterranean. The high degree of divergence in the COI dataset (> 7%) suggests the existence of potential cryptic speciation that needs to be further explored with a more comprehensive sampling. Such patterns are only congruent with a scenario where C. calyculata populations were maintained during glacial/interglacial cycles, supporting the role of the studied archipelagos as drivers of diversity for marine biota. We stress the importance of developing studies for species with various life history and dispersal modes. In such a way, a more profound understanding of the biogeographic and evolutionary significance of oceanic islands can catalyse directed conservation efforts, especially in the context of the ongoing climate crisis.

Animals↗
PubMed2007

Dissecting the genetic history of São Tomé e Príncipe: a new window from Y-chromosome biallelic markers.

Twenty biallelic Y chromosome markers were analyzed in Angolares, Forros and Tongas, three population groups from the African archipelago of São Tomé e Príncipe. While most male lineages belonged to sub-Saharan haplogroups, the component of European origin added up 23.9% in the archipelago. This contrasts with the reported absence of European mtDNA lineages, and the combined findings testify to a strong sex-biased admixture process during the long-lasting colonial period in São Tomé e Príncipe. Furthermore, the male mediated European component was clearly found to be out of proportion to the small demographic impact of the Portuguese on the islands, reflecting high variance in the reproductive success of the individuals that contributed to its peopling. The male portion of European ancestry was 33.3% in Forros, 27.3% in Tongas and approximately two-fold less, 14.5%, in Angolares. The Angolares also showed the lowest haplogroup diversity and the most reduced number of different haplogroups. The current results reinforce our previous evidence pointing to remarkable restrictions in gene flow between Angolares and other São Tomean inhabitants, in agreement with their considerable isolation and confinement to the south-eastern tip of São Tomé until recently.

Africa↗
PubMed2006

Contralateral recurrence and prognostic factors in familial non-BRCA1/2-associated breast cancer.

BACKGROUND: A higher incidence of contralateral breast cancer and ipsilateral recurrence has been reported in familial breast cancer than in sporadic cancer. This study investigated the influence of contralateral cancer and tumour stage on survival in patients with familial non-BRCA1/BRCA2-associated breast cancer. METHODS: The incidences of contralateral breast cancer, ipsilateral recurrence, distant disease-free and overall survival were assessed in 327 patients from families with three or more breast and/or ovarian cancers, but no BRCA1 or BRCA2 gene mutation (familial non-BRCA1/2), and in 327 control subjects with sporadic breast cancer, matched for year and age at detection. RESULTS: Mean follow-up was 7.3 years for patients with familial-non-BRCA1/2 cancers and 6.5 years for patients with sporadic breast cancer. Tumours were stage T1 or lower in 62.1 per cent of familial non-BRCA1/2 cancers versus 49.9 per cent in sporadic breast cancers (P = 0.003), and node negative in 55.8 versus 52.1 per cent, respectively (P = 0.477). After 10 years the incidence of metachronous contralateral breast cancer was 6.4 per cent for familial non-BRCA1/2 tumours versus 5.4 per cent for sporadic cancers. The rate of ipsilateral recurrence was not significantly increased (17.0 versus 14.2 per cent, respectively, at 10 years; P = 0.132). Tumour size (hazard ratio (HR) 1.02 per mm increase, P = 0.016) and node status (HR 2.6 for three or more involved nodes versus node negative, P = 0.017) were independent predictors of overall survival in the familial non-BRCA1/2 group, and in the whole group, whereas contralateral breast cancer (HR 0.7, P = 0.503) and risk-reducing contralateral mastectomy (HR 0.4, P = 0.163) were not. CONCLUSION: Stage at detection was a key determinant of prognosis in familial non-BRCA1/2 breast cancer, whereas contralateral cancer was not. Risk-reducing contralateral mastectomy did not significantly improve survival, but early detection can. Decisions on breast-conserving treatment can be made on the same grounds in patients with familial and sporadic breast cancer.

Adult↗
PubMed2005

Population data on 15 autosomal STRs in a sample from East Timor.

Allele frequencies for the fifteen STRs included in the AmpF/STR Identifiler (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) were estimated from a sample of 186 unrelated individuals from East Timor. No deviations from Hardy-Weinberg equilibrium were observed (only after applying the Bonferroni correction in the cases of D2S1338, TPO and D5S818). Genetic parameters of forensic interest were calculated and comparison with geographically nearby populations was performed.

DNA Fingerprinting↗
PubMed2005

Data for 15 autosomal STR markers (Powerplex 16 System) from two Tunisian populations: Kesra (Berber) and Zriba (Arab).

Allele frequencies, together with some parameters of forensic interest, for 15 STRs included in the Powerplex 16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPO and VWA) were estimated from two samples of unrelated individuals from Tunisia, of different ethnicity: Kesra (Berber) and Zriba (Arab). No deviations from Hardy-Weinberg equilibrium were observed after Bonferroni's correction for the number of loci analysed. Comparative analyses between our population data and other North African databases showed that significant differences were concentrated on loci with lowest values of diversity (mainly CSF1PO and D13S317), irrespective of ethnicity and geographic location.

DNA Fingerprinting↗
PubMed2005

Mutation rates at Y chromosome specific microsatellites.

A collaborative work was carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG) to estimate Y-STR mutation rates. Seventeen Y chromosome STR loci (DYS19, DYS385, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635 [GATA C4], GATA H4, and GATA A10) were analyzed in a sample of 3,026 father/son pairs. Among 27,029 allele transfers, 54 mutations were observed, with an overall mutation rate across the 17 loci of 1.998 x 10(-3) (95% CI, 1.501 x 10(-3) to 2.606 x 10(-3)). With just one exception, all of the mutations were single-step, and they were observed only once per gametogenesis. Repeat gains were more frequent than losses, longer alleles were found to be more mutable, and the mutation rate seemed to increase with the father's age. Hum Mutat 26(6), 520-528, 2005. (c) 2005 Wiley-Liss, Inc.

Age Factors↗
PubMed2005

Mitochondrial DNA haplotyping revealed the presence of mixed up benign and neoplastic tissue sections from two individuals on the same prostatic biopsy slide.

DNA typing was requested to investigate a presumptive cancer diagnosis error by confirming whether benign and cancerous prostatic tissue in the same presurgical haematoxylin and eosin stained slide belonged to the same person. After independent histological re-examination of the slide by a pathologist, manual slide dissection was used to guarantee independent and high recovery DNA isolation from each tissue section, avoiding carryover and background contamination. Nuclear DNA quantification performed by real time polymerase chain reaction (PCR) revealed the absence of human DNA for short tandem repeat (STR) typing. Mitochondrial DNA was only obtained by performing PCR of very short fragments ( approximately 100 bp), indicating high DNA degradation. Different low frequency hypervariable region I haplotypes were obtained from each tissue section (normal tissue section haplotype: 16224C, 16234T, 16311C, 16356C; cancer tissue section haplotype: 16256T, 16270T, 16293G). Only the normal tissue section haplotype matched that obtained from the patient's blood sample, indicating that the cancer tissue section originated from an unknown patient. These results supported the hypothesis of sample mix up during block processing or slide preparation by a carryover mechanism. Mitochondrial genetic typing is recommended to exclude the possibility of carryover artefacts when low DNA content and high degradation compromise conventional STR typing.

Artifacts↗
PubMed2004

AZF and DAZ gene copy-specific deletion analysis in maturation arrest and Sertoli cell-only syndrome.

Deletions of the AZFc region in Yq11.2, which include the DAZ gene family, are responsible for most cases of male infertility and were associated with severe oligozoospermia and also with a variable testicular pathology. To uncover the functional contribution of DAZ to human spermatogenesis, a DAZ gene copy-specific deletion analysis was previously established and showed that DAZ1/DAZ2 deletions associate with oligozoospermia. In this study we applied the same screening method to 50 control fertile males and 91 non-obstructive azoospermic males, 39 with Sertoli cell-only syndrome (SCOS) and 52 with meiotic arrest (MA). Samples were also screened with 24 sequence-tagged sites to the different AZF regions, including 114 control fertile males. After biopsy (testicular sperm extraction, TESE), residual spermiogenesis was found in 57.7% MA and 30.8% SCOS cases (incomplete syndromes). DAZ1/DAZ2 deletions were associated with the testicular phenotype of residual spermiogenesis as they were only found in two patients (8%) with incomplete MA. Differences between incomplete (23.3%) and complete (4.5%) MA cases regarding AZFc and DAZ1/DAZ2 deletion frequencies, and between incomplete (58.3%) and complete (11.1%) SCOS cases for AZFc deletions, suggest that incomplete syndromes might represent an aggravation of the oligozoospermic phenotype. As successful TESE was achieved in 87.5% of MA cases with AZFc and DAZ1/DAZ2 deletions and in 58.3% of SCOS cases with AZFc deletions, the present results also suggest that these molecular markers might be used for the establishment of a prognosis before TESE.

Deleted in Azoospermia 1 Protein↗
PubMed2004

17 STR data (AmpF/STR Identifiler and Powerplex 16 System) from Cabinda (Angola).

Allele frequencies for seventeen STRs included in the AmpF/STR Identifiler (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPOX, and VWA) and Powerplex 16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPOX, and VWA) were estimated from a sample of 110 unrelated individuals from Cabinda, Angola. Comparative analyses between our population data and other African databases, namely Promega's African-Americans, AB Applied Biosystems African-Americans and five other population samples gathered from the literature are also presented.

Angola↗
PubMed2004

Application of GEANT4 radiation transport toolkit to dose calculations in anthropomorphic phantoms.

In this paper, we present a novel implementation of a dose calculation application, based on the GEANT4 Monte Carlo toolkit. Validation studies were performed with an homogeneous water phantom and an Alderson-Rando anthropomorphic phantom both irradiated with high-energy photon beams produced by a clinical linear accelerator. As input, this tool requires computer tomography images for automatic codification of voxel-based geometries and phase-space distributions to characterize the incident radiation field. Simulation results were compared with ionization chamber, thermoluminescent dosimetry data and commercial treatment planning system calculations. In homogeneous water phantom, overall agreement with measurements were within 1-2%. For anthropomorphic simulated setups (thorax and head irradiation) mean differences between GEANT4 and TLD measurements were less than 2%. Significant differences between GEANT4 and a semi-analytical algorithm implemented in the treatment planning system, were found in low-density regions, such as air cavities with strong electronic disequilibrium.

Algorithms↗
PubMed2003

Phylogeography of the Madeiran endemic lizard Lacerta dugesii inferred from mtDNA sequences.

Partial sequences from two mitochondrial DNA genes, cytochrome b and 12S rRNA, were used to assess the phylogenetic relationships of populations of Lacerta dugesii from the volcanic Atlantic islands of Madeira, the Desertas, Porto Santo, and the Selvagens. All four-island groups are genetically distinguishable and populations within each contain similar degrees of genetic diversity. Molecular clock estimates suggest that the islands were colonized much later after their emergence compared to other Atlantic islands, possibly due to their greater geographical isolation. Mismatch analysis of all populations is consistent with exponential growth, as expected after colonization of empty niches. The Selvagens contain genetic substructuring between the islets.

Animals↗
PubMed2002

Extending STR markers in Y chromosome haplotypes.

Two multiplex reactions were developed to amplify 16 Y-STRs (DYS19, DYS385, DYS389 I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, GATA A7.1, GATA A7.2, GATA A10, GATA C4, GATA H4). Here we extend previous population studies done in a sample from northern Portugal for the GATA A7.1, GATA A7.2, GATA C4 and GATA H4 loci. A total of 199 different haplotypes identified by the 16 Y-STR markers were observed in a sample of 208 male individuals, of which 190 were unique and 9 were found twice. The overall haplotype diversity was 0.9996. The haplotype diversity of the Y-STR set composed of the 8 new markers is higher than the Y-STR core set included in the Y-STR haplotype reference database. Sequence structure of new alleles for GATA C4 and GATA H4 is reported. The usefulness of the inclusion of this new set of Y-STRs in forensic casework was also assessed. The increase in haplotype diversity with the addition of any new Y-STR marker to the 8 Y-STR core set is dependent not only on the gene diversity (positively) but also (negatively) on the degree of gametic association between the markers and the haplotypes previously defined. For instance, in our sample the addition of the DYS437, DYS438 and GATA A7.2 to a 13-locus set increased haplotype diversity only by 0.0001.

Base Sequence↗
PubMed2002

A comparison of AT1 angiotensin II antagonists at pre- and postjunctional angiotensin II receptors of the rat tail artery.

A comparison was made of the influence of candesartan, ZD7155, losartan and eprosartan on angiotensin II effects at pre- and postjunctional AT(1) receptors of the rat tail artery. To study the anti-angiotensin II effect at prejunctional receptors, the tissues were preincubated with [(3)H]noradrenaline and then superfused and electrically stimulated (1 Hz, 2 ms, 50 mA, during 5 min); to study the angiotensin II effect at postjunctional receptors, non-cumulative concentration-response curves to angiotensin II were determined in the absence and in the presence of the antagonist. p A(2) values were calculated for competitive antagonists and p D'(2) values for insurmountable antagonists. At the prejunctional level, losartan and eprosartan displayed competitive antagonism with p A(2) values of 6.50 and 8.08, respectively, whereas candesartan and ZD7155 displayed non-competitive antagonism with p D'(2) values of 8.71 and 7.98, respectively. At the postjunctional level, the four antagonists displayed the same kind of antagonism as prejunctionally with p A(2) values for losartan and eprosartan of 8.52 and 8.22, respectively, and p D'(2) values of 10.62 and 9.01, for candesartan and ZD7155, respectively. The ratios between post- and prejunctional potencies were: losartan 101, candesartan 81, ZD7155 11, and eprosartan 1.4. We conclude that, at least functionally, pre- and postjunctional angiotensin II AT(1) receptors are different and propose that the prejunctional receptors in this tissue belong to the AT(1B)-subtype.

Angiotensin II↗
PubMed2002

Genetic diversity of Y-specific STRs in chimpanzees (Pan troglodytes).

Using the primers described for humans, sequences for 11 Y-specific microsatellites (DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, GATA A10, A7.1, A7.2, C4, and H4 [Gusmão et al., in press]), previously described in 10 male chimpanzees (Pan troglodytes), were confirmed in nine additional male chimpanzees. Sequences for nine additional microsatellites (DYS19, DYS385I and II, DYS389I and II, DYS390, DYS391, DYS392, and DYS393) were determined in all 19 male chimpanzees; homology to human Y-Short Tandem Repeat (STRs) was confirmed by sequencing. Good amplification results were not obtained for DYS19 and DYS385I/II. Two amplicons were obtained for DYS389I/II, but in contrast to humans, the larger fragment was not Y-specific. Moreover, no polymorphism was observed for DYS434, DYS435, or GATA A10. Consequently, these eight STRs were eliminated from further analyses, and haplotype and allele frequencies were estimated for the remaining 12 STRs. A high haplotype diversity value was found (1.000 +/- 0.017), demonstrating the usefulness and informative power of these Y-STRs for future studies on chimpanzee population genetics.

Amino Acid Sequence↗
PubMed2002

Bantu and European Y-lineages in Sub-Saharan Africa.

Ancient diversity in Sub-Saharan Africa is known to have been re-modulated to a large extent by Bantu migrations in the sub-Sahel region, in two southwards waves of advance through both the west and east coasts. Haplotype matching performed for Y-STR haplotypes in several sub-Saharan populations, both inside and outside the migration path, allowed the confirmation of a putative founder haplotype, and its one-step neighbours, of Bantu origin, and detected an increasing drift towards the south, with a stronger reduction of diversity along the western coast. A mixed frequency distribution for the Bantu haplotype core in South Africa, relative to the western and eastern pools, seems to provide evidence for the intermingling between both Bantu waves in that region. The proportion of male lineages considered as predating the Bantu expansion reached 8.8% in Mozambique. Further influence on sub-Saharan diversity may have occurred during the colonial period; in Mozambique, the European genetic impact in the male component was estimated to be around 5.9%, in significant contrast with the female counterpart where no European lineages were detected.

Africa South of the Sahara↗
PubMed2002

Current aetiology of unilateral vocal fold paralysis in a teaching hospital in the West of Scotland.

Between May 1997 and May 2001 all patients presenting with a unilateral vocal fold palsy at Gartnavel General hospital were entered into a prospective observational study. The sex, age, side of palsy and aetiology were documented. The aim of the study was to assess the current aetiology of vocal fold palsy in a large teaching hospital in the West of Scotland, and to compare this with the established aetiology in other parts of the world. Seventy-seven patients were studied. Eighty-three per cent were found to have a left and 17 per cent a right vocal fold palsy. The male to female ratio was 2:1, with an age range of 23-85, mean 61. Forty-three per cent of all vocal fold palsies were secondary to an underlying bronchogenic carcinoma and a further nine per cent due to other malignancies. This contrasted with figures quoted in other studies, that gave lung cancer causes of vocal fold palsies ranging from four to 22 per cent. Surgical trauma accounted for 24 per cent and in 11 per cent no cause was found. In conclusion, in our hospital population there is a high rate of vocal fold palsy secondary to bronchogenic carcinoma. This is likely to be associated with the high levels of smoking found in Scotland. Lung cancer rates in Scotland are 1.6 times greater for men, and two times greater for women than the world standard. Malignancies overall cause over 50 per cent of our vocal fold palsies. Vigilance is required in any patient presenting with a vocal fold palsy to ensure a malignancy is not overlooked.

Adult↗
PubMed2001

STR data for the AmpFlSTR profiler plus loci from Macau (China).

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 87 unrelated individuals living in the region of Macau, a territory located in the southeastern coast of China.

Alleles↗