Sequence and Structural Analysis of the 5 ` Noncoding Region of Hepatitis C Virus in Patients With Chronic Infection

Hepatitis C virus (HCV), exhibits considerable genetic diversity, but presents a relatively well conserved 5 ` noncoding region (5 ` NCR) among all genotypes. In this study, the structural features and translational efficiency of the HCV 5 ` NCR sequences were analyzed using the programs RNAfold, RNAshapes and RNApdist and with a bicistronic dual luciferase expression system, respectively. RNA structure prediction software indicated that base substitutions will alter potentially the 5 ` NCR structure. The heterogeneous sequence observed on 5 ` NCR led to important changes in their translation efficiency in different cell culture lines. Interactions of the viral RNA with cellular transacting factors may vary according to the cell type and viral genome polymorphisms that may result in the translational efficiency observed. J. Med. Virol. 81: 1212-1219, 2009. (C) 2009 Wiley-Liss, Inc.

Structural Investigation of MFe(2)O(4) (M = Fe, Co) Magnetic Fluids

Ferrites of the type M(II)Fe(2)O(4) (M = Fe and Co) have been prepared by the traditional coprecipitation method. These ferrites were modified by the adsorption of fatty acids derived from soybean and castor oil and were then dispersed in cyclohexane, providing very stable magnetic fluids, readily usable in nonpolar media. The structural properties of the ferrites and modified ferrites as well as the magnetic fluids were characterized by XRD (X-ray powder diffraction), TEM (transmission electron microscopy), DRIFTS (diffusion reflectance infrared Fourier transform spectroscopy), FTMR (Fourier transform near-infrared), UV-vis, normal Raman spectroscopy, and surface-enhanced Raman scattering (SERS). XRD and TEM analysis have shown that the magnetic nanoparticles (nonmodified and modified) present diameters in the range of 10-15 nm. DRIFTS measurements have shown that the carboxylate groups of soybean and castor oil fatty acids adsorb on the ferrite surface, forming three different structures: a bridging bidentate, a bridging monodentate, and a bidentate chelate structure. The FTIR and Raman spectra of nonmodified Fe(3)O(4) and CoFe(2)O(4) nanoparticles have shown that the number of observed phonons is not compatible with the expected O(h)(7) symmetry, since IR-only active phonons were observed. in the Raman spectra and vice versa. SERS measurements of a CoFe(2)O(4) thin film on a SERS-active gold electrode at different applied potentials made possible the assignment of the signals near 550 and 630 cm(-1) to Co-O motions and the signals near 470 and 680 cm(-1) to Fe-O motions.

Structural studies of prephenate dehydratase from Mycobacterium tuberculosis H37Rv by SAXS, ultracentrifugation, and computational analysis

Tuberculosis (TB) is one of the most common infectious diseases known to man and responsible for millions of human deaths in the world. The increasing incidence of TB in developing countries, the proliferation of multidrug resistant strains, and the absence of resources for treatment have highlighted the need of developing new drugs against TB. The shikimate pathway leads to the biosynthesis of chorismate, a precursor of aromatic amino acids. This pathway is absent from mammals and shown to be essential for the survival of Mycobacterium tuberculosis, the causative agent of TB. Accordingly, enzymes of aromatic amino acid biosynthesis pathway represent promising targets for structure-based drug design. The first reaction in phenylalanine biosynthesis involves the conversion of chorismate to prephenate, catalyzed by chorismate mutase. The second reaction is catalyzed by prephenate dehydratase (PDT) and involves decarboxylation and dehydratation of prephenate to form phenylpyruvate, the precursor of phenylalanine. Here, we describe utilization of different techniques to infer the structure of M. tuberculosis PDT (MtbPDT) in solution. Small angle X-ray scattering and ultracentrifugation analysis showed that the protein oligomeric state is a tetramer and MtbPDT is a flat disk protein. Bioinformatics tools were used to infer the structure of MtbPDT A molecular model for MtbPDT is presented and molecular dynamics simulations indicate that MtbPDT i.s stable. Experimental and molecular modeling results were in agreement and provide evidence for a tetrameric state of MtbPDT in solution.

A dynamic model of price competition with switching and search costs

Em modelos de competição de preços, somente um custo de procura positivo por parte do consumidor não gera equilíbrio com dispersão de preços. Já modelos dinâmicos de switching cost consistentemente geram este fenômeno bastante documentado para preços no varejo. Embora ambas as literaturas sejam vastas, poucos modelos tentaram combinar as duas fricções em um só modelo. Este trabalho apresenta um modelo dinâmico de competição de preços em que consumidores idênticos enfrentam custos de procura e de switching. O equilíbrio gera dispersão nos preços. Ainda, como os consumidores são obrigados a se comprometer com uma amostra fixa de firmas antes dos preços serem definidos, somente dois preços serão considerados antes de cada compra. Este resultado independe do tamanho do custo de procura individual do consumidor.

Structural analysis of the place of wine in Brazil

With the constant decrease of the wine consumption in traditional winemaking countries, more and more Brazil is seen as an appealing market. But the country also pretends to become an international player of winemaking in its own right. Both the participants of the Brazilian wine industry and the foreigners trying to get advantage of this promising market are facing new challenges to develop the consumption of wine in the world’s fifth largest country. Among all the possible actions to be taken in that sense, it also is worth taking time for a collective thought on the place of wine in the country, as well as the factors that shape it. What are these factors, which ones really make the difference, and what is their respective impact on the evolution of the place of wine in the country? After drawing the big picture of the wine market situation, this thesis tries to identify the levers of the evolution of the place of wine in Brazil. Using the tools of prospective, it aims at putting into perspective the different driving forces that influence its development, and in particular the relative influence of the political drivers. This paper also intends to be a first step of a prospective study as it constitutes a solid base for scenario planning. This paper is divided in five chapters starting with “introduction”, followed by chapter 2 “Theoretical framework”. Chapter 3 is “Methodology”, followed by chapter 4 “Description and analysis of the results”. Finally the results are discussed and concluded in the last part “Conclusions and implications for future studies”.

A dynamic model of simultaneous price competition with switching and search costs

Esse artigo apresenta um modelo dinâmico de competição em precos que incorpora tanto custos de procura quanto custos de switching e onde que as decisões do consumidor e das firmas são simultâneas. Dadas as hipóteses feitas n ós veremos que este modelo possui equilí brio. As principais propriedades do equil íbrio deste modelo são: Se os custos de procura forem baixos o suficiente, em equilí brio o consumidor vai procurar todas as firmas no mercado enquanto que o aumento dos custos de procura vai reduzir a propor cão de firmas que o consumidor busca. Um resultado contraintuitivo e que os pre cos esperados pagos pelo consumidor normalmente decresce em nossas computa cões numéricas do equil íbrio quando os custos de procura aumentam. Enquanto que aumentar os custos de switching tamb ém vai produzir o resultado contraituitivo que as firmas unmatched vão diminuir suas ofertas de modo a atrair o consumidor.

KittyCat: a cognitive model of structure-form discovery

Cognition is a core subject to understand how humans think and behave. In that sense, it is clear that Cognition is a great ally to Management, as the later deals with people and is very interested in how they behave, think, and make decisions. However, even though Cognition shows great promise as a field, there are still many topics to be explored and learned in this fairly new area. Kemp & Tenembaum (2008) tried to a model graph-structure problem in which, given a dataset, the best underlying structure and form would emerge from said dataset by using bayesian probabilistic inferences. This work is very interesting because it addresses a key cognition problem: learning. According to the authors, analogous insights and discoveries, understanding the relationships of elements and how they are organized, play a very important part in cognitive development. That is, this are very basic phenomena that allow learning. Human beings minds do not function as computer that uses bayesian probabilistic inferences. People seem to think differently. Thus, we present a cognitively inspired method, KittyCat, based on FARG computer models (like Copycat and Numbo), to solve the proposed problem of discovery the underlying structural-form of a dataset.

Tailoring the Structural Properties of PVDF and P(VDF-TrFE) by Using Natural Polymers as Additives

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

Structural analysis of fertilization in the fish Brycon orbignyanus

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Structural aspects of the fermion-boson mapping in two-dimensional gauge and anomalous gauge theories with massive fermions

Using a synthesis of the functional integral and operator approaches we discuss the fermion-buson mapping and the role played by the Bose field algebra in the Hilbert space of two-dimensional gauge and anomalous gauge field theories with massive fermions. In QED, with quartic self-interaction among massive fermions, the use of an auxiliary vector field introduces a redundant Bose field algebra that should not be considered as an element of the intrinsic algebraic structure defining the model. In anomalous chiral QED, with massive fermions the effect of the chiral anomaly leads to the appearance in the mass operator of a spurious Bose field combination. This phase factor carries no fermion selection rule and the expected absence of Theta-vacuum in the anomalous model is displayed from the operator solution. Even in the anomalous model with massive Fermi fields, the introduction of the Wess-Zumino field replicates the theory, changing neither its algebraic content nor its physical content. (C) 2002 Elsevier B.V. (USA).

Structural analysis of the embryonic development in Brycon cephalus (Gunther, 1869)

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

Structural characteristics of the tendinous cord-papillary muscle junction in healthy and hypertensive rats

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

Molecular approaches for structural characterization of Bothrops L-amino acid oxidases with antiprotozoal activity: cDNA cloning, comparative sequence analysis, and molecular modeling

Two L-amino acid oxidases (LAAOs) were identified by random sequencing of cDNA libraries from the venom glands of Bothrops moojeni (BmooLAAO) and Bothrops jararacussu (Bjussu LAAO). Phylogenetic analysis involving other SV-LAAOs showed sequence identities within the range 83-87% being closely related to those from Agkistrodon and Trimeresurus. Molecular modeling experiments indicated the FAD-binding, substrate-binding, and helical domains of Bmoo and Bjussu LAAOs. The RMS deviations obtained by the superposition of those domains and that from Calloselasma rhodostoma LAAO crystal structure confirm the high degree of structural similarity between these enzymes. Purified BjussuLAAO-I and BmooLAAO-I exhibited antiprotozoal activities which were demonstrated to be hydrogen-peroxide mediated. This is the first report on the isolation and identification of cDNAs encoding LAAOs from Bothrops venom. The findings here reported contribute to the overall structural elucidation of SV-LAAOs and will advance the understanding on their mode of action. (c) 2006 Elsevier B.V. All rights reserved.

Structural description of humic substances from subtropical coastal environments using elemental analysis, FT-IR and C-13-solid state NMR data

Elemental composition and spectroscopic properties (FT-IR and CP/MAS C-13-NMR) of sedimentary humic substances (HS) from aquatic subtropical environments (a lake, an estuary and two marine sites) are investigated. Humic acids (HA) are relatively richer in nitrogen and in aliphatic chains than fulvic acids (FA) from the same sediments. Conversely, FA are richer in carboxylic groups and in ring polysaccharides than HA. Nitrogen is mostly present as amide groups and for lake and marine HS the FT-IR peaks around 1640 cm(-1) and 1540 cm(-1) identify polypeptides. Estuarine HS exhibit mixed continental-marine influences, these being highly influenced by site location. Overall, the data suggest that aquatic and mixed HS are more aliphatic than has been proposed in current models and also that amide linkages form an important part of their structural configuration.

Molecular, kinetic, thermodynamic, and structural analyses of Mycobacterium tuberculosis hisD-encoded metal-dependent dimeric histidinol dehydrogenase (EC 1.1.1.23)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)