Percorrer por autor "Carlier, Jorge"
A mostrar 1 - 10 de 41
Resultados por página
Opções de ordenação
- A genetic map of pineapple (Ananas comosus (L.) Merr.) including SCAR, CAPS, SSR and EST-SSR markersPublication . Carlier, Jorge; Sousa, N. H.; Santo, Tatiana; d'Eeckenbrugge, G. C.; Leitão, JoséDespite the paramount importance of pineapple (Ananas comosus L.) in world production and trade of tropical fruits, the genomics of this crop is still lagging behind that of other tropical fruit crops such as banana or papaya. A genetic map of pineapple was constructed using an F2 segregating population obtained from a single selfed F1 plant of a cross A. comosus var. comosus (cv. Rondon, clone BR 50) x A. comosus var. bracteatus (Branco do mato, clone BR 20). Multiple randomly amplified markers (RAPD, ISSR and AFLP) were brought together with SSR and EST-SSR markers identified among sequences uploaded to public databases and with sequence-specific markers (SCAR, SSR and CAPS) derived from random amplified markers. Sixty-three randomly amplified markers (RAPD, ISSR and AFLP) were selected and cloned, resulting in 71 sequences which were used to generate sequence-specific SCAR and CAPS markers. The present map includes 492 DNA markers: 57 RAPD, 22 ISSR, 348 AFLP, 20 SSR, 12 EST-SSR, 25 SCARs, 8 CAPS, and the morphological trait locus "piping", gathered into 33 linkage groups that integrate markers inherited from both botanical varieties, four linkage groups with markers only from var. comosus and three linkage groups with markers exclusively from var. bracteatus. The relatively higher mapping efficiency of sequence-specific markers derived from randomly amplified markers (50.7%) versus SSR (31.4%) and EST-SSR (28.9%) markers is discussed. Spanning over 80% of the 2,470 cM estimated average length of the genome, the present map constitutes a useful research tool for molecular breeding and genomics projects in pineapple and other Bromeliaceae species.
- Acid mine drainage bioremediation using bacteria enriched from the confluence zone between its flow and treated sewagePublication . Nobahar, Amir; Fitas, Eduardo Trindadde; Costa, Maria Clara; Carlier, JorgeSediments from the confuence zone between an acid mine drainage stream and a water stream receiving the efuent from a municipal wastewater treatment plant were inoculated in a Postgate B medium base having methanol, glycerol, or etha[1]nol as carbon source/electron donor, over a pH range between 2.00 and 6.00, aiming to obtain native cultures enriched in acidophilic/acid-tolerant sulfate-reducing bacteria. The most efective sulfate reduction observed in acidic conditions was in the enrichment cultures with methanol. Thus, the microbial consortium enriched in these conditions was further used in acid mine drainage bioremediation experiments at an initial pH of 4.50 and using diferent doses of nutrients medium base and methanol as carbon source/electron donor. The most promising results, with more than 99% removal of metals, were obtained in the mixture of 20% Postgate B medium base plus 80% acid mine drainage (v/v), which corresponds to 0.115% basal salts and 0.02% yeast extract (w/v). Metataxonomic analysis based on 16S rRNA gene sequences showed the presence of Desulfosporosinus spp. in all enrichment cultures, with the highest relative abundance in cultures at pH 4.00 with methanol. Furthermore, metataxonomic analysis in the acid mine drainage remediation tests revealed the presence of Desulfosporosi[1]nus spp. in all tested conditions. In addition, the study also revealed Clostridium members in all tests. Plus, their relative abundances were related to the dose of nutrient medium base and in balance with the abundances of Desulfosporosinus spp.
- An autochthonous aerobic bacterial community and its cultivable isolates capable of degrading fluoxetinePublication . Palma, Tânia Cristina da Luz; Shylova, Anastasiia; Carlier, Jorge; Costa, Maria ClaraBACKGROUND Fluoxetine is an antidepressant and recalcitrant fluorine pharmaceutical that is poorly biodegraded, so it enters the hydric resources and causes hazardous effects to aquatic environments. According to these fluoxetine features, the main aim of the present research was to find resistant bacteria in environmental samples with a high degradation efficiency. RESULTS The results obtained from raw municipal wastewater spiked with fluoxetine and inoculated with aerobic sludge from a Portuguese wastewater treatment plant under highly aerobic conditions showed that more than half and approximate to 89% of the drug was degraded after 48 and 144 h, respectively. During the assay, the initial population (mainly composed of Arcobacter, Bacteroides, and Macellibacteroides) shifted with an increase of members of the Acinetobacter, Rheinheimera, Shewanella, Pseudomonas, Methylobacillus, Piscinobacter genera and Aeromonadales order and the Pseudomonadaceae family, all of which were likely responsible for fluoxetine biodegradation. From the same sludge, six bacterial isolates were selected and identified as follows: Pseudomonas putida, Enterobacter ludwigii, Pseudomonas nitritireducens, Alcaligenes faecalis, Pseudomonas aeruginosa, and Pseudomonas nitroreducens; all of them grew with fluoxetine as sole carbon source. Pseudomonas nitroreducens showed the highest removal of 55 +/- 1% at 20 mg L-1 fluoxetine after 24 h. CONCLUSION An autochthonous aerobic bacterial community and its cultivable isolates showed the capacity to biodegrade fluoxetine. Biodegradation, rather than adsorption, appears to play the main role in the fluoxetine removal in aerobic conditions using bacteria simply obtained from an environmental sample. As far as is known, those bacteria are reported for the first time as fluoxetine biodegraders; thus, these bacteria are a promising option to integrate into new bioremediation processes aiming at the removal of fluoxetine.
- An integrated genetic map of pineapple (Ananas comosus (L.) Merr.)Publication . de Sousa, N.; Carlier, Jorge; Santo, Tatiana; Leitão, J. M.The inclusion of multiple new markers, in particular 41 sequence specific markers, resulted in drastically improved version of a previously published F1-based genetic map of pineapple (Ananas comosus). The integration of the new version of this map with a more recently published F2-based map resulted in a map that assembles 741 loci: 739 DNA markers (25 SSR, 12 EST_SSR, 22 SCAR, 8 CAPS, 20 ISSR, 109 RAPD, and 543 AFLP), one isozyme (PGM) locus and the morphological trait 'piping', in 28 integrated linkage groups, spanning 2113 centimorgans (cM) and covering approximately 86% of the genome. Four small F1-based linkage groups and 5 small F2-based linkage groups assembling more than two markers, totalling 292 cM, remained not integrated. The present integrated genetic map is expected to be a helpful tool in genomic studies on pineapple and other Bromeliaceae genera and species. (c) 2013 Elsevier B.V. All rights reserved.
- Antioxidant activity and enzyme inhibitory potential of Euphorbia resinifera and E. officinarum honeys from Morocco and plant aqueous extractsPublication . Boutoub, Oumaima; EL-Geundouz, Soukaina; Estevinho, Leticia M.; Paula, Vanessa B.; Aazza, Smail; El Ghadraoui, Lahsen; Rodrigues, Brígida; Raposo, Sara; Carlier, Jorge; Costa, Maria Clara; Miguel, MariaNatural products may be applied in a wide range of domains, from agriculture to food and pharmaceutical industries. In this study, the antioxidant properties and the capacity to inhibit some enzymatic activities ofEuphorbia resiniferaandEuphorbia officinarumaqueous extracts and honeys were assessed. The physicochemical characteristics were also evaluated. Higher amounts of iron, copper and aluminium were detected inE. officinarumhoney, which may indicate environmental pollution around the beehives or inadequate storage of honey samples. This honey sample showed higher amounts of total phenols and better capacity for scavenging superoxide anion free radicals and DPPH free radicals as compared withE. resiniferahoney, but poorer capacity for inhibiting lipoxygenase, acetylcholinesterase, tyrosinase and xanthine oxidase. The ratio plant mass:solvent volume (1:100) and extraction time (1 - 2 h) were associated with higher total phenols and better antioxidant activities and lipoxygenase, acetylcholinesterase and tyrosinase inhibitory activities, regardless of the plant species. The aqueous extracts had systematically higher in vitro activities than the respective honey samples.
- Application of urea-agarose gel electrophoresis to select non-redundant 16S rRNAs for taxonomic studies: palladium(II) removal bacteriaPublication . Assunção, Ana; Costa, Maria Clara; Carlier, JorgeThe 16S ribosomal RNA (rRNA) gene has been the most commonly used sequence to characterize bacterial communities. The classical approach to obtain gene sequences to study bacterial diversity implies cloning amplicons, selecting clones, and Sanger sequencing cloned fragments. A more recent approach is direct sequencing of millions of genes using massive parallel technologies, allowing a large-scale biodiversity analysis of many samples simultaneously. However, currently, this technique is still expensive when applied to few samples; therefore, the classical approach is still used. Recently, we found a community able to remove 50 mg/L Pd(II). In this work, aiming to identify the bacteria potentially involved in Pd(II) removal, the separation of urea/heat-denatured DNA fragments by urea-agarose gel electrophoresis was applied for the first time to select 16S rRNA-cloned amplicons for taxonomic studies. The major raise in the percentage of bacteria belonging to genus Clostridium sensu stricto from undetected to 21 and 41 %, respectively, for cultures without, with 5 and 50 mg/L Pd(II) accompanying Pd(II) removal point to this taxa as a potential key agent for the bio-recovery of this metal. Despite sulfate-reducing bacteria were not detected, the hypothesis of Pd(II) removal by activity of these bacteria cannot be ruled out because a slight decrease of sulfate concentration of the medium was verified and the formation of PbS precipitates seems to occur. This work also contributes with knowledge about suitable partial 16S rRNA gene regions for taxonomic studies and shows that unidirectional sequencing is enough when Sanger sequencing cloned 16S rRNA genes for taxonomic studies to genus level.
- Bacterial bioaugmentation for paracetamol removal from water and sewage sludge. Genomic approaches to elucidate biodegradation pathway.Publication . Lara-Moreno, A.; Vargas-Ordóñez, A.; Villaverde, J.; Madrid, F.; Carlier, Jorge; Santos, J. L.; Alonso, E.; Morillo, E.Wastewater treatment plants (WWTPs) are recognized as significant contributors of paracetamol (APAP) into the environment due to their limited ability to degrade it. This study used a bioaugmentation strategy with Pseudomonas extremaustralis CSW01 and Stutzerimonas stutzeri CSW02 to achieve APAP biodegradation in solution in wide ranges of temperature (10-40 °C) and pH (5-9), reaching DT values < 1.5 h to degrade 500 mg L APAP. Bacterial strains also mineralized APAP in solution (<30 %), but when forming consortia with Mycolicibacterium aubagnense HPB1.1, mineralization significantly increased (up to 74 % and 58 % for CSW01 +HPB1.1 and CSW02 +HPB1.1, respectively), decreasing DT values to only 1 and 9 days. Despite the complete degradation of APAP and its high mineralization, residual toxicity throughout the process was observed. Three APAP metabolites were identified (4-aminophenol, hydroquinone and trans-2-hexenoic acid) that quickly disappeared, but residual toxicity remained, indicating the presence of other non-detected intermediates. CSW01 and CSW02 degraded also 100 % APAP (50 mg kg) adsorbed on sewage sludge, with DT values of only 0.7 and 0.3 days, respectively, but < 15 % APAP was mineralized. A genome-based analysis of CSW01 and CSW02 revealed that amidases, deaminases, hydroxylases, and dioxygenases enzymes were involved in APAP biodegradation, and a possible metabolic pathway was proposed.
- Batch studies on the biodegradation of paracetamol and 1,4-hydroquinone by novel bacterial strains isolated from extreme environmental samples and the identification of candidate catabolic genesPublication . Lara-Moreno, Alba; Fatma El-Sayed; Cox, Cymon; Costa, Maria Clara; Carlier, JorgeThe emerging pollutant paracetamol (APAP) is one of the most prescribed drugs worldwide. In addition, APAP and its main metabolites, namely, 4-aminophenol (4-AP), hydroquinone (H2Q), benzoquinone (BQ), and 2,5-dihydroxy-1,4-benzoquinone (2,5-OH-BQ), among others, are frequently detected in wastewater treatment plants (WWTPs) influents, effluents, and the environment. Thus, continuous release into the environment, especially aquatic environments, is a source of general concern. Six APAP-degrading bacterial strains were isolated from two mine samples from the Iberian Pyrite Belt (Lousal and Poderosa mines). Mycolicibacterium aubagnense HPB1.1, which was isolated using enrichment cultures from the Poderosa mine sample in the presence of H2Q as the sole carbon source, also showed APAP biodegrading capabilities. Pure cultures of this strain degraded 34.3 mg L-1 of APAP in 5 days and 9.4 mg L-1 of H2Q in 4 days. Interestingly, BQ and 2,5-OH-BQ were detected as metabolites resulting from H2Q abiotic degradation, but these compounds were removed in the strain's cultures. Furthermore, M. aubagnense HPB1.1 whole-genome was sequenced, and its encoded proteins were aligned with enzymes of APAP-degrading bacteria recovered from databases and literature aiming to identify candidate catabolic genes. Putative amidases, deaminases, hydroxylases, and dioxygenases, responsible for the degradation of APAP by the HPB1.1 strain, were identified by similarity, corroborating its ability to transform APAP and its intermediate metabolite H2Q into less toxic metabolic compounds due to their capacity to break the aromatic ring of these molecules.
- Biometal demonstration plant for the biological rehabilitation of metal bearing-wastewaters (Biometal Demo)Publication . Jimeno, Manuel Román; Ballester, Antonio; García Roig, Manuel; Guibal, Eric; Costa, Maria Clara; Castro, Laura; Carlier, Jorge; Perez Galande, Patricia; Alvarez, Angela; Bertagnolli, Caroline; Guibal, EricHeavy metal pollution is one of the most important environmental problems today even threatening human life. A large number of industries produce and discharge wastes containing different heavy metals into the environment and do not comply with current EU directives. European project BIOMETAL DEMO (www.biometaldemo.eu) aims to demonstrate the feasibility of the application of novel biotechnologies for the treatment of metal polluted wastewaters through the development of three pilot plants to be implemented in metal polluting representative industries.The biotechnologies that have been evaluated in project BIOMETAL DEMO are: metal bioprecipitation by sulphate-reducing bacteria and immobilized phytase biocatalysis, and metal biosorption on agricultural industry by-products and biopolymers such as alginate & chitosan based materials.After the evaluation of these techniques, an optimized bioprocess or a synergy of two integrated bioprocesses will be selected to design and build two demonstration pilot plants for scaling-up the metal removal biotreatment.Finally, an economic, social and technical analysis of the benefits of such biotreatment of metal polluted industrial wastewater will be carried out for the corresponding and related industrial sectors.
- Chemical characterization and biological properties assessment of Euphorbia resinifera and Euphorbia officinarum Moroccan PropolisPublication . Boutoub, Oumaima; El-Guendouz, Soukaina; Matos, Isabel; El Ghadraoui, Lahsen; Costa, Maria Clara; Carlier, Jorge; Faleiro, Maria Leonor; Figueiredo, Ana Cristina; Estevinho, Letícia M.; Miguel, MariaAlthough the plants of the genus Euphorbia are largely exploited by therapists in Morocco, the composition and antibacterial activities of propolis from these plants are still unknown. To address this gap, this study aimed to characterize the pollen type, the volatile compounds, and the phenolic and mineral profiles of three Euphorbia propolis samples collected in Morocco and evaluate their antimicrobial activities. The minimum inhibitory concentration of the propolis samples was determined by the microdilution method, and the anti-adherence activity was evaluated by the crystal violet assay. The examination of anti-quorum-sensing proprieties was performed using the biosensor Chromobacterium violaceum CV026. Pollen analysis revealed that Euphorbia resinifera pollen dominated in the P1 sample (58%), while E. officinarum pollen dominated in the P2 and P3 samples (44%). The volatile compounds were primarily composed of monoterpene hydrocarbons, constituting 35% in P1 and 31% in P2, with α-pinene being the major component in both cases, at 16% in P1 and 15% in P2. Calcium (Ca) was the predominant mineral element in both E. resinifera (P1) and E. officinarum (P2 and P3) propolis samples. Higher levels of phenols, flavonoids and dihydroflavonoids were detected in the E. officinarum P2 sample. The minimum inhibitory concentration (MIC) value ranged from 50 to 450 µL/mL against Gram-positive and Gram-negative bacteria. Euphorbia propolis displayed the ability to inhibit quorum sensing in the biosensor C. violaceum CV026 and disrupted bacterial biofilm formation, including that of resistant bacterial pathogens. In summary, the current study evidences the potential use of E. officinarum propolis (P2 and P3) to combat important features of resistant pathogenic bacteria, such as quorum sensing and biofilm formation.