Reversal of a single base pair step controls guanine photo-oxidation by an intercalating Ru(II) dipyridophenazine complex

Small changes in DNA sequence can often have major biological effects. Here the rates and yields of guanine photo-oxidation by Λ [Ru(TAP)2(dppz)]2+ have been compared in 5′-{CCGGATCCGG}2 and 5′-{CCGGTACCGG}2 using ps/ns transient visible and time-resolved IR (TRIR) spectroscopy. The inefficiency of electron transfer in the TA sequence is consistent with the 5′-TA-3′ vs. 5′-AT-3′ binding preference predicted by X-ray crystallography. The TRIR spectra also reveal the differences in binding sites in the two oligonucleotides.

Controlled variation of monomer sequence-distribution in the synthesis of aromatic poly(ether ketone)s

The effects of varying the alkali metal cation in the high-temperature nucleophilic synthesis of a semi-crystalline, aromatic poly(ether ketone) have been systematically investigated, and striking variations in the sequence-distributions and thermal characteristics of the resulting polymers were found. Polycondensation of 4,4'-dihydroxybenzophenone with 1,3-bis(4-fluorobenzoyl)benzene in diphenylsulfone as solvent, in the presence of an alkali metal carbonate M2CO3 (M= Li, Na, K, or Rb) as base, affords a range of different polymers that vary in the distribution pattern of 2-ring and 3-ring monomer units along the chain. Lithium carbonate gives an essentially alternating and highly crystalline polymer, but the degree of sequence-randomisation increases progressively as the alkali metal series is descended, with rubidium carbonate giving a fully random and non-thermally-crystallisable polymer. Randomisation during polycondensation is shown to result from reversible cleavage of the ether linkages in the polymer by fluoride ions, and an isolated sample of alternating-sequence polymer is thus converted to a fully randomised material on heating with rubidium fluoride.

Sequence diversity and evolutionary dynamics of the dimorphic antigen merozoite surface protein-6 and other Msp genes of Plasmodium falciparum

Immune evasion by Plasmodium falciparum is favored by extensive allelic diversity of surface antigens. Some of them, most notably the vaccine-candidate merozoite surface protein (MSP)-1, exhibit a poorly understood pattern of allelic dimorphism, in which all observed alleles group into two highly diverged allelic families with few or no inter-family recombinants. Here we describe contrasting levels and patterns of sequence diversity in genes encoding three MSP-1-associated surface antigens of P. falciparum, ranging from an ancient allelic dimorphism in the Msp-6 gene to a near lack of allelic divergence in Msp-9 to a more classical multi-allele polymorphism in Msp-7 Other members of the Msp-7 gene family exhibit very little polymorphism in non-repetitive regions. A comparison of P. falciparum Msp-6 sequences to an orthologous sequence from P. reichenowi provided evidence for distinct evolutionary histories of the 5` and 3` segments of the dimorphic region in PfMsp-6, consistent with one dimorphic lineage having arisen from recombination between now-extinct ancestral alleles. In addition. we uncovered two surprising patterns of evolution in repetitive sequence. Firsts in Msp-6, large deletions are associated with (nearly) identical sequence motifs at their borders. Second, a comparison of PfMsp-9 with the P. reichenowi ortholog indicated retention of a significant inter-unit diversity within an 18-base pair repeat within the coding region of P. falciparum, but homogenization in P. reichenowi. (C) 2009 Elsevier B.V. All rights reserved.

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.

The mitochondrial transcription factor A functions in mitochondrial base excision repair

Mitochondrial transcription factor A (TFAM) is an essential component of mitochondrial nucleoids TFAM plays an important role in mitochondrial transcription and replication TFAM has been previously reported to inhibit nucleotide excision repair (NER) in vitro but NER has not yet been detected in mitochondria, whereas base excision repair (BER) has been comprehensively characterized in these organelles The BER proteins are associated with the inner membrane in mitochondria and thus with the mitochondrial nucleoid, where TFAM is also situated However, a function for TFAM in BER has not yet been investigated This study examines the role of TFAM in BER In vitro studies with purified recombinant TFAM indicate that it preferentially binds to DNA containing 8-oxoguanines, but not to abasic sites, uracils, or a gap in the sequence TFAM inhibited the in vitro incision activity of 8-oxoguanine DNA glycosylase (OGG1), uracil-DNA glycosylase (UDG), apurinic endonuclease 1 (APE1), and nucleotide incorporation by DNA polymerase gamma (pol gamma) On the other hand, a DNA binding-defective TFAM mutant, L58A, showed less inhibition of BER in vitro Characterization of TFAM knockdown (KD) cells revealed that these lysates had higher 8oxoG incision activity without changes in alpha OGG1 protein levels TFAM KD cells had mild resistance to menadione and increased damage accumulation in the mtDNA when compared to the control cells In addition, we found that the tumor suppressor p53, which has been shown to interact with and alter the DNA binding activity of TFAM, alleviates TFAM-Induced inhibition of BER proteins Together, the results suggest that TFAM modulates BER in mitochondria by virtue of its DNA binding activity and protein interactions Published by Elsevier B V

Oxindole-Schiff base copper(II) complexes interactions with human serum albumin: Spectroscopic, oxidative damage, and computational studies

CD and EPR were used to characterize interactions of oxindole-Schiff base copper(II) complexes with human serum albumin (HSA). These imine ligands form very stable complexes with copper, and can efficiently compete for this metal ion towards the specific N-terminal binding site of the protein, consisting of the amino acid sequence Asp-Ala-His. Relative stability constants for the corresponding complexes were estimated from CD data, using the protein as competitive ligand, with values of log K(CuL) in the range 15.7-18.1, very close to that of [Cu(HSA)] itself, with log K(CuHSA) 16.2. Some of the complexes are also able to interfere in the a-helix structure of the protein, while others seem not to affect it. EPR spectra corroborate those results, indicating at least two different metal species in solution, depending on the imine ligand. Oxidative damage to the protein after incubation with these copper(II) complexes, particularly in the presence of hydrogen peroxide, was monitored by carbonyl groups formation, and was observed to be more severe when conformational features of the protein were modified. Complementary EPR spin-trapping data indicated significant formation of hydroxyl and carbon centered radicals, consistent with an oxidative mechanism. Theoretical calculations at density functional theory (DFT) level were employed to evaluate Cu(II)-L binding energies, L -> Cu(II) donation, and Cu(II) -> L back-donation, by considering the Schiff bases and the N-terminal site of HSA as ligands. These results complement previous studies on cytotoxicity, nuclease and pro-apoptotic properties of this kind of copper(II) complexes, providing additional information about their possibilities of transport and disposition in blood plasma. (C) 2009 Elsevier Inc. All rights reserved.

Análise estratigráfica do Campo de Namorado (Bacia de Campos) com base na interpretação sísmica tridimensional

O presente trabalho analisa os reservatórios turbidíticos do Campo de Namorado, Bacia de Campos – RJ, com a apresentação de um novo modelo evolutivo para o intervalo entre o Albiano superior e Cenomaniano, na área do referido campo. As ferramentas utilizadas neste estudo consistiram da interpretação sísmica em ambiente tridimensional com o software VoxelGeo®, e da análise faciológica junto à perfilagem de poços do referido campo. A análise desenvolvida permitiu a individualização e a posterior visualização tridimensional de um paleocanal meandrante na base do intervalo estudado, feição esta até então não relatada em interpretações anteriores neste reservatório. Como resultado das análises sísmicas e faciológicas, foi possível elaborar um modelo deposicional, onde foram definidos quatro sistemas turbidíticos distintos, inclusos em duas seqüências de 3ª Ordem. Esses sistemas turbidíticos estariam, portanto, associados às seqüências de 4ª Ordem, que são interpretadas como parasseqüências, inseridas nos dois ciclos de 3ª Ordem. As seqüências de 3ª Ordem, que englobam os reservatórios do Campo de Namorado, representariam intervalos de alta freqüência no registro estratigráfico, dentro do contexto de afogamento (2ª Ordem) da Bacia de Campos. Pelas características da calha deposicional observada para o Campo de Namorado, é possível concluir que o sistema, como um todo, foi depositado em um complexo de canais, junto a sistemas de frentes deltaicas. Esses canais, provavelmente, foram esculpidos por fluxos hiperpicnais, formados a partir de inundações catastróficas. As informações provenientes deste estudo, proporcionaram uma melhor compreensão da gênese dos depósitos turbidíticos, acumuladores de hidrocarbonetos, no intervalo estudado, e cuja ocorrência está relacionada com etapas de rebaixamento relativo do nível do mar.

Controle on-line por atributos para o número de não-conformidades no item inspecionado com base em uma sequência de inspeção

This paper proposes a procedure to control on-line processes for attributes, using an Shewhart control chart with two control limits (warning limit and control limit) and will be based on a sequence of inspection (h). The inspection procedure is based on Taguchi et al. (1989), in which to inspect the item, if the number of non-conformities is higher than an upper control limit, the process needs to be stopped and some adjustment is required; and, if the last inspection h, from all items inspected present a number of non-conformities between the control limit and warning limit. The items inspected will suffer destructive inspection, being discarded after inspection. Properties of an ergodic Markov chain are used to get the expression of average cost per item and the aim was the determination of four optimized parameters: the sampling interval of the inspections (m); the constant W to draw the warning limit (W); the constant C to draw the control limit (C), where W £ C, and the length of sequence of inspections (h). Numerical examples illustrate the proposed procedure

Preparation, characterization, and CuX2 and CoX2 (X = Cl-, Br-, ClO4-) adsorption behavior of a polyhedral oligomer silsesquioxane functionalized with an organic base

In this paper we report on the synthesis, characterization, and adsorption properties of the first 3-amino-1,2,4-triazole-modified porous silsesquioxane (ATPS). The isotherms of adsorption of MX2 (M = Cu(II), Co(II); X = Cl-, Br-, ClO4-) by ATPS were studied in ethanol and aqueous solutions at 298 K. The results showed that there is a good fit between the experimental data and the Langmuir isotherm. The adsorption capacity in both solvents followed the sequence Cu(II) >> Co(II). The lowest adsorption for Co(II) should be related to the largest hydration volume, which obstructs the adsorption capacity of the surface, and consequently causes a decrease in the number of cations adsorbed. For the salts with different anions the sequence was MCl2 > MBr2 > M(ClO4)2 in both solvents. The low affinity for M(ClO4)(2) toward the solid phase is a consequence of the poorer coordination ability of the ClO4-. Adsorptions from ethanol solutions were higher than those from aqueous solutions due to the higher polarity of water, which can more strongly solvate the solute and the basic sites on the surface. The following adsorption capacities (in mmol g(-1)) were determined: 0.24 (aq) and 0.84 (eth) for CuCl2, 0.09 (aq) and 0.16 (eth) for CuBr2, and 0.08 (aq) and 0.11 (eth) for Cu(ClO4)(2); 0.02 (aq) and 0.07 (eth) for CoCl2, 0.02 (aq) and 0.06 (eth) for CoBr2, and 0.01 (aq) and 0.05 (eth) for Co(ClO4)(2). (c) 2007 Elsevier B.V. All rights reserved.

Interpretação de dados de GPR com base na hierarquização de superfícies limitantes e na adaptação de critérios sismoestratigráficos

Due to its high resolution, Ground Penetrating Radar (GPR) has been used to image subsurface sedimentary deposits. Because GPR and Seismic methods share some principles of image construction, the classic seismostratigraphic interpretation method has been also applied as an attempt to interpret GPR data. Nonetheless some advances in few particular contexts, the adaptations from seismic to GPR of seismostratigraphic tools and concepts unsuitable because the meaning given to the termination criteria in seismic stratigraphy do not represent the adequate geologic record in the GPR scale. Essentially, the open question relies in proposing a interpretation method for GPR data which allow not only relating product and sedimentary process in the GPR scale but also identifying or proposing depositional environments and correlating these results with the well known Sequence Stratigraphy cornerstones. The goal of this dissertation is to propose an interpretation methodology of GPR data able to perform this task at least for siliciclastic deposits. In order to do so, the proposed GPR interpretation method is based both on seismostratigraphic concepts and on the bounding surface hierarchy tool from Miall (1988). As consequence of this joint use, the results of GPR interpretation can be associated to the sedimentary facies in a genetic context, so that it is possible to: (i) individualize radar facies and correlate them to the sedimentary facies by using depositional models; (ii) characterize a given depositional system, and (iii) determine its stratigraphic framework highligthing how it evolved through geologic time. To illustrate its use the proposed methodology was applied in a GPR data set from Galos area which is part of the Galinhos spit, located in Rio Grande do Norte state, Northeastern Brazil. This spit presents high lateral sedimentary facies variation, containing in its sedimentary record from 4th to 6th cicles caused by high frequency sea level oscillation. The interpretation process was done throughout the following phases: (i) identification of a vertical facies succession, (ii) characterization of radar facies and its associated sedimentary products, (iii) recognition of the associated sedimentary process in a genetic context, and finally (iv) proposal of an evolutionay model for the Galinhos spit. This model proposes that the Galinhos spit is a barrier island constituted, from base to top, of the following sedimentary facies: tidal channel facies, tidal flat facies, shore facies, and aeolic facies (dunes). The tidal channel facies, in the base, is constituted of lateral accretion bars and filling deposits of the channels. The base facies is laterally truncated by the tidal flat facies. In the foreshore zone, the tidal flat facies is covered by the shore facies which is the register of a sea transgression. Finally, on the top of the stratigraphic column, aeolic dunes are deposited due to areal exposition caused by a sea regression

Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities

BaP1 is a 22.7-kD P-I-type zinc-dependent metalloproteinase isolated from the venom of the snake Bothrops asper, a medically relevant species in Central America. This enzyme exerts multiple tissue-damaging activities, including hemorrhage, myonecrosis, dermonecrosis, blistering, and edema. BaP1 is a single chain of 202 amino acids that shows highest sequence identity with metalloproteinases isolated front the venoms of snakes of the subfamily Crotalinae. It has six Cys residues involved in three disulfide bridges (Cys 117-Cys 197, Cys 159-Cys 181, Cys 157-Cys 164). It has the consensus sequence H(142)E(143)XXH(146)XXGXXH(152), as well as the sequence C164I165M166, which characterize the metzincin superfamily of metalloproteinases. The active-site cleft separates a major subdomain (residues 1-152), comprising four a-helices and a five-stranded beta-sheet, from the minor subdomain, which is formed by a single a-helix and several loops. The catalytic zinc ion is coordinated by the N-epsilon2 nitrogen atoms of His 142, His 146, and His 152, in addition to a solvent water molecule, which in turn is bound to Glu 143. Several conserved residues contribute to the formation of the hydrophobic pocket, and Met 166 serves as a hydrophobic base for the active-site groups. Sequence and structural comparisons of hemorrhagic and nonhemorrhagic P-I metalloproteinases from snake venoms revealed differences in several regions. In particular, the loop comprising residues 153 to 176 has marked structural differences between metalloproteinases with very different hemorrhagic activities. Because this region lies in close proximity to the active-site microenvironment, it may influence the interaction of these enzymes with physiologically relevant substrates in the extracellular matrix.

Aprendizado não-supervisionado em redes neurais pulsadas de base radial: um estudo da capacidade de agrupamento para a classificação de pixels

Redes neurais pulsadas - redes que utilizam uma codificação temporal da informação - têm despontado como uma promissora abordagem dentro do paradigma conexionista, emergente da ciência cognitiva. Um desses novos modelos é a rede neural pulsada com função de base radial, que é capaz de armazenar informação nos tempos de atraso axonais dos neurônios. Um algoritmo de aprendizado foi aplicado com sucesso nesta rede pulsada, que se mostrou capaz de mapear uma seqüência de pulsos de entrada em uma seqüência de pulsos de saída. Mais recentemente, um método baseado no uso de campos receptivos gaussianos foi proposto para codificar dados constantes em uma seqüência de pulsos temporais. Este método tornou possível a essa rede lidar com dados computacionais. O processo de aprendizado desta nova rede não se encontra plenamente compreendido e investigações mais profundas são necessárias para situar este modelo dentro do contexto do aprendizado de máquinas e também para estabelecer as habilidades e limitações desta rede. Este trabalho apresenta uma investigação desse novo classificador e um estudo de sua capacidade de agrupar dados em três dimensões, particularmente procurando estabelecer seus domínios de aplicação e horizontes no campo da visão computacional.

Nucleotide sequence, genomic organization and chromosome localization of 5S rDNA in two species of Curimatidae (Teleostei, Characiformes)

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

The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

Evidências moleculares dos padrões evolutivos e filogeográficos de populações de Astyanax paranae (Pisces : Characidae) com base em caracteres do DNA mitocondrial

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)