Mutations in the small subunit of the Drosophila U2AF splicing factor cause lethality and developmental defects.

The essential eukaryotic pre-mRNA splicing factor U2AF (U2 small nuclear ribonucleoprotein auxiliary factor) is required to specify the 3' splice at an early step in spliceosome assembly. U2AF binds site-specifically to the intron polypyrimidine tract and recruits U2 small nuclear ribonucleoprotein to the branch site. Human U2AF (hU2AF) is a heterodimer composed of a large (hU2AF65) and small (hU2AF35) subunit. Although these proteins associate in a tight complex, the biochemical requirement for U2AF activity can be satisfied solely by the large subunit. The requirement for the small subunit in splicing has remained enigmatic. No biochemical activity has been found for hU2AF35 and it has been implicated in splicing only indirectly by its interaction with known splicing factors. In the absence of a biochemical assay, we have taken a genetic approach to investigate the function of the small subunit in the fruit fly Drosophila melanogaster. A cDNA clone encoding the small subunit of Drosophila U2AF (dU2AF38) has been isolated and sequenced. The dU2AF38 protein is highly homologous to hU2AF35 containing a conserved central arginine- and serine-rich (RS) domain. A recessive P-element insertion mutation affecting dU2AF38 causes a reduction in viability and fertility and morphological bristle defects. Consistent with a general role in splicing, a null allele of dU2AF38 is fully penetrant recessive lethal, like null alleles of the Drosophila U2AF large subunit.

The embryonic transcription factor stage specific activator protein contains a potent bipartite activation domain that interacts with several RNA polymerase II basal transcription factors.

Stage specific activator protein (SSAP) is a member of a newly discovered class of transcription factors that contain motifs more commonly found in RNA-binding proteins. Previously, we have shown that SSAP specifically binds to its recognition sequence in both the double strand and the single strand form and that this DNA-binding activity is localized to the N-terminal RNA recognition motif domain. Three copies of this recognition sequence constitute an enhancer element that is directly responsible for directing the transcriptional activation of the sea urchin late histone H1 gene at the midblastula stage of embryogenesis. Here we show that the remainder of the SSAP polypeptide constitutes an extremely potent bipartite transcription activation domain that can function in a variety of mammalian cell lines. This activity is as much as 3 to 5 times stronger than VP16 at activating transcription and requires a large stretch of amino acids that contain glutamine-glycine rich and serine-threonine-basic amino acid rich regions. We present evidence that SSAP's activation domain shares targets that are also necessary for activation by E1a and VP16. Finally, SSAP's activation domain is found to participate in specific interactions in vitro with the basal transcription factors TATA-binding protein, TFIIB, TFIIF74, and dTAF(II) 110.

Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases.

The regions surrounding the catalytic amino acids previously identified in a few "retaining" O-glycosyl hydrolases (EC 3.2.1) have been analyzed by hydrophobic cluster analysis and have been used to define sequence motifs. These motifs have been found in more than 150 glycosyl hydrolase sequences representing at least eight established protein families that act on a large variety of substrates. This allows the localization and the precise role of the catalytic residues (nucleophile and acid catalyst) to be predicted for each of these enzymes, including several lysosomal glycosidases. An identical arrangement of the catalytic nucleophile was also found for S-glycosyl hydrolases (myrosinases; EC 3.2.3.1) for which the acid catalyst is lacking. A (beta/alpha)8 barrel structure has been reported for two of the eight families of proteins that have been grouped. It is suggested that the six other families also share this fold at their catalytic domain. These enzymes illustrate how evolutionary events led to a wide diversification of substrate specificity with a similar disposition of identical catalytic residues onto the same ancestral (beta/alpha)8 barrel structure.

Structure and stability of a second molten globule intermediate in the apomyoglobin folding pathway.

Apomyoglobin folding proceeds through a molten globule intermediate (low-salt form; I1) that has been characterized by equilibrium (pH 4) and kinetic (pH 6) folding experiments. Of the eight alpha-helices in myoglobin, three (A, G, and H) are structured in I1, while the rest appear to be unfolded. Here we report on the structure and stability of a second intermediate, the trichloroacetate form of the molten globule intermediate (I2), which is induced either from the acid-unfolded protein or from I1 by > or = 5 mM sodium trichloroacetate. Circular dichroism measurements monitoring urea- and acid-induced unfolding indicate that I2 is more highly structured and more stable than I1. Although I2 exhibits properties closer to those of the native protein, one-dimensional NMR spectra show that it maintains the lack of fixed side-chain structure that is the hallmark of a molten globule. Amide proton exchange and 1H-15N two-dimensional NMR experiments are used to identify the source of the extra helicity observed in I2. The results reveal that the existing A, G, and H helices present in I1 have become more stable in I2 and that a fourth helix--the B helix--has been incorporated into the molten globule. Available evidence is consistent with I2 being an on-pathway intermediate. The data support the view that apomyoglobin folds in a sequential fashion through a single pathway populated by intermediates of increasing structure and stability.

Hairpins are formed by the single DNA strands of the fragile X triplet repeats: structure and biological implications.

Inordinate expansion and hypermethylation of the fragile X DNA triplet repeat, (GGC)n.(GCC)n, are correlated with the ability of the individual G- and C-rich single strands to form hairpin structures. Two-dimensional NMR and gel electrophoresis studies show that both the G- and C-rich single strands form hairpins under physiological conditions. This propensity of hairpin formation is more pronounced for the C-rich strand than for the G-rich strand. This observation suggests that the C-rich strand is more likely to form hairpin or "slippage" structure and show asymmetric strand expansion during replication. NMR data also show that the hairpins formed by the C-rich strands fold in such a way that the cytosine at the CpG step of the stem is C.C paired. The presence of a C.C mismatch at the CpG site generates local flexibility, thereby providing analogs of the transition to the methyltransferase. In other words, the hairpins of the C-rich strand act as better substrates for the human methyltransferase than the Watson-Crick duplex or the G-rich strand. Therefore, hairpin formation could account for the specific methylation of the CpG island in the fragile X repeat that occurs during inactivation of the FMR1 gene during the onset of the disease.

Estratégias para conservação de carne armazenada sob refrigeração: embalagem em atmosfera modificada e processamento em alta pressão

A busca por produtos mais saudáveis e minimamente processados tem levado indústrias e pesquisadores a estudarem novas formas de preservação de alimentos. Os objetivos deste trabalho foram: 1) avaliar o efeito da embalagem com atmosfera modificada (ATM) na preservação de lombo ovino armazenado sob refrigeração e 2) Avaliar o efeito do processamento em alta pressão na conservação de carne bovina marinada e com teor de sódio reduzido. Em ambas as pesquisas, músculos Longissimus lumborum foram submetidos à contagem microbiana, avaliação de cor, pH, oxidação lipídica (TBARS), perdas por cocção (PPC) e força de cisalhamento. Para o estudo do efeito da embalagem em atmosfera modificada, as amostras foram acondicionadas em cinco sistemas de ATM, 15% O2 + 85% CO2; 30% de O2 + 70% de CO2; 45% de O2 + 55% de CO2; 60% de O2 + 40% de CO2 e Vácuo (controle) e armazenadas a 1°C durante 21 dias. As análises de cor, pH, TBARS, PPC e força de cisalhamento foram realizadas a cada sete dias e as microbiológicas duas vezes por semana. Diferentes concentrações de oxigênio dentro da embalagem trouxeram diferença significativa na intensidade de cor vermelha das carnes armazenadas em ATM. Até o sétimo dia de estocagem tratamentos com maior quantidade de O2 apresentaram melhor coloração, após esse período embalagens a vácuo conseguiram preservar melhor a mioglobina. Diferentes concentrações gasosas não trouxeram causaram diferença (p> 0,05) no pH da carne entre tratamentos. Nenhuma diferença significativa entre tratamentos foi encontrada para amostras embaladas em ATM nos parâmetros perda de peso por cocção e força de cisalhamento. A embalagem em atmosfera modificada foi capaz de retardar o crescimento da microbiota presente na carne. Isso levou á preservação da amostra por até 18 dias sob refrigeração, enquanto amostras a vácuo tiveram uma vida útil de 11 dias. Para o estudo do efeito da alta pressão em carne marinada com baixo teor de sódio, as carnes foram inoculadas com 106 UFC/g de carne com E. faecium e Listeria innocua e em seguida marinadas durante 18 horas, a 4°C, em diferentes soluções: 1% NaCl + 1% ácido cítrico, 1% NaCl + 2% ácido cítrico, 2% NaCl + 2% ácido cítrico e 2% NaCl + 2% ácido cítrico. Após a marinação as amostras foram submetidas ao tratamento nas seguintes pressões: Zero (controle), 300MPa, 450Mpa, 600MPa. As análises físico-químicas e microbiológicas foram realizadas logo após o tratamento. O tratamento em alta pressão foi capaz de reduzir a população microbiana em até seis ciclos logarítmicos quando 600Mpa foram aplicados em todas as soluções estudadas. A não aplicação de alta pressão proporcionou a redução de apenas um ciclo log na população de E. faecium quando as carnes foram marinadas com 2% NaCl + 2% ácido cítrico. A alta pressão e as diferentes concentrações de sal e ácido, não trouxeram diferença significativa na coloração das amostras. Já o maior teor de ácido cítrico na marinada causou maior (p<0,05) redução do pH da carne em comparação com as amostras em baixa concentração de ácido. Os experimentos demonstraram que a tanto embalagem a vácuo quanto a aplicação de ácido cítrico foram eficientes em retardar a oxidação lipídica. Pressões de 600Mpa tornaram a carne significativamente mais dura que as demais pressões aplicadas. Os resultados demonstraram a possibilidade de extensão da vida útil da carne refrigerada através da aplicação de diferentes tecnologias: a embalagem com atmosfera modificada para carne fresca e processamento em alta pressão de carnes marinadas com reduzido teor de sal.

Complex learning: the role of knowledge, intelligence, motivation and learning strategies

This work presents the main theories and models formulated with the purpose of offering a global overview on the acquisition of knowledge and skills involved in the initial development of expert competence. Setting from this background, we developed an empirical work whose main purpose is to define those factors in a complex learning situation such as chapter-sized in a knowledge-rich domain. The results obtained in a sample of Master students reveal that the several variables intervening, such as the qualitative organization of knowledge, intellectual ability, motivation, the deliberate use of strategies, and a rich learning environment, contribute in an independent way to provide an explanation for the acquired knowledge.

Successful functionalization of superporous zeolite templated carbon using aminobenzene acids and electrochemical methods

A novel and selective electrochemical functionalization of a highly reactive superporous zeolite templated carbon (ZTC) with two different aminobenzene acids (2-aminobenzoic and 4-aminobenzoic acid) was achieved. The functionalization was done through potentiodynamic treatment in acid media under oxidative conditions, which were optimized to preserve the unique ZTC structure. Interestingly, it was possible to avoid the electrochemical oxidation of the highly reactive ZTC structure by controlling the potential limit of the potentiodynamic experiment in presence of aminobenzene acids. The electrochemical characterization demonstrated the formation of polymer chains along with covalently bonded functionalities to the ZTC surface. The functionalized ZTCs showed several redox processes, producing a capacitance increase in both basic and acid media. The rate performance showed that the capacitance increase is retained at scan rates as high as 100 mV s−1, indicating that there is a fast charge transfer between the polymer chains formed inside the ZTC porosity or the new surface functionalities and the ZTC itself. The success of the proposed approach was also confirmed by using other characterization techniques, which confirmed the presence of different nitrogen groups in the ZTC surface. This promising method could be used to achieve highly selective functionalization of highly porous carbon materials.

Mineralogy and geochemistry of contrasting hydrothermal systems on the Arctic Mid Ocean Ridge (AMOR) : the Jan Mayen and Loki’s Castle vent fields

Tese de doutoramento, Ciências do Mar, Universidade de Lisboa, Faculdade de Ciências, 2016

Scenarios for the Agricultural Sector in the Southern and Eastern Mediterranean. MEDPRO Report No. 4, March 2013

The paper builds predictive scenarios for the agricultural sector of eleven southern and eastern Mediterranean countries (SEMCs), namely Algeria, Egypt, Israel, Jordan, Lebanon, Libya, Morocco, Palestine, Syria, Tunisia and Turkey. First, it assesses the performance trends of the SEMCs’ agricultural sector, with a focus on production, consumption and trade patterns, incentives, trade protection policies and trade relations with the EU, productivity dynamics and their determinants. Second, it presents four scenarios based on the main value chains of the SEMCs’ agriculture sector: animal products, fruit and vegetables, sugar and edible oils, cereals, fish and other sea products. The four scenarios are: business as usual, Mediterranean – one global player, the EU-Mediterranean area under threat and the EU and SEMCs as regional players on the global stage.

O mel, os açúcares e os adoçantes sob diferentes perspetivas

A alimentação sempre constituiu e constitui um fator de grande importância para a espécie humana. A qualidade alimentar, o valor nutricional e a saúde estão extremamente interligados e são cada vez mais importantes para a tomada de decisão no acto de compra por parte dos consumidores. Os escândalos alimentares têm causado um maior estado de atenção por parte das autoridades e dos consumidores. A importância da informação da origem e modo de produção dos produtos alimentares assim como a rotulagem dos alimentos processados e dos suplementos alimentares também tem vindo a ter cada vez importância e demanda por parte dos consumidores e da indústria alimentar. Este trabalho pretende destacar o mel como alimento e como adoçante de grande valor nutricional com potenciais efeitos benéficos para a saúde humana. Por outro lado pretende identificar e descrever os açúcares e os adoçantes alternativos, sejam eles naturais ou artificiais. Este trabalho, aborda, também, o papel controverso do açúcar refinado na dieta alimentar assim como de alguns dos adoçantes artificiais mais utilizados pela indústria alimentar atualmente. Nos últimos anos tem-se verificado um interesse crescente por produtos naturais com efeitos benéficos para a saúde e tem havido um aumento do consumo de mel, sobretudo nos países industrializados. O objetivo é que este trabalho seja uma ferramenta de auxílio e orientação no mundo dos adoçantes, para opções alimentares mais saudáveis.

(Table 1) Stable-isotopes of mineral separates and whole-rock powders from altered volcanic rocks of DSDP Hole 62-465A

Hess Rise, in the western Pacific Ocean, formed in the mid-Cretaceous south of the equator and moved north with the Pacific Plate (Lancelot and Larson, 1975; Lancelot, 1978; Valuer et al., 1979). Southern Hess Rise was a volcanic archipelago, at least until late Albian time, after which it subsided to become one of the major aseismic rises in the present western Pacific. A second pulse of volcanic activity apparently occurred in the Campanian-Maastrichtian interval, which may be related to tectonic uplift of Hess Rise (Valuer and Jefferson, this volume). Trachytic rocks underlie 412 meters of carbonate sediments at Site 465 on southern Hess Rise. Twenty-four meters of trachyte were recovered from a 64-meter cored interval. The rocks are relatively homogeneous in texture, color, and composition, indicating that the cored sequence was probably part of only one magmatic event (Seifert et al., this volume). Large (> 5-mm) vesicles and oxidized parts of some flows suggest subaerial or shallow-water extrusions. The rocks are high in silica and relatively rich in Na2O, K2O, and light rare-earth elements. The upper part of the volcanic-rock sequence is a breccia, the fragments cemented by calcite, pyrite, and rare barite. Some of the resultant veins are more than 1 cm thick. In addition to the veins, many vesicles are also filled with these minerals. Brecciation and the number and thickness of veins decrease with depth in the hole. The degree of weathering, as indicated by water content, also decreases with depth.

Sedimentology, organic geochemistry, and stable isotopes of core PS2138-1

We studied variations in terrigenous (TOM) and marine organic matter (MOM) input in a sediment core on the northern Barents Sea margin over the last 30 ka. Using a multiproxy approach, we reconstructed processes controlling organic carbon deposition and investigated their paleoceanographic significance in the North Atlantic-Arctic Gateways. Variations in paleo-surface-water productivity are not documented in amount and composition of organic carbon. The highest level of MOM was deposited during 25-23 ka as a result of scavenging on fine-grained, reworked, and TOM-rich material released by the retreating Svalbard/Barents Sea ice sheet during the late Weichselian. A second peak of MOM is preserved because of sorptive protection by detrital and terrigenous organic matter, higher surface-water productivity due to permanent intrusion of Atlantic water, and high suspension load release by melting sea ice during 15.9-11.2 ka.