| 1. |
- Araujo, Mario Jorge, et al.
(författare)
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Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species
- 2021
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Ingår i: Proteomes. - : MDPI. - 2227-7382. ; 9:4
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Tidskriftsartikel (refereegranskat)abstract
- Proteomics has been recently introduced in aquaculture research, and more methodological studies are needed to improve the quality of proteomics studies. Therefore, this work aims to compare three sample preparation methods for shotgun LC-MS/MS proteomics using tissues of two aquaculture species: liver of turbot Scophthalmus maximus and hepatopancreas of Mediterranean mussel Mytilus galloprovincialis. We compared the three most common sample preparation workflows for shotgun analysis: filter-aided sample preparation (FASP), suspension-trapping (S-Trap), and solid-phase-enhanced sample preparations (SP3). FASP showed the highest number of protein identifications for turbot samples, and S-Trap outperformed other methods for mussel samples. Subsequent functional analysis revealed a large number of Gene Ontology (GO) terms in turbot liver proteins (nearly 300 GO terms), while fewer GOs were found in mussel proteins (nearly 150 GO terms for FASP and S-Trap and 107 for SP3). This result may reflect the poor annotation of the genomic information in this specific group of animals. FASP was confirmed as the most consistent method for shotgun proteomic studies; however, the use of the other two methods might be important in specific experimental conditions (e.g., when samples have a very low amount of protein).
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| 2. |
- Araújo, Mário J, et al.
(författare)
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Proteomics reveals multiple effects of titanium dioxide and silver nanoparticles in the metabolism of turbot, Scophthalmus maximus
- 2022
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Ingår i: Chemosphere. - : Pergamon-Elsevier Science Ltd. - 0045-6535 .- 1879-1298. ; 308
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Tidskriftsartikel (refereegranskat)abstract
- Titanium dioxide (TiO2) and silver (Ag) NPs are among the most used engineered inorganic nanoparticles (NPs); however, their potential effects to marine demersal fish species, are not fully understood. Therefore, this study aimed to assess the proteomic alterations induced by sub-lethal concentrations citrate-coated 25 nm ("P25") TiO2 or polyvinylpyrrolidone (PVP) coated 15 nm Ag NPs to turbot, Scophthalmus maximus. Juvenile fish were exposed to the NPs through daily feeding for 14 days. The tested concentrations were 0, 0.75 or 1.5 mg of each NPs per kg of fish per day. The determination of NPs, Titanium and Ag levels (sp-ICP-MS/ICP-MS) and histological alterations (Transmission Electron Microscopy) supported proteomic analysis performed in the liver and kidney. Proteomic sample preparation procedure (SP3) was followed by LC-MS/MS. Label-free MS quantification methods were employed to assess differences in protein expression. Functional analysis was performed using STRING web-tool. KEGG Gene Ontology suggested terms were discussed and potential biomarkers of exposure were proposed. Overall, data shows that liver accumulated more elements than kidney, presented more histological alterations (lipid droplets counts and size) and proteomic alterations. The Differentially Expressed Proteins (DEPs) were higher in Ag NPs trial. The functional analysis revealed that both NPs caused enrichment of proteins related to generic processes (metabolic pathways). Ag NPs also affected protein synthesis and nucleic acid transcription, among other processes. Proteins related to thyroid hormone transport (Serpina7) and calcium ion binding (FAT2) were suggested as biomarkers of TiO2 NPs in liver. For Ag NPs, in kidney (and at a lower degree in liver) proteins related with metabolic activity, metabolism of exogenous substances and oxidative stress (e.g.: NADH dehydrogenase and Cytochrome P450) were suggested as potential biomarkers. Data suggests adverse effects in turbot after medium/long-term exposures and the need for additional studies to validate specific biological applications of these NPs.
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| 3. |
- Brodic, Bojan, et al.
(författare)
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Innovative seismic imaging of volcanogenic massive sulfide deposits, Neves-Corvo, Portugal - Part 1 : In-mine array
- 2021
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Ingår i: Geophysics. - : Society of Exploration Geophysicists. - 0016-8033 .- 1942-2156. ; 86:3, s. B165-B179
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Tidskriftsartikel (refereegranskat)abstract
- To evaluate and upscale the feasibility of using exploration tunnels in an operating mine for active-source seismic imaging, a seismic experiment was conducted at the Neves-Corvo mine, in southern Portugal. Four seismic profiles were deployed in exploration drifts approximately 650 m beneath the ground surface, above the world-class Lombador volcanogenic massive sulfide deposit. In addition to the tunnel profiles, two perpendicular surface seismic profiles were deployed above the exploration tunnels. The survey was possible due to a newly developed prototype global positioning system (GPS) time transmitter enabling accurate GPS synchronization of cabled and nodal seismic recorders, below and on the surface. Another innovative acquisition aspect was a 1.65 t broadband, linear synchronous motor (LSM) driven - electric seismic vibrator (e-vib) used as the seismic source along two of the exploration tunnels. We have evaluated the challenges and innovations necessary for active-source tunnel seismic acquisition, characterized by high levels of vibrational noise from the mining activities. In addition, we evaluated the LSM vibrator's signal and overall seismic-data quality in this hard rock mining environment. Our processing results from the tunnel data and 3D reflection imaging of the Lombador deposit below the exploration tunnels were checked for consistency through constant-velocity 3D ray-tracing traveltime forward modeling. For imaging purposes, 3D Kirchhoff prestack depth and poststack time-migration algorithms were used, with both successfully imaging the targeted deposit. The results obtained show that active-source-seismic imaging using subsurface mining infrastructure of operational mines is possible. However, it requires innovative exploration strategies, a broadband seismic source, an accurate GPS-time system capable of transmitting GPS-time hundreds of meters below the surface, and careful processing. The results obtained open up possibilities for similar studies in different mining or tunneling projects.
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| 4. |
- Carvalho, Joao, et al.
(författare)
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A drill-hole, geological and geophysical data-based 3D model for target generation in Neves-Corvo mine region, Portugal
- 2022
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Ingår i: International journal of earth sciences. - : Springer Nature. - 1437-3254 .- 1437-3262. ; 111, s. 403-424
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Tidskriftsartikel (refereegranskat)abstract
- The Neves-Corvo world class Iberian Pyrite Belt volcanogenic massive sulphide (VMS) deposit located in southern Portugal, constitutes an important Cu-Zn-Pb active mine. Seven deposits are currently known, among which the Lombador deposit alone has estimated 150 Mt of massive sulphides. The life-time of the mine is dependent on the discovery of new exploration targets and it is vital to have accurate 3D geological models, not only to guide drilling campaigns but also to drive a winning/new strategy, which in the past has led to Semblana and Monte Branco discoveries: geophysical inversion and modelling. Furthermore, 3D geological models can contribute to the understanding of the tectonic and stratigraphic evolution of the region. Therefore, the goal of this study is to produce a realistic 3D geological model of the Neves-Corvo region, as only one model is presently publicly available: the PROMINE model, which includes the study area of this work and extends from Aljustrel to the border with Spain. Lundin Mining has also produced two unpublished, confidential models in 2007 and 2017. The latest Lundin model incorporates the same geophysical data used in this work (2D and 3D seismic reflection and time-domain electromagnetic (TEM) ground loop data) and approximately 7500 surface and underground drill-holes. The model presented in this research has much more detail than the 2012 PROMINE model in the Neves-Corvo region and uses an updated and revised drill-hole database with approximately 8000 drill-holes, revised geological cross-sections built from surface geology and drill-hole logs, new geological outcrop data, petrophysical and reprocessed geophysical data, and is therefore more detailed and accurate than any of the previous models, in particular the 2007 and PROMINE models. Land gravimetric and aeromagnetic data are also available in the study area but were not directly used to build the geological model but rather to investigate and check the model produced. Modelling was performed with industry standard software and the 3D curves resulting from the geological/geophysical interpretation were interpolated using different approaches to respect the hard data (interpretation lines and drill-holes). The resulting 3D stratigraphic surfaces required strong manual editing to respect the interpretation, due to the presence of folds, thrusts and tectonic nappes in the study area. The surfaces were afterwards tied to the drill-holes, resulting in a 3D model with great accuracy and detail in the near mining area and covering a larger area than previously available 3D geological models. The model has three major stratigraphic layers: the Mertola Flysch Formation and the Volcano-Sedimentary Complex (VSC), overlying the Phyllite-Quartzite Formation basement, and also the known VMS deposits (underlying the top of the Lower VSC) geometries according to drill-hole data. In the central part of the study area, where more drill-holes are available, the top of the Lower VSC sequence surface was also built. This approach will contribute to a better exploration drill-hole planning and the generation of new targets for exploration.
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| 5. |
- Dias, Pedro, et al.
(författare)
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Geophysical investigation of the down-dip extension of the Lombador massive sulphide deposit, Neves-Corvo, Portugal
- 2021
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Ingår i: International journal of earth sciences. - : Springer Nature. - 1437-3254 .- 1437-3262. ; 110:3, s. 911-922
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Tidskriftsartikel (refereegranskat)abstract
- The 150 Mt Lombador massive sulphide deposit is one of the seven known deposits of the Neves-Corvo mine. The deposit dips approximately 30o-35o to the NE and is open down dip, with current exploitation reaching down at 1 km depth. To investigate the possible downwards continuation of the deposit, a 1D constrained inversion of time-domain electromagnetic (TEM) ground loop data was conducted, followed by 3D electromagnetic (EM) forward modeling and a constrained 3D gravimetric inversion over the same area. To perform the EM and gravity modeling/inversion, a 3D geologic model was built using a density database comprising of approximately 300 drill-holes, and an electrical conductivity database with measurements from resistivity surveys and 1D inversion of the TEM data. The EM modeling shows that the Neves Formation shales are a regional conductive layer extending down to approximately 1.6 km depth in the Lombador area. This layer, often topped by massive sulphides, has an average density of 2.83 g/cm(3), whereas stockwork and massive sulphide reach on average 3.1 g/cm(3) and 4.5 g/cm(3), respectively. The 3D constrained gravity inversion results do not support the hypothesis of the presence of massive sulphides located in the down-dip direction of the Lombador deposit in the immediate vicinity of the known deposit. The lack of spatial resolution of the gravity grid, the study area limited size and the lack of information from within the basement suggest further studies are required to confirm the presence and amount of stockwork mineralization down-dip the Lombador deposit inside the Neves-Formation or the Phyllite-Quartzite basement.
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| 6. |
- Donoso, George A., et al.
(författare)
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3D reflection seismic imaging of volcanogenic massive sulphides at Neves-Corvo, Portugal
- 2023
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Ingår i: Geophysical Prospecting. - : John Wiley & Sons. - 0016-8025 .- 1365-2478. ; 71:7, s. 1116-1131
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Tidskriftsartikel (refereegranskat)abstract
- Three-dimensional reflection seismic data from the Neves-Corvo area, southern Portugal, were reprocessed with the main objective of improving the seismic signature of the Lombador and Semblana volcanogenic massive sulphide deposits. The sensitivity for choosing adequate parameters for targeted imaging, even during the pre-processing stage, such as common-depth point binning size, was studied in detail before the main processing work began helping to optimize bin size parameters; preliminary stacking results from this analysis presented severe acquisition footprint, and seismic targets were not clearly identifiable. Processing results using pre-stack dip move-out and post-stack migration methods show strong moderate to steeply dipping reflections. Several of the observed reflections can be correlated with known lithological contacts, some of which are interpreted to originate from the Semblana and Lombador deposits. Despite the mixed signal-to-noise ratio, the seismic cube reveals both shallow and deep three-dimensional structures, allowing to account for the deposits’ lateral extension beyond the capabilities of two-dimensional seismic imaging alone. Given the data processing approach taken it was possible to distinguish strong diffraction patterns, interpreted as originating from faults and edges of the Lombador deposit, illustrating the usefulness of diffraction patterns for better interpretation of geological features in hard-rock environments.
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| 7. |
- Donoso, George A., et al.
(författare)
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Innovative seismic imaging of volcanogenic massive sulfide deposits, Neves-Corvo, Portugal – Part 2 : Surface array
- 2021
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Ingår i: Geophysics. - : Society of Exploration Geophysicists. - 0016-8033 .- 1942-2156. ; 86:3, s. B181-B191
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Tidskriftsartikel (refereegranskat)abstract
- Seismic methods are an affordable and effective way of studying the subsurface for mineral exploration. With the goal of testing new technologies for mineral exploration in highly challenging mining areas, in early 2019, an innovative seismic survey was conducted at the Neves-Corvo mine, south Portugal. We have focused on the data and results from the surface array data, whereas other work deals with the underground seismic data. The surface seismic survey consisted of two perpendicular 2D profiles positioned above the known world-class tier-1 Lombador deposit. Simultaneously, a survey inside the active underground mine took place, being unique because it included the testing of a prototype system that enabled accurate GPS-time (microsecond accuracy) synchronization inside the mine tunnels, approximately 650 m below the surface profiles. Due to the active mining operations, the surface data are noisy. To handle this, a carefully tailored processing algorithm was developed and applied to enhance reflections in the data, interpreted to originate from lithologic contacts and the Lombador deposit. The results and interpretations from 2D processing were validated taking advantage of the known deposit geometry using 3D exploding reflector modeling and pseudo-3D cross-dip analysis. These analyses suggest that there is an out-of-plane signature of the Lombador deposit on the surface data. Additionally, source points activated in the exploration tunnels and simultaneously recorded on the surface profiles allowed for the creation of a 2D velocity model that was used for migration and time-to depth conversion, providing a reliable 2D seismic section of the subsurface under the surface profiles. We determine that limited surface coverage 2D surveys and a velocity model derived from the tunnel-to-surface seismic recordings allow for imaging of key subsurface geologic structures and delineating mineral deposits of economic interest.
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| 8. |
- Donoso, George A., et al.
(författare)
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Potential of legacy 2D seismic data for deep targeting and structural imaging at the Neves-Corvo massive sulphide-bearing deposit, Portugal
- 2020
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Ingår i: Geophysical Prospecting. - : WILEY. - 0016-8025 .- 1365-2478. ; 68:1, s. 44-61
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Tidskriftsartikel (refereegranskat)abstract
- Seismic methods are becoming an established choice for deep mineral exploration after being extensively tested and employed for the past two decades. To investigate whether the early European mineral-exploration datasets had potential for seismic imaging that was overlooked, we recovered a low-fold legacy seismic dataset from the Neves-Corvo mine site in the Iberian Pyrite Belt in southern Portugal. This dataset comprises six 4-6 km long profiles acquired in 1996 for deep targeting. Using today's industry-scale processing algorithms, the world-class, ca. 150 Mt, Lombador massive sulphide and other smaller deposits were better imaged. Additionally, we also reveal a number of shallow but steeply dipping reflections that were absent in the original processing results. This study highlights that legacy seismic data are valuable and should be revisited regularly to take advantage of new processing algorithms and the experiences gained from processing such data in hard-rock environments elsewhere. Remembering that an initial processing job in hard rock should always aim to first obtain an overall image of the subsurface and make reflections visible, and then subsequent goals of the workflow could be set to, for example understanding relative amplitude ratios. The imaging of the known mineralization implies that this survey could likely have been among one of the pioneer studies in the world that demonstrated the capability of directly imaging massive sulphide deposits using the seismic method.
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| 9. |
- Householder, John Ethan, et al.
(författare)
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One sixth of Amazonian tree diversity is dependent on river floodplains
- 2024
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Ingår i: NATURE ECOLOGY & EVOLUTION. - 2397-334X.
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Tidskriftsartikel (refereegranskat)abstract
- Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.
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| 10. |
- Luize, Bruno Garcia, et al.
(författare)
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Geography and ecology shape the phylogenetic composition of Amazonian tree communities
- 2024
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Ingår i: JOURNAL OF BIOGEOGRAPHY. - 0305-0270 .- 1365-2699.
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Tidskriftsartikel (refereegranskat)abstract
- Aim: Amazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and v & aacute;rzea forest types, the phylogenetic composition varies by geographic region, but the igap & oacute; and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R-2 = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R-2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main Conclusion: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions.
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