Nominal anchors and macroeconomic coordination options in MERCOSUR

Includes bibliography

Alguns aspectos sobre a geração dinâmica de massa em modelos de Technicolor

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Potentiated Electron Transference in alpha-Ag2WO4 Microcrystals with Ag Nanofilaments as Microbial Agent

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Abordagem alternativa para síntese de melanina

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Cytochrome c-promoted cardiolipin oxidation generates singlet molecular oxygen

The interaction of cytochrome c (cyt c) with cardiolipin (CL) induces protein conformational changes that favor peroxidase activity. This process has been correlated with CL oxidation and the induction of cell death. Here we report evidence demonstrating the generation of singlet molecular oxygen [O-2((1)Delta(g))] by a cyt c-CL complex in a model membrane containing CL. The formation of singlet oxygen was directly evidenced by luminescence measurements at 1270 nm and by chemical trapping experiments. Singlet oxygen generation required cyt c-CL binding and occurred at pH values higher than 6, consistent with lipid-protein interactions involving fully deprotonated CL species and positively charged residues in the protein. Moreover, singlet oxygen formation was specifically observed for tetralinoleoyl CL species and was not observed with monounsaturated and saturated CL species. Our results show that there are at least two mechanisms leading to singlet oxygen formation: one with fast kinetics involving the generation of singlet oxygen directly from CL hydroperoxide decomposition and the other involving CL oxidation. The contribution of the first mechanism was clearly evidenced by the detection of labeled singlet oxygen [O-18(2)((1)Delta(g))] from liposomes supplemented with 18-oxygen-labeled CL hydroperoxides. However quantitative analysis showed that singlet oxygen yield from CL hydroperoxides was minor (<5%) and that most of the singlet oxygen is formed from the second mechanism. Based on these data and previous findings we propose a mechanism of singlet oxygen generation through reactions involving peroxyl radicals (Russell mechanism) and excited triplet carbonyl intermediates (energy transfer mechanism).

Realistic fluids as source for dynamically accreting black holes in a cosmological background

We show that a single imperfect fluid can be used as a source to obtain a mass-varying black hole in an expanding universe. This approach generalizes the well-known McVittie spacetime, by allowing the mass to vary thanks to a novel mechanism based on the presence of a temperature gradient. This fully dynamical solution, which does not require phantom fields or fine-tuning, is a step forward in a new direction in the study of systems whose local gravitational attraction is coupled to the expansion of the universe. We present a simple but instructive example for the mass function and briefly discuss the structure of the apparent horizons and the past singularity.

The Cysteine-Rich Protein Thimet Oligopeptidase as a Model of the Structural Requirements for S-glutathiolation and Oxidative Oligomerization

Thimet oligopeptidase (EP24.15) is a cysteine-rich metallopeptidase containing fifteen Cys residues and no intra-protein disulfide bonds. Previous work on this enzyme revealed that the oxidative oligomerization of EP24.15 is triggered by S-glutathiolation at physiological GSSG levels (10-50 mu M) via a mechanism based on thiol-disulfide exchange. In the present work, our aim was to identify EP24.15 Cys residues that are prone to S-glutathiolation and to determine which structural features in the cysteinyl bulk are responsible for the formation of mixed disulfides through the reaction with GSSG and, in this particular case, the Cys residues within EP24.15 that favor either S-glutathiolation or inter-protein thiol-disulfide exchange. These studies were conducted by in silico structural analyses and simulations as well as site-specific mutation. S-glutathiolation was determined by mass spectrometric analyses and western blotting with anti-glutathione antibody. The results indicated that the stabilization of a thiolate sulfhydryl and the solvent accessibility of the cysteines are necessary for S-thiolation. The Solvent Access Surface analysis of the Cys residues prone to glutathione modification showed that the S-glutathiolated Cys residues are located inside pockets where the sulfur atom comes into contact with the solvent and that the positively charged amino acids are directed toward these Cys residues. The simulation of a covalent glutathione docking onto the same Cys residues allowed for perfect glutathione posing. A mutation of the Arg residue 263 that forms a saline bridge to the Cys residue 175 significantly decreased the overall S-glutathiolation and oligomerization of EP24.15. The present results show for the first time the structural requirements for protein S-glutathiolation by GSSG and are consistent with our previous hypothesis that EP24.15 oligomerization is dependent on the electron transfer from specific protonated Cys residues of one molecule to previously S-glutathionylated Cys residues of another one.

A UML profile for the OBO relation ontology

Background: Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain. Results: We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO). Conclusions: The use of an established and well-known graphical language in the development of biomedical ontologies provides a more intuitive form of capturing and representing knowledge than using only text-based notations. The use of the profile requires the domain expert to reason about the underlying semantics of the concepts and relationships being modeled, which helps preventing the introduction of inconsistencies in an ontology under development and facilitates the identification and correction of errors in an already defined ontology.

Generation of the Cape Ghir upwelling filament: a numerical study

[EN] Filaments are narrow, shallow structures of cool water originating from the coast. They are typical features of the four main eastern boundary upwelling systems (EBUS). In spite of their significant biological and chemical roles, through the offshore exportation of nutrient-rich waters, the physical processes that generate them are still not completely understood. This paper is a process-oriented study of filament generation mechanisms. Our goal is twofold: firstly, to obtain a numerical solution able to well represent the characteristics of the filament off Cape Ghir (30°38'N, northwestern Africa) in the Canary EBUS and secondly, to explain its formation by a simple mechanism based on the balance of potential vorticity. The first goal is achieved by the use of the ROMS model (Regional Ocean Modeling System) in embedded domains around Cape Ghir, with a horizontal resolution going up to 1.5 km for the finest domain. The latter gets its initial and boundary conditions from a parent solution and is forced by climatological, high-resolution atmospheric fields. The modeled filaments display spatial, temporal and physical characteristics in agreement with the available in situ and satellite observations. This model solution is used as a reference to compare the results with a set of process-oriented experiments. These experiments allow us to reach the second objective. Their respective solution serves to highlight the contribution of various processes in the filament generation. Since the study is focused on general processes present under climatological forcing conditions, inter-annual forcing is not necessary. The underlying idea for the filament generation is the balance of potential vorticity in the Canary EBUS: the upwelling jet is characterized by negative relative vorticity and flows southward along a narrow band of uniform potential vorticity. In the vicinity of the cape, an injection of relative vorticity induced by the wind breaks the existing vorticity balance. The upwelling jet is prevented from continuing its way southward and has to turn offshore to follow lines of equal potential vorticity. The model results highlight the essential role of wind, associated with the particular topography (coastline and bottom) around the cape. The mechanism presented here is general and thus can be applied to other EBUS.

Knowledge management in intelligent tutoring systems

In the last years, Intelligent Tutoring Systems have been a very successful way for improving learning experience. Many issues must be addressed until this technology can be defined mature. One of the main problems within the Intelligent Tutoring Systems is the process of contents authoring: knowledge acquisition and manipulation processes are difficult tasks because they require a specialised skills on computer programming and knowledge engineering. In this thesis we discuss a general framework for knowledge management in an Intelligent Tutoring System and propose a mechanism based on first order data mining to partially automate the process of knowledge acquisition that have to be used in the ITS during the tutoring process. Such a mechanism can be applied in Constraint Based Tutor and in the Pseudo-Cognitive Tutor. We design and implement a part of the proposed architecture, mainly the module of knowledge acquisition from examples based on first order data mining. We then show that the algorithm can be applied at least two different domains: first order algebra equation and some topics of C programming language. Finally we discuss the limitation of current approach and the possible improvements of the whole framework.

The effect of osmolytes on protein fold stability at the single-molecule level

By pulling and releasing the tension on protein homomers with the Atomic Force Miscroscope (AFM) at different pulling speeds, dwell times and dwell distances, the observed force-response of the protein can be fitted with suitable theoretical models. In this respect we developed mathematical procedures and open-source computer codes for driving such experiments and fitting Bell’s model to experimental protein unfolding forces and protein folding frequencies. We applied the above techniques to the study of proteins GB1 (the B1 IgG-binding domain of protein G from Streptococcus) and I27 (a module of human cardiac titin) in aqueous solutions of protecting osmolytes such as dimethyl sulfoxide (DMSO), glycerol and trimethylamine N-oxide (TMAO). In order to get a molecular understanding of the experimental results we developed an Ising-like model for proteins that incorporates the osmophobic nature of their backbone. The model benefits from analytical thermodynamics and kinetics amenable to Monte-Carlo simulation. The prevailing view used to be that small protecting osmolytes bridge the separating beta-strands of proteins with mechanical resistance, presumably shifting the transition state to significantly higher distances that correlate with the molecular size of the osmolyte molecules. Our experiments showed instead that protecting osmolytes slow down protein unfolding and speed-up protein folding at physiological pH without shifting the protein transition state on the mechanical reaction coordinate. Together with the theoretical results of the Ising-model, our results lend support to the osmophobic theory according to which osmolyte stabilisation is a result of the preferential exclusion of the osmolyte molecules from the protein backbone. The results obtained during this thesis work have markedly improved our understanding of the strategy selected by Nature to strengthen protein stability in hostile environments, shifting the focus from hypothetical protein-osmolyte interactions to the more general mechanism based on the osmophobicity of the protein backbone.

Isoprene oxidation and its impacts on the atmospheric composition

Terrestrische Vegetation, vor allem tropischer Regenwald, emittiert grosse Mengen flüchtiger organischer Verbindungen (VOCs) in die rnAtmosphäre, die durch Oxidationsreaktionen und Deposition der Reaktionsprodukte wieder entfernt werden. Die Oxidation wird vor allem durch Hydroxyl-Radikale (OH) initiiert, die hauptsächlich durch Photodissoziation von Ozon gebildet werden. Zuvor ging man davon aus, dass biogene VOCs OH in unverschmutzter Luft abbauen und dadurch die atmosphärische Oxidationskapazität verringern. Umgekehrt, führt rndie Oxidation von VOCs in verschmutzter Luft durch die katalytische Wirkung von Stickstoffoxiden (NOx = NO + NO2) zu schädlicher Oxidationsmittelbildung. Flugzeugmessungen atmosphärischer Spurengase, die über dem unberührten Amazonas-Regenwald durchgeführt worden sind, haben jedoch unerwartet hohe OH-Konzentrationen aufgezeigt. Das VOC mit der höchsten Emission in dieser Region war Isopren, dessen Oxidation als stärkeste OH-Senke berechnet wurde. In dieser Arbeit wurde die Hypothese genauestens untersucht, dass die natürliche Isopren-Oxidation in niedrig-NOx Luft OH effizient erneuert. Es wurde ein sehr detaillierter Oxidationsmechanismus für Isopren entwickelt, in dem neueste experimentelle und theoretische Fortschritte umgesetzt worden sind. Die Haupt-OH-Rückgewinnungswege wurden angewendet wodurch gezeigt wurde, dass sie wesentlich zur Oxidation unter niedrig-NOx Bedingungen beitragen. Verstärkte OH-Konzentrationen blieben unter verminderten Lichtverhältnissen, wie sie unter dichten Vegetationsdächern typisch sind, dauerhaft erhalten. Im Vergleich zu Flugzeugmessungen, der neue Oxidationsmechanismus reproduziert die OH-Konzentrationen innerhalb des Unsicherheitsbereiches. Darüber hinaus zeigten Simulationen eine erhebliche Produktion eines Isopren-Dihydroxyepoxids, das ein potenziell wichtiger Vorläufer organischer Aerosole in der Atmosphäre sein könnte. Es wurde einen neuen vereinfachten Oxidationsmechanismus auf Basis des traditionellen Wissenstands entwickelt und seine Anwendung für globale atmosphärische Studien getestet. Die Eingliederung der neuen Oxidationswege in diesen Mechanismus ermöglicht es folgende Auswirkungen der verstärkten VOC-Oxidation zu studieren die Zusammensetzung der Atmosphäre, den Austausch zwischen Erdoberfläche und Atmosphäre, Aerosole und Klima.

Ginger phenylpropanoids inhibit IL-1beta and prostanoid secretion and disrupt arachidonate-phospholipid remodeling by targeting phospholipases A2

The rhizome of ginger (Zingiber officinale) is employed in Asian traditional medicine to treat mild forms of rheumatoid arthritis and fever. We have profiled ginger constituents for robust effects on proinflammatory signaling and cytokine expression in a validated assay using human whole blood. Independent of the stimulus used (LPS, PMA, anti-CD28 Ab, anti-CD3 Ab, and thapsigargin), ginger constituents potently and specifically inhibited IL-1β expression in monocytes/macrophages. Both the calcium-independent phospholipase A(2) (iPLA(2))-triggered maturation and the cytosolic phospholipase A(2) (cPLA(2))-dependent secretion of IL-1β from isolated human monocytes were inhibited. In a fluorescence-coupled PLA(2) assay, most major ginger phenylpropanoids directly inhibited i/cPLA(2) from U937 macrophages, but not hog pancreas secretory phospholipase A(2). The effects of the ginger constituents were additive and the potency comparable to the mechanism-based inhibitor bromoenol lactone for iPLA(2) and methyl arachidonyl fluorophosphonate for cPLA(2), with 10-gingerol/-shogaol being most effective. Furthermore, a ginger extract (2 μg/ml) and 10-shogaol (2 μM) potently inhibited the release of PGE(2) and thromboxane B2 (>50%) and partially also leukotriene B(4) in LPS-stimulated macrophages. Intriguingly, the total cellular arachidonic acid was increased 2- to 3-fold in U937 cells under all experimental conditions. Our data show that the concurrent inhibition of iPLA(2) and prostanoid production causes an accumulation of free intracellular arachidonic acid by disrupting the phospholipid deacylation-reacylation cycle. The inhibition of i/cPLA(2), the resulting attenuation of IL-1β secretion, and the simultaneous inhibition of prostanoid production by common ginger phenylpropanoids uncover a new anti-inflammatory molecular mechanism of dietary ginger that may be exploited therapeutically.

Phosphatidylinositol 3-kinase isoforms as novel drug targets

Phosphatidylinositol 3-kinases (PI3Ks) are key molecules in the signal transduction pathways initiated by the binding of extracellular signals to their cell surface receptors. The PI3K family of enzymes comprises eight catalytic isoforms subdivided into three classes and control a variety of cellular processes including proliferation, growth, apoptosis, migration and metabolism. Deregulation of the PI3K pathway has been extensively investigated in connection to cancer, but is also involved in other commonly occurring diseases such as chronic inflammation, autoimmunity, allergy, atherosclerosis, cardiovascular and metabolic diseases. The fact that the PI3K pathway is deregulated in a large number of human diseases, and its importance for different cellular responses, makes it an attractive drug target. Pharmacological PI3K inhibitors have played a very important role in studying cellular responses involving these enzymes. Currently, a wide range of selective PI3K inhibitors have been tested in preclinical studies and some have entered clinical trials in oncology. However, due to the complexity of PI3K signaling pathways, developing an effective anti-cancer therapy may be difficult. The biggest challenge in curing cancer patients with various signaling pathway abnormalities is to target multiple components of different signal transduction pathways with mechanism-based combinatorial treatments. In this article we will give an overview of the complex role of PI3K isoforms in human diseases and discuss their potential as drug targets. In addition, we will describe the drugs currently used in clinical trials, as well as promising emerging candidates.

Controlling electronic and magnetic properties of ultra narrow multilayered nanowires

Interest in the study of magnetic/non-magnetic multilayered structures took a giant leap since Grünberg and his group established that the interlayer exchange coupling (IEC) is a function of the non-magnetic spacer width. This interest was further fuelled by the discovery of the phenomenal Giant Magnetoresistance (GMR) effect. In fact, in 2007 Albert Fert and Peter Grünberg were awarded the Nobel Prize in Physics for their contribution to the discovery of GMR. GMR is the key property that is being used in the read-head of the present day computer hard drive as it requires a high sensitivity in the detection of magnetic field. The recent increase in demand for device miniaturization encouraged researchers to look for GMR in nanoscale multilayered structures. In this context, one dimensional(1-D) multilayerd nanowire structure has shown tremendous promise as a viable candidate for ultra sensitive read head sensors. In fact, the phenomenal giant magnetoresistance(GMR) effect, which is the novel feature of the currently used multilayered thin film, has already been observed in multilayered nanowire systems at ambient temperature. Geometrical confinement of the supper lattice along the 2-dimensions (2-D) to construct the 1-D multilayered nanowire prohibits the minimization of magnetic interaction- offering a rich variety of magnetic properties in nanowire that can be exploited for novel functionality. In addition, introduction of non-magnetic spacer between the magnetic layers presents additional advantage in controlling magnetic properties via tuning the interlayer magnetic interaction. Despite of a large volume of theoretical works devoted towards the understanding of GMR and IEC in super lattice structures, limited theoretical calculations are reported in 1-D multilayered systems. Thus to gauge their potential application in new generation magneto-electronic devices, in this thesis, I have discussed the usage of first principles density functional theory (DFT) in predicting the equilibrium structure, stability as well as electronic and magnetic properties of one dimensional multilayered nanowires. Particularly, I have focused on the electronic and magnetic properties of Fe/Pt multilayered nanowire structures and the role of non-magnetic Pt spacer in modulating the magnetic properties of the wire. It is found that the average magnetic moment per atom in the nanowire increases monotonically with an ~1/(N(Fe)) dependance, where N(Fe) is the number of iron layers in the nanowire. A simple model based upon the interfacial structure is given to explain the 1/(N(Fe)) trend in magnetic moment obtained from the first principle calculations. A new mechanism, based upon spin flip with in the layer and multistep electron transfer between the layers, is proposed to elucidate the enhancement of magnetic moment of Iron atom at the Platinum interface. The calculated IEC in the Fe/Pt multilayered nanowire is found to switch sign as the width of the non-magnetic spacer varies. The competition among short and long range direct exchange and the super exchange has been found to play a key role for the non-monotonous sign in IEC depending upon the width of the Platinum spacer layer. The calculated magnetoresistance from Julliere's model also exhibit similar switching behavior as that of IEC. The universality of the behavior of exchange coupling has also been looked into by introducing different non-magnetic spacers like Palladium, Copper, Silver, and Gold in between magnetic Iron layers. The nature of hybridization between Fe and other non-magnetic spacer is found to dictate the inter layer magnetic interaction. For example, in Fe/Pd nanowire the d-p hybridization in two spacer layer case favors anti-ferromagnetic (AFM) configuration over ferromagnetic (FM) configuration. However, the hybridization between half-filled Fe(d) and filled Cu(p) state in Fe/Cu nanowire favors FM coupling in the 2-spacer system.