Análise estrutural da deformação cenozóica na Bacia de Cumuruxatiba (BA)

The Cumuruxatiba basin is located at the southern coast State of Bahia in northeastern of Brazil. This basin was formed in distensional context, with rifting and subsequent thermal phase during Neocomian to late Cretaceous. At Cenozoic ages, the Abrolhos magmatism occurs in the basin with peaks during the Paleocene and Eocene. In this period, there was a kinematic inversion in the basin represented by folds related to reverse faults. Structural restoration of regional 2D seismic sections revealed that most of the deformation was concentrated at the beginning of the Cenozoic time with the peak at the Lower Eocene. The post-Eocene is marked by a decrease of strain rate to the present. The 3D structural modeling revealed a fold belt (trending EW to NE-SW) accommodating the deformation between the Royal Charlotte and Sulphur Minerva volcanic highs. The volcanic eruptions have caused a differential overburden on the borders of the basin. This acted as the trigger for halokinesis, as demonstrated by physical modeling in literature. Consequently, the deformation tends to be higher in the edges of the basin. The volcanic rocks occur mainly as concordant structures (sills) in the syn-tectonic sediment deposition showing a concomitant deformation. The isopach maps and diagrams of axis orientation of deformation revealed that most of the folds were activated and reactivated at different times during the Cenozoic. The folds exhibit diverse kinematic patterns over time as response to behavior of adjacent volcanic highs. These interpretations allied with information on the petroleum system of the basin are important in mapping the prospects for hydrocarbons

Aplicação da modelagem estrutural computacional direta na análise da geometria de falhas: exemplo da falha de Baixa Grande (Bacia Potiguar - NE do Brasil)

The Baixa grande fault is located on the edge of the S-SW Potiguar Rift. It limits the south part of Umbuzeiro Graben and the Apodi Graben. Although a number of studies have associated the complex deformation styles in the hanging wall of the Baixa Grande Fault with geometry and displacement variations, none have applied the modern computational techniques such as geometrical and kinematic validations to address this problem. This work proposes a geometric analysis of the Baixa Fault using seismic interpretation. The interpretation was made on 3D seismic data of the Baixa Grande fault using the software OpendTect (dGB Earth Sciences). It was also used direct structural modeling, such as Analog Direct Modeling know as Folding Vectors and, 2D and 3D Direct Computational Modeling. The Folding Vectors Modeling presented great similarity with the conventional structural seismic interpretations of the Baixa Grande Fault, thus, the conventional interpretation was validated geometrically. The 2D direct computational modeling was made on some sections of the 3D data of the Baixa Grande Fault on software Move (Midland Valley Ltd) using the horizon modeling tool. The modeling confirms the influence of fault geometry on the hanging wall. The Baixa Grande Fault ramp-flat-ramp geometry generates synform on the concave segments of the fault and antiform in the convex segments. On the fault region that does not have segments angle change, the beds are dislocated without deformation, and on the listric faults occur rollover. On the direct 3D computational modeling, structural attributes were obtained as horizons on the hanging wall of the main fault, after the simulation of several levels of deformation along the fault. The occurrence of structures that indicates shortening in this modeling, also indicates that the antiforms on the Baixa Grande Fault were influenced by fault geometry

Modelagem estrutural física de semigrábens ortogonais e oblíquos à distenção regional: influência da trama do embasamento e comparação com analógicos no nordeste brasileiro

The physical structural modeling tool is being increasingly used in geology to provide information about the evolutionary stages (nucleation, growth) and geometry of geological structures at various scales. During the simulations of extensional tectonics, modeling provides a better understanding of fault geometry and evolution of the tectonic-stratigraphic architecture of rift basins. In this study a sandbox type apparatus was used to study the nucleation and development of basins influenced by previous structures within the basement, variably oriented as regards to the main extensional axis. Two types of experiments were conducted in order to: (i) simulate the individual (independent) development of half-grabens oriented orthogonal or oblique to the extension direction; (ii) simulate the simultaneous development of such half-grabens, orthogonal or oblique to the extension direction. In both cases the same materials (sand mixed with gypsum) were used and the same boundary conditions were maintained. The results were compared with a natural analogue represented by the Rio do Peixe Basin (one of the eocretaceous interior basins of Northeast Brazil). The obtained models allowed to observe the development of segmented border faults with listric geometry, often forming relay ramps, and the development of inner basins faults that affect only the basal strata, like the ones observed in the seismic sections of the natural analogue. The results confirm the importance of basement tectonic heritage in the geometry of rift depocenters

Expression, purification and molecular analysis of the human ZNF706 protein

Background: The ZNF706 gene encodes a protein that belongs to the zinc finger family of proteins and was found to be highly expressed in laryngeal cancer, making the structure and function of ZNF706 worthy of investigation. In this study, we expressed and purified recombinant human ZNF706 that was suitable for structural analysis in Escherichia coli BL21(DH3). Findings. ZNF706 mRNA was extracted from a larynx tissue sample, and cDNA was ligated into a cloning vector using the TOPO method. ZNF706 protein was expressed according to the E. coli expression system procedures and was purified using a nickel-affinity column. The structural qualities of recombinant ZNF706 and quantification alpha, beta sheet, and other structures were obtained by spectroscopy of circular dichroism. ZNF706's structural modeling showed that it is composed of α-helices (28.3%), β-strands (19.4%), and turns (20.9%), in agreement with the spectral data from the dichroism analysis. Conclusions: We used circular dichroism and molecular modeling to examine the structure of ZNF706. The results suggest that human recombinant ZNF706 keeps its secondary structures and is appropriate for functional and structural studies. The method of expressing ZNF706 protein used in this study can be used to direct various functional and structural studies that will contribute to the understanding of its function as well as its relationship with other biological molecules and its putative role in carcinogenesis. © 2013 Colombo et al.; licensee BioMed Central Ltd.

Análise estática de um guindaste de torre, utilizando o método dos elementos finitos

The finite element method is of great importance for the development and analysis of a new product being designed or already on the market, and that requires some specific request or special application. The tower crane, being an essential equipment for modern construction to increase productivity and safety on construction sites, is required for many types of special applications day after day, in many kinds of work. Paying attention to this growing need for handling special projects for the tower crane, faced with the importance and necessity of development and improvement of knowledge in more accurate and practical calculation methods such as the finite element method , for greater agility and precision in the response to a new project. The tower crane is defined by the maximum load moment that it can act with a certain amount of load. The tower crane which will be analyzed in this work , for example, is a tower crane with a resulting capacity of 85 Metric Tons which are considered basic dimensions data of a fisical tower crane of a crane company Liebherr in Guaratinguetá . Thus, the project analysis will begin with the threedimensional representation of the crane lines with AutoCAD software , conversion of this model to the format accepted ANSYS Workbench and completion of 3D modeling of structural components in Design module ANSYS software. After structural modeling is completed, the simulation is performed in static simulation of ANSYS Workbench software mode. The standards will be adopted to DIN (Deutsches Institut für Normung) and EN 14439 (Europäische Normung 14439) and some NR 's related to specific security class of tower cranes, which will be referred throughout the work

Elementos de interoperabilidade na perspectiva da catalogação descritiva

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

Expression, purification and molecular analysis of the human ZNF706 protein

Background: The ZNF706 gene encodes a protein that belongs to the zinc finger family of proteins and was found to be highly expressed in laryngeal cancer, making the structure and function of ZNF706 worthy of investigation. In this study, we expressed and purified recombinant human ZNF706 that was suitable for structural analysis in Escherichia coli BL21(DH3). Findings: ZNF706 mRNA was extracted from a larynx tissue sample, and cDNA was ligated into a cloning vector using the TOPO method. ZNF706 protein was expressed according to the E. coli expression system procedures and was purified using a nickel-affinity column. The structural qualities of recombinant ZNF706 and quantification alpha, beta sheet, and other structures were obtained by spectroscopy of circular dichroism. ZNF706's structural modeling showed that it is composed of α-helices (28.3%), β-strands (19.4%), and turns (20.9%), in agreement with the spectral data from the dichroism analysis. Conclusions: We used circular dichroism and molecular modeling to examine the structure of ZNF706. The results suggest that human recombinant ZNF706 keeps its secondary structures and is appropriate for functional and structural studies. The method of expressing ZNF706 protein used in this study can be used to direct various functional and structural studies that will contribute to the understanding of its function as well as its relationship with other biological molecules and its putative role in carcinogenesis.

Hexose-6-phosphate dehydrogenase modulates 11beta-hydroxysteroid dehydrogenase type 1-dependent metabolism of 7-keto- and 7beta-hydroxy-neurosteroids

BACKGROUND: The role of 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1) in the regulation of energy metabolism and immune system by locally reactivating glucocorticoids has been extensively studied. Experiments determining initial rates of enzyme activity revealed that 11beta-HSD1 can catalyze both the reductase and the dehydrogenase reaction in cell lysates, whereas it predominantly catalyzes the reduction of cortisone to cortisol in intact cells that also express hexose-6-phosphate dehydrogenase (H6PDH), which provides cofactor NADPH. Besides its role in glucocorticoid metabolism, there is evidence that 11beta-HSD1 is involved in the metabolism of 7-keto- and 7-hydroxy-steroids; however the impact of H6PDH on this alternative function of 11beta-HSD1 has not been assessed. METHODOLOGY: We investigated the 11beta-HSD1-dependent metabolism of the neurosteroids 7-keto-, 7alpha-hydroxy- and 7beta-hydroxy-dehydroepiandrosterone (DHEA) and 7-keto- and 7beta-hydroxy-pregnenolone, respectively, in the absence or presence of H6PDH in intact cells. 3D-structural modeling was applied to study the binding of ligands in 11beta-HSD1. PRINCIPAL FINDINGS: We demonstrated that 11beta-HSD1 functions in a reversible way and efficiently catalyzed the interconversion of these 7-keto- and 7-hydroxy-neurosteroids in intact cells. In the presence of H6PDH, 11beta-HSD1 predominantly converted 7-keto-DHEA and 7-ketopregnenolone into their corresponding 7beta-hydroxy metabolites, indicating a role for H6PDH and 11beta-HSD1 in the local generation of 7beta-hydroxy-neurosteroids. 3D-structural modeling offered an explanation for the preferred formation of 7beta-hydroxy-neurosteroids. CONCLUSIONS: Our results from experiments determining the steady state concentrations of glucocorticoids or 7-oxygenated neurosteroids suggested that the equilibrium between cortisone and cortisol and between 7-keto- and 7-hydroxy-neurosteroids is regulated by 11beta-HSD1 and greatly depends on the coexpression with H6PDH. Thus, the impact of H6PDH on 11beta-HSD1 activity has to be considered for understanding both glucocorticoid and neurosteroid action in different tissues.

PHYLOGENETIC ANALYSES, GENE DOSAGE EFFECT AND SELECTION IN MEMBERS OF THE LATERAL BOUNDARY DOMAIN (LBD) GENES TRANSCRIPTION FACTOR FAMILY

Wood formation is an economically and environmentally important process and has played a significant role in the evolution of terrestrial plants. Despite its significance, the molecular underpinnings of the process are still poorly understood. We have previously shown that four Lateral Boundary Domain (LBD) transcription factors have important roles in the regulation of wood formation with two (LBD1 and LBD4) involved in secondary phloem and ray cell development and two (LBD15 and LBD18) in secondary xylem formation. Here, we used comparative phylogenetic analyses to test potential roles of the four LBD genes in the evolution of woodiness. We studied the copy number and variation in DNA and amino acid sequences of the four LBDs in a wide range of woody and herbaceous plant taxa with fully sequenced and annotated genomes. LBD1 showed the highest gene copy number across the studied species, and LBD1 gene copy number was strongly and significantly correlated with the level of ray seriation. The lianas, cucumber and grape, with multiseriate ray cells showed the highest gene copy number (12 and 11, respectively). Because lianas’ growth habit requires significant twisting and bending, the less lignified ray parenchyma cells likely facilitate stem flexibility and maintenance of xylem conductivity. We further demonstrate conservation of amino acids in the LBD18 protein sequences that are specific to woody taxa. Neutrality tests showed evidence for strong purifying selection on these gene regions across various orders, indicating adaptive convergent evolution of LBD18. Structural modeling demonstrates that the conserved amino acids have a significant impact on the tertiary protein structure and thus are likely of significant functional importance.

A novel FIP1L1-PDGFRA mutant destabilizing the inactive conformation of the kinase domain in chronic eosinophilic leukemia/hypereosinophilic syndrome

BACKGROUND: The Fip1-like-1-platelet-derived growth factor receptor alpha (FIP1L1-PDGFRA) gene fusion is a common cause of chronic eosinophilic leukemia (CEL)/hypereosinophilic syndrome (HES), and patients suffering from this particular subgroup of CEL/HES respond to low-dose imatinib therapy. However, some patients may develop imatinib resistance because of an acquired T674I mutation, which is believed to prevent drug binding through steric hindrance. METHODS: In an imatinib resistant FIP1L1-PDGFRA positive patient, we analyzed the molecular structure of the fusion gene and analyzed the effect of several kinase inhibitors on FIP1L1-PDGFRA-mediated proliferative responses in vitro. RESULTS: Sequencing of the FIP1L1-PDGFRA fusion gene revealed the occurrence of a S601P mutation, which is located within the nucleotide binding loop. In agreement with the clinical observations, imatinib did not inhibit the proliferation of S601P mutant FIP1L1-PDGFRA-transduced Ba/F3 cells. Moreover, sorafenib, which has been described to inhibit T674I mutant FIP1L1-PDGFRA, failed to block S601P mutant FIP1L1-PDGFRA. Structural modeling revealed that the newly identified S601P mutated form of PDGFRA destabilizes the inactive conformation of the kinase domain that is necessary to bind imatinib as well as sorafenib. CONCLUSIONS: We identified a novel mutation in FIP1L1-PDGFRA resulting in both imatinib and sorafenib resistance. The identification of novel drug-resistant FIP1L1-PDGFRA variants may help to develop the next generation of target-directed compounds for CEL/HES and other leukemias.

Understanding the role of argininosuccinate lyase transcript variants in the clinical and biochemical variability of the urea cycle disorder argininosuccinic aciduria

Argininosuccinic aciduria (ASA) is an autosomal recessive urea cycle disorder caused by deficiency of argininosuccinate lyase (ASL) with a wide clinical spectrum from asymptomatic to severe hyperammonemic neonatal onset life-threatening courses. We investigated the role of ASL transcript variants in the clinical and biochemical variability of ASA. Recombinant proteins for ASL wild type, mutant p.E189G, and the frequently occurring transcript variants with exon 2 or 7 deletions were (co-)expressed in human embryonic kidney 293T cells. We found that exon 2-deleted ASL forms a stable truncated protein with no relevant activity but a dose-dependent dominant negative effect on enzymatic activity after co-expression with wild type or mutant ASL, whereas exon 7-deleted ASL is unstable but seems to have, nevertheless, a dominant negative effect on mutant ASL. These findings were supported by structural modeling predictions for ASL heterotetramer/homotetramer formation. Illustrating the physiological relevance, the predominant occurrence of exon 7-deleted ASL was found in two patients who were both heterozygous for the ASL mutant p.E189G. Our results suggest that ASL transcripts can contribute to the highly variable phenotype in ASA patients if expressed at high levels. Especially, the exon 2-deleted ASL variant may form a heterotetramer with wild type or mutant ASL, causing markedly reduced ASL activity.

Whole-exome sequencing reveals a C-terminal germline variant in CEBPA-associated acute myeloid leukemia: 45-year follow-up of a large family.

Familial acute myeloid leukemia is rare and linked to germline mutations in RUNX1, GATA2 or CCAAT/enhancer binding protein-α (CEBPA). We re-evaluated a large family with acute myeloid leukemia originally seen at NIH in 1969. We utilized whole-exome sequencing to study this family, and conducted in silico bioinformatics analysis, protein structural modeling and laboratory experiments to assess the impact of the identified CEBPA Q311P mutation. Unlike most previously identified germline mutations in CEBPA, which were N-terminal frameshift mutations, we identified a novel Q311P variant that was located in the C-terminal bZip domain of C/EBPα. Protein structural modeling suggested that the Q311P mutation alters the ability of the CEBPA dimer to bind DNA. Electrophoretic mobility shift assays showed that the Q311P mutant had attenuated binding to DNA, as predicted by the protein modeling. Consistent with these findings, we found that the Q311P mutation has reduced transactivation, consistent with a loss-of-function mutation. From 45 years of follow-up, we observed incomplete penetrance (46%) of CEBPA Q311P. This study of a large multi-generational pedigree reveals that a germline mutation in the C-terminal bZip domain can alter the ability of C/EBP-α to bind DNA and reduces transactivation, leading to acute myeloid leukemia.

Beam Spectral Element with FRP Debonding

The behaviour of the interface between the FRP and the concrete is the key factor controlling debonding failures in FRP-strengthened RC structures. This defect can cause reductions in static strength, structural integrity and the change in the dynamic behavior of the structure. The adverse effect on the dynamic behavior of the defects can be utilized as an effective means for identifying and assessing both the location and size of debonding at its earliest stages. The presence of debonding changes the structural dynamic characteristics and might be traced in modal parameters, dynamic strain and wave patterns etc. Detection of minor local defects, as those origin of a future debonding, requires working at high frequencies so that the wavelength of the excited is small and sensitive enough to detect local damage. The development of a spectral element method gives a large potential in high-frequency structural modeling. In contrast to the conventional finite element, since inertial properties are modeled exactly few elements are necessary to capture very accurate solutions at the highest frequencies in large regions. A wide variety of spectral elements have been developed for structural members over finite and semi-infinite regions. The objective of this paper is to develop a Spectral Finite Element Model to efficiently capture the behavior of intermediate debonding of a FRP strengthened RC beam during wave-based diagnostics.

Conversion of cucumber linoleate 13-lipoxygenase to a 9-lipoxygenating species by site-directed mutagenesis

Multiple lipoxygenase sequence alignments and structural modeling of the enzyme/substrate interaction of the cucumber lipid body lipoxygenase suggested histidine 608 as the primary determinant of positional specificity. Replacement of this amino acid by a less-space-filling valine altered the positional specificity of this linoleate 13-lipoxygenase in favor of 9-lipoxygenation. These alterations may be explained by the fact that H608V mutation may demask the positively charged guanidino group of R758, which, in turn, may force an inverse head-to-tail orientation of the fatty acid substrate. The R758L+H608V double mutant exhibited a strongly reduced reaction rate and a random positional specificity. Trilinolein, which lacks free carboxylic groups, was oxygenated to the corresponding (13S)-hydro(pero)xy derivatives by both the wild-type enzyme and the linoleate 9-lipoxygenating H608V mutant. These data indicate the complete conversion of a linoleate 13-lipoxygenase to a 9-lipoxygenating species by a single point mutation. It is hypothesized that H608V exchange may alter the orientation of the substrate at the active site and/or its steric configuration in such a way that a stereospecific dioxygen insertion at C-9 may exclusively take place.

A family of lysozyme-like virulence factors in bacterial pathogens of plants and animals.

We describe a conserved family of bacterial gene products that includes the VirB1 virulence factor encoded by tumor-inducing plasmids of Agrobacterium spp., proteins involved in conjugative DNA transfer of broad-host-range bacterial plasmids, and gene products that may be involved in invasion by Shigella spp. and Salmonella enterica. Sequence analysis and structural modeling show that the proteins in this group are related to chicken egg white lysozyme and are likely to adopt a lysozyme-like structural fold. Based on their similarity to lysozyme, we predict that these proteins have glycosidase activity. Iterative data base searches with three conserved sequence motifs from this protein family detect a more distant relationship to bacterial and bacteriophage lytic transglycosylases, and goose egg white lysozyme. Two acidic residues in the VirB1 protein of Agrobacterium tumefaciens form a putative catalytic dyad, Each of these residues was changed into the corresponding amide by site-directed mutagenesis. Strains of A. tumefaciens that express mutated VirB1 proteins have a significantly reduced virulence. We hypothesize that many bacterial proteins involved in export of macromolecules belong to a widespread class of hydrolases and cleave beta-1,4-glycosidic bonds as part of their function.