| 1. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 2. |
- Almeida, Joana R., et al.
(författare)
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Structure-Antifouling Activity Relationship and Molecular Targets of Bio-Inspired(thio)xanthones
- 2020
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Ingår i: Biomolecules. - : MDPI. - 2218-273X. ; 10:8
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Tidskriftsartikel (refereegranskat)abstract
- The development of alternative ecological and effective antifouling technologies is still challenging. Synthesis of nature-inspired compounds has been exploited, given the potential to assure commercial supplies of potential ecofriendly antifouling agents. In this direction, the antifouling activity of a series of nineteen synthetic small molecules, with chemical similarities with natural products, were exploited in this work. Six (4,5,7,10,15and17) of the tested xanthones showed in vivo activity toward the settlement ofMytilus galloprovincialislarvae (EC50: 3.53-28.60 mu M) and low toxicity to this macrofouling species (LC50> 500 mu M and LC50/EC50: 17.42-141.64), and two of them (7and10) showed no general marine ecotoxicity (Artemia salinamortality) after 48 h of exposure. Regarding the mechanism of action in mussel larvae, the best performance compounds4and5might be acting by the inhibition of acetylcholinesterase activity (in vitro and in silico studies), while7and10showed specific targets (proteomic studies) directly related with the mussel adhesive structure (byssal threads), given by the alterations in the expression ofMytiluscollagen proteins (PreCols) and proximal thread proteins (TMPs). A quantitative structure-activity relationship (QSAR) model was built with predictive capacity to enable speeding the design of new potential active compounds.
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| 3. |
- 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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| 4. |
- 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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| 5. |
- Campos, Alexandre B., et al.
(författare)
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Adaptive Target Enhancer : Bridging the Gap between Synthetic and Measured SAR Images for Automatic Target Recognition
- 2023
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Ingår i: Proceedings of the IEEE Radar Conference. - : Institute of Electrical and Electronics Engineers (IEEE). - 9781665436694
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Konferensbidrag (refereegranskat)abstract
- Automatic target recognition (ATR) algorithms have been successfully used for vehicle classification in synthetic aperture radar (SAR) images over the past few decades. For this application, however, the scarcity of labeled data is often a limiting factor for supervised approaches. While the advent of computer-simulated images may result in additional data for ATR, there is still a substantial gap between synthetic and measured images. In this paper, we propose the so-called adaptive target enhancer (ATE), a tool designed to automatically delimit and weight the region of an image that contains or is affected by the presence of a target. Results for the publicly released Synthetic and Measured Paired and Labeled Experiment (SAMPLE) dataset show that, by defining regions of interest and suppressing the background, we can increase the classification accuracy from 68% to 84% while only using artificially generated images for training. © 2023 IEEE.
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| 6. |
- Campos, Alexandre Becker, 1997-, et al.
(författare)
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False Alarm Reduction in Wavelength-Resolution SAR Change Detection Schemes by Using a Convolutional Neural Network
- 2022
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Ingår i: IEEE Geoscience and Remote Sensing Letters. - : Institute of Electrical and Electronics Engineers Inc.. - 1545-598X .- 1558-0571. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- In this letter, we propose a method to reduce the number of false alarms in a wavelength-resolution synthetic aperture radar (SAR) change detection scheme by using a convolutional neural network (CNN). The detection is performed in two steps: change analysis and object classification. A simple technique for wavelength-resolution SAR change detection is implemented to extract potential targets from the image of interest. A CNN is then used for classifying the change map detections as either a target or nontarget, further reducing the false alarm rate (FAR). The scheme is tested for the CARABAS-II data set, where only three false alarms over a testing area of 96 km² are reported while still sustaining a probability of detection above 96%. We also show that the network can still reduce the FAR even when the flight heading of the SAR system measurement campaign differs by up to 100° between the images used for training and test. CCBY
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| 7. |
- Campos, Alexandre Becker, 1997-, et al.
(författare)
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UNSUPERVISED AUTOMATIC TARGET DETECTION FOR MULTITEMPORAL SAR IMAGES BASED ON ADAPTIVE K-MEANS ALGORITHM
- 2020
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Konferensbidrag (refereegranskat)abstract
- In this paper, we present an unsupervised automatic target detection algorithm for multitemporal SAR images. The proposed two-fold method is expected to reduce processing time for large scene sizes with sparse targets while still improving detection performance. Firstly, pixel blocks are extracted from an initial change map to reduce the algorithm's search space and favor target detection. Secondly, an adaptive k-means algorithm selects the number of clusters that better separates targets from false alarms, which are discarded. Preliminary results show the advantages of the proposed method in processing time and detection performance over a recently proposed supervised method for the CARABAS-II dataset.
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| 8. |
- Campos, Alexandre, et al.
(författare)
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Proteomic research in bivalves Towards the identification of molecular markers of aquatic pollution
- 2012
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Ingår i: Journal of Proteomics. - : Elsevier. - 1874-3919 .- 1876-7737. ; 75:14, s. 4346-4359
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Forskningsöversikt (refereegranskat)abstract
- Biomonitoring of aquatic environment and assessment of ecosystem health play essential roles in the development of effective strategies for the protection of the environment, human health and sustainable development. Biomarkers of pollution exposure have been extensively utilized in the last few decades to monitor the health of organisms and hence assess environmental status. However, the use of single biomarkers against biotic or abiotic stressors may be limited by the lack of sensitivity and specificity. Therefore, more recently, the search for novel biomarkers has been focused on the application of OMICS methodologies. Environmental proteomics focuses on the analysis of an organisms proteome and the detection of changes in the level of individual proteins/peptides in response to environmental stressors. Proteomics can provide a more robust approach for the assessment of environmental stress and therefore exposure to pollutants. This review aims to summarize the proteomic research in bivalves, a group of sessile and filter feeding organisms that play an important function as "sentinels" of the aquatic environment. A description of the main proteomic methodologies is provided. The current knowledge in bivalves toxicology, achieved with proteomics, is reported describing the main biochemical markers identified. A brief discussion regarding future challenges in this area of research emphasizing the development of more descriptive gene/protein databases that could support the OMICs approaches is presented. less thanbrgreater than less thanbrgreater thanThis article is part of a Special Issue entitled: Farm animal proteomics.
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| 9. |
- Campos, Alexandre, et al.
(författare)
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Shotgun analysis of the marine mussel Mytilus edulis hemolymph proteome and mapping the innate immunity elements
- 2015
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 15:23-24, s. 4021-4029
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Tidskriftsartikel (refereegranskat)abstract
- The marine mussel innate immunity provides protection to pathogen invasion and inflammation. In this regard, the mussel hemolymph takes a main role in the animal innate response. Despite the importance of this body fluid in determining the physiological condition of the animal, little is known about the molecular mechanisms underlying the cellular and humoral responses. In this work, we have applied a MS (nano-LC-MS/MS) strategy integrating genomic and transcriptomic data with the aim to: (i) identify the main protein functional groups that characterize hemolymph and (ii) to map the elements of innate immunity in the marine mussel Mytilus edulis hemolymph proteome. After sample analysis and first protein identification based on MS/MS data comparison, proteins with unknown functions were annotated with blast using public database (nrNCBI) information. Overall 595 hemolymph proteins were identified with high confidence and annotated. These proteins encompass primary cellular metabolic processes: energy production and metabolism of biomolecules, as well as processes related to oxidative stress defence, xenobiotic detoxification, drug metabolism, and immune response. A group of proteins was identified with putative immune effector, receptor, and signaling functions in M. edulis. Data are available via ProteomeXchange with identifier PXD001951 (http://proteomecentral.proteomexchange.org/dataset/PXD001951).
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| 10. |
- Campos, Alexandre, et al.
(författare)
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Shotgun proteomics to unravel marine mussel (Mytilus edulis) response to long-term exposure to low salinity and propranolol in a Baltic Sea microcosm
- 2016
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Ingår i: Journal of Proteomics. - : Elsevier. - 1874-3919 .- 1876-7737. ; 137, s. 97-106
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Tidskriftsartikel (refereegranskat)abstract
- Pharmaceuticals, among them the β-adrenoreceptor blocker propranolol, are an important group of environmental contaminants reported in European waters. Laboratory exposure to pharmaceuticals on marine species has been performed without considering the input of the ecosystem flow. To unravel the ecosystem response to long-term exposure to propranolol we have performed long-term exposure to propranolol and low salinity in microcosms. We applied shotgun proteomic analysis to gills of Mytilus edulis from those Baltic Sea microcosms and identified 2071 proteins with a proteogenomic strategy. The proteome profiling patterns from the 587 highly reproductive proteins among groups define salinity as a key factor in the mussel´s response to propranolol. Exposure at low salinity drives molecular mechanisms of adaptation based on a decrease in the abundance of several cytoskeletal proteins, signalling and intracellular membrane trafficking pathway combined with a response towards the maintenance of transcription and translation. The exposure to propranolol combined with low salinity modulates the expression of structural proteins including cilia functions and decrease the expression membrane protein transporters. This study reinforces the environment concerns of the impact of low salinity in combination with anthropogenic pollutants and anticipate critical physiological conditions for the survival of the blue mussel in the northern areas.
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