Browsing by Author "Rocha, F."
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- Characterization of the sedimentary environment of the Gilão River Mouth, based on sedimentological and mineralogical analysisPublication . Rocha, F.; Boski, T.; Gomes, Celso; Moura, Delminda; Veiga-Pires, C.The main objective of this paper is to use the mineralogical composition of the fine and clay fractions of the sediments from the studied borehole to a better characterization of the Gilão Estuary sedimentary environment.
- Correction of the misclassification of species in the Portuguese collection of Cucurbita pepo L. using DNA markersPublication . Rodrigues, R.; Veiga, I.; Marreiros, A.; Rocha, F.; Leitão, J. M.In this study, the genetic variability among 130 accessions of the Portuguese germplasm collection of Cucurbita pepo L. maintained at the Banco Portugues de Germoplasma Vegetal was assessed using AFLP (amplified fragment length polymorphism) and RAPD (random amplified polymorphic DNA) techniques for the identification of a genetically diverse core group of accessions for field phenotypic analysis. The surprisingly completely different molecular patterns exhibited by multiple accessions was later confirmed in the distribution of the putative C. pepo plants into two clusters drastically separated at a very low level of genetic similarity (DICE coefficient = 0.37). Additional analyses with RAPD and ISSR (inter single sequence repeat) markers and the introduction of standard genotypes of C. maxima L. and C. moschata L. into the analyses allowed the identification of multiple accessions of the last species wrongly included in the C. pepo collection. This study is a good example of the usefulness of DNA markers in the establishment and management of plant germplasm collections.
- Ensaio de caracterização do meio sedimentar do estuário do Rio Gilão, com base em análises de parâmetros mineralógicos e sedimentológicosPublication . Rocha, F.; Boski, T.; Gomes, Celso; Moura, Delminda; Veiga-Pires, C.Foram realizadas análises sedimentológicas e mineralógicas ao sedimento recolhido numa sondagem realizada no estuário do Rio Gilão próximo do Arraial Ferreira Neto. A sondagem atingiu o substrato rochoso pré-holocénico aos 18 m de profundidade.
- Geochemical characterization of surficial sediments from the southwestern Iberian continental shelfPublication . Machado, A.; Rocha, F.; Araujo, M. F.; Vitali, F.; Gomes, C.; Dias, João A.The impact of trace elements (Ba, Nb, Zr, Y, Sr, Rb, Pb, As, Zn, Cu, Ni, Co, Cr, V, La, Ce, Nd, Sm, Eu, Th, Yb and Lu) transported by the Guadiana, Tinto-Odiel and Guadalquivir rivers on sediments from the southwestern Iberian continental shelf has been studied. Shelf surficial sediments from three transects established right in front of the river estuaries were characterized by specific signatures relative to those trace elements. The Guadiana transect shows high Zr concentration values; the Tinto-Odiel transect shows high heavy metal (Pb, As, Zn and Cu) concentration values; and the Guadalquivir transect shows high Sr concentration values. Data from the statistical analysis indicate three distinct sources for trace elements: lithogenic, biogenic and anthropogenic.
- Geochemistry, luminescence and innovative dose rate determination of a Chalcolithic calcite-rich negative featurePublication . Rodrigues, A. L.; Dias, M., I; Carlos Valera, António; Rocha, F.; Prudencio, M., I; Marques, R.; Cardoso, G.; Russo, D.An interdisciplinary approach comprising archaeological, chemical, mineralogical, and luminescence data was applied to a better understanding of the fill dynamic and chronologies of a calcite-rich negative archaeological feature from Southern Portugal. This work aims to contribute to the assessment of the human involvement in the backfilling actions of a negative archaeological feature from a Chalcolithic site, thus better defining the moments of its destruction and/or abandonment. There are well-known limitations of luminescence dating of calcite-rich materials, particularly in the dose rate determination. In this work, a proposal of two innovative protocols to determine the dose rate of calcite-rich contexts is discussed. A clear improvement of the dose rate estimation was obtained by using the "radionuclide weighed" protocol. The comprehensive used methodologies enabled to define the infill phases and the sources of the infill materials. The luminescence profiling studies were also useful to describe the infill processes, highlighting their discontinuity and pointing to different deposition rates. The luminescence ages obtained, when using the "radionuclide weighed" protocol proposed in this work, are closer to the archaeological evidence of a Chalcolithic occupation.
- Influence of Aveiro Lagoon heavy metal contents in the adjacent continental shelf (Portugal)Publication . Abrantes, I.; Rocha, F.; Vidinha, J.; Dias, João A.A chemical analysis of Al, Ca, Fe, Mg, Cu, Pb, Zn, Cr, Co, Ni and Cd was carried out in 22 surface sediment samples of the continental shelf and upper slope between Espinho and Aveiro (Portugal). To reduce the disturbing effects of grain size, all samples were size-normalized by wet sieving (< 63 mu m). The fine fraction was digested with concentrated acids and analyzed by flame atomic absorption spectrometry. The Al and heavy metal concentrations displayed a similar distribution pattern, decreasing seaward. Exceptions to this general pattern are Ca, Mg and Pb distributions. The Ca contents are related to carbonated biogenic particles that are very abundant in the outer shelf. Multivariate statistical analysis was applied to all data to assess the behaviour and sources of each element analyzed. The results from factor analysis showed that terrigenous supply (from Aveiro Lagoon flow, coastal erosion and littoral drift), grain size (clay) sorting and anthropogenic influences from Aveiro Lagoon are the major factors controlling spatial variations of chemical elements in the continental shelf between Espinho and Aveiro. Unusually high contents of Pb were found in the middle shelf off Furadouro, but we could not determine the possible source of this contamination.
- Programming the metabolic gene expression in zebrafish juveniles (Danio rerio) by supra-physiological glucose level during embryogenesisPublication . Rocha, F.; Dias, J.; Engrola, S.; Gavaia, Paulo J.; Geurden, Inge; Dinis, Maria Teresa; Panserat, S.Using zebrafish as a model organism, assess the effect of high glucose levels during early embryonic stages as a lifelong moderator of metabolic pathways.
- The response of benthic foraminifera to pollution and environmental stress in Ria de Aveiro (N Portugal)Publication . Martins, V.; Yamashita, C.; Sousa, S. H. M.; Martins, P.; Laut, L. L. M.; Figueira, R. C. L.; Mahiques, M. M.; Ferreira da Silva, E.; Dias, J. M. Alveirinho; Rocha, F.This work evaluates the quality of the sediment in Ria de Aveiro, a coastal lagoon located at N of Portugal that is under strong anthropic influence, and the effects of the contamination on benthic foraminifera. The initial approach for measuring pollution was done through the load pollution index (LPI), based on As, Cd, Cr, Cu, Ni, Pb and Zn concentrations, and determined by total digestion of the sediments (TDS). This information was complemented by conducting a metal fractionation technique (sequential chemical extraction - SCE) in some of the most contaminated samples in order to define the relevance of different metal bearing- phases (exchangeable cations adsorbed by clay and co-precipitated with carbonates, absorbed by organic matter and retained in the mineralogical phase) and to evaluate the toxic heavy metal availability. Multivariable statistical analyses were carried out taking into consideration the geochemical results, as well as the biotic (percentage of species/groups of species; foraminifer abundance and diversity) and abiotic variables, such as sediment content in mud, total organic carbon (TOC) and Eh. SCE results show that most of the element concentration in the sediments is retained in the resistant mineralogical phase. However, the higher bioavailability of some toxic elements, such as As, Cd, Cu, Hg, Ni, Pb and Zn, found in Laranjo Bay, Aveiro City, Aveiro Harbours and Espinheiro Channel, have a generic negative impact on benthic foraminifera of the Aveiro lagoon. Differential sensitivity of benthic foraminifera to high concentrations of heavy metals may exist. quinqueloculina seminulum, for instance, seems to be more tolerant to higher bioavailable concentrations of Pb and Cu than Ammonia tepida or Haynesina germanica. Both species were previously considered to be the most heavy metal-tolerant foraminifer species. This study confirmed the use of benthic foraminifera as an important tool for the evaluation of the environmental quality of an ecosystem and for monitoring and restoring it.
- Tolerance of zebrafish embryos to supra-physiologic yolk levels of glucosePublication . Rocha, F.; Dias, J.; Engrola, S.; Gavaia, Paulo J.; Dinis, Maria Teresa; Panserat, S.Once spawned and fertilized the oviparous fish eggs operate as closed systems; only respiratory gases, heat and negligible amounts of solutes and water are exchanged freely, as a result of an extremely low permeability of the egg surface membranes. Currently, the opportunities to exert a nutritional stimulus during a stage of high metabolic plasticity, such as fish embryogenesis, are restricted to maternal transfer and the onset of exogenous feeding.
- Whole exome sequencing of patients with diffuse idiopathic skeletal hyperostosis and calcium pyrophosphate crystal chondrocalcinosisPublication . Parreira, B.; Couto, A. R.; Rocha, F.; Sousa, M.; Faustino, V.; Power, Deborah; Bruges-Armas, J.Objectives: DISH/CC is a poorly understood phenotype characterised by peripheral and axial enthesopathic calcifications, frequently fulfilling the radiological criteria for Diffuse Idiopathic Skeletal Hyperostosis (DISH, MIM 106400), and in some cases associated with Calcium Pyrophosphate Dihydrate (CPPD) Chondrocalcinosis (CC). The concurrence of DISH and CC suggests a shared pathogenic mechanism. In order to identify genetic variants for susceptibility we performed whole exome sequencing in four patients showing this phenotype. Materials and methods: Exome data were filtered in order to find a variant or a group of variants that could be associated with the DISH/CC phenotype. Variants of interest were subsequently confirmed by Sanger sequencing. Selected variants were screened in a cohort of 65 DISH/CC patients vs 118 controls from Azores. The statistical analysis was performed using PLINK V1.07. Results:We identified 21 genetic variants in 17 genes that were directly or indirectly related to mineralization, several are predicted to have a strong effect at a protein level. Phylogenetic analysis of altered amino acids indicates that these are either highly conserved in vertebrates or conserved in mammals. In case-control analyses, variant rs34473884 in PPP2R2D was significantly associated with the DISH/CC phenotype (p=0.028; OR=1.789, 95% CI= 1.060 - 3.021)). Conclusion: The results of the present and preceding studies with the DISH/CC families suggests that the phenotype has a polygenic basis. The PPP2R2D gene could be involved in this phenotype in an as yet unknown way.