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A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

Publication . Pereira-Leal, José B.; Abreu, Isabel A.; Alabaça, Cláudia S.; Almeida, Maria H.; Almeida, Paulo; Almeida, Tânia; Amorim, Maria I.; Araújo, Susana; Azevedo, Herlânder; Badia, Aleix; Batista, Dora; Bohn, Andreas; Capote, Tiago; Carrasquinho, Isabel; Chaves, Inês; Coelho, A. C.; Costa, Maria M. R.; Costa, Rita; Cravador, A.; Egas, Conceição; Faro, Carlos; Fortes, Ana M.; Fortunato, Ana S.; Gaspar, Maria J.; Gonçalves, Sónia; Graça, José; Horta, Marília; Inácio, Vera; Leitão, J. M.; Lino-Neto, Teresa; Marum, Liliana; Matos, José; Mendonça, Diogo; Miguel, Andreia; Miguel, Célia M.; Morais-Cecílio, Leonor; Neves, Isabel; Nóbrega, Filomena; Oliveira, Maria M.; Oliveira, Rute; Pais, Maria S.; Paiva, Jorge A.; Paulo, O. S.; Pinheiro, Miguel; Raimundo, João A. P.; Ramalho, J. C.; Ribeiro, Ana I.; Ribeiro, Teresa; Rocheta, Margarida; Rodrigues, Ana I.; Rodrigues, José C.; Saibo, Nelson J. M.; Santo, Tatiana; Santos, Ana M.; Sá-Pereira, Paula; Sebastiana, Mónica; Simões, Fernanda; Sobral, Rómulo S.; Tavares, Rui; Teixeira, Rita; Varela, Carolina; Veloso, Maria M.; Ricardo, Cândido P. P.

Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.

2014-05-15Journal article

Open Access

Green synthesis of covellite nanocrystals using biologically generated sulfide: potential for bioremediation systems

Publication . Costa, J. P. da; Girão, Ana Violeta; Lourenço, J. P.; Monteiro, O. C.; Trindade, Tito; Costa, Maria Clara

This work describes the synthesis of CuS powders in high yield and via an environmentally friendly and straightforward process, under ambient conditions (temperature and pressure), by adding to aqueous copper (II) a nutrient solution containing biologically generated sulfide from sulfate-reducing bacteria (SRB). The powders obtained were composed of CuS (covellite) nanoparticles (NPs) exhibiting a spheroid morphology (<5 nm). The relevance of this method to obtain CuS supported solid substrates has been demonstrated by performing the synthesis in the presence of TiO2 and SiO2 submicron particles. We further extended the work carried out, which substantiates the potential of using biogenic sulfide for the production of covellite nanocrystals and composites, using the effluent of a bioremediation column. Hence, such process results in the synthesis of added value products obtained from metal rich effluents, such as metallurgical and industrial ones, or Acid Mine Drainage (AMD), when associated with bioremediation processes.

2013-10Journal article

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Tris(pyrazolyl)methane molybdenum tricarbonyl complexes as catalyst precursors for olefin epoxidation

Publication . Gomes, Ana C.; Neves, Patrícia; Figueiredo, Sónia; Fernandes, José A.; Valente, Anabela A.; Almeida Paz, Filipe A.; Pillinger, Martyn; Lopes, Andre D.; Gonçalves, Isabel S.

The molybdenum tricarbonyl complexes [Mo(CO)3(HC(3,5-Me2pz)3)] (1) and [Mo(CO)3(HC(pz)3)] (2)(HC(3,5-Me2pz)3 = tris(3,5-dimethyl-1-pyrazolyl)methane, HC(pz)3 = tris(1-pyrazolyl)methane) were obtained in good yields by the microwave-assisted reaction of Mo(CO)6 with the respective organic ligand. Complete oxidative decarbonylation of 1 and 2 was achieved by reaction with excess tert-butylhydroperoxide (TBHP) in 1,2-dichloroethane at 55 ◦C. For complex 1, the (2-oxo)bis[dioxomolybdenum(VI)] hexamolybdate of composition [{MoO2(HC(3,5-Me2pz)3)}2(2- O)][Mo6O19] (3) was obtained in good yield, and its structure was determined by single crystal X-ray diffraction. The compound (4) obtained by oxidative decarbonylation of 2 was not unambiguously identified, but may be chemically analogous to 3. Compounds 1–4 were examined for the first time as homogeneous (pre)catalysts for the epoxidation of olefins with TBHP, using different types of cosolvents at 55 ◦C. During the catalytic reactions 1 and 2 transform in situ into 3 and 4, respectively, and the latter two are fairly stable catalysts. Catalytic tests and characterization studies of the recovered catalysts were carried out in an attempt to understand the kinetic differences observed between the compounds prepared in situ during the catalytic reaction and those prepared prior to the catalytic reaction, from the same precursor complex.

2013-04Journal article

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Bis(pyrazolyl)methanetetracarbonyl-molybdenum(0) as precursor to a molybdenum(VI) catalyst for olefin epoxidation

Publication . Figueiredo, Sónia; Gomes, Ana C.; Fernandes, José A.; Paz, Filipe A. Almeida; Lopes, Andre D.; Lourenço, J. P.; Pillinger, Martyn; Gonçalves, Isabel S.

Bis(pyrazolyl)methanetetracarbonyl-molybdenum(0), cis-[Mo(CO)4(BPM)] (1), was prepared from Mo(CO)6 and the ligand bis(pyrazolyl)methane (BPM), and examined as a catalyst precursor for the epoxidation of olefins using tert-butylhydroperoxide (TBHP) as oxidant. Catalytic activities followed the sequence 1-octene < trans-2-octene < a-pinene < (R)-(þ)-limonene < cis-cyclooctene, and, with the exception of a-pinene and limonene, the corresponding epoxide was always the only reaction product. Turnover frequencies for the epoxidation of cyclooctene were 580 mol molMo 1 h 1 at 55 C and 1175 mol molMo 1 h 1 at 75 C, which compare favourably with those found for other molybdenum carbonyl complexes used as catalyst precursors for the same reaction under similar conditions. Catalytic activities were lower in the presence of organic co-solvents, decreasing in the sequence 1,2-dichloroethane > nitromethane > ethanol > hexane > acetonitrile. It is proposed that the oxodiperoxo complex [MoO(O2)2(BPM)] (2) may be the active catalyst formed in situ by oxidative decarbonylation of 1, since crystals of 2 suitable for structure determination by X-ray diffraction were obtained from the reaction solution recovered after a catalytic run at 55 C with cis-cyclooctene as substrate. In support of this hypothesis, the catalytic performance of 2 for the epoxidation of cyclooctene at 55 C is very similar to that for 1.

2013Journal article

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