Origins of sequence diversity in the malaria vaccine candidate merozoite surface protein-2 (MSP-2) in Amazonian isolates of Plasmodium falciparum

The recent evolution of Plasmodium falciparum is at odds with the extensive polymorphism found in most genes coding for antigens. Here, we examined the patterns and putative mechanisms of sequence diversification in the merozoite surface protein-2 (MSP-2), a major malarial repetitive surface antigen. We compared the msp-2 gene sequences from closely related clones derived from sympatric parasite isolates from Brazilian Amazonia and used microsatellite typing to examine, in these same clones, the haplotype background of chromosome 2, where msp-2 is located. We found examples of msp-2 sequence rearrangements putatively created by nonreciprocal recombinational events, such as replication slippage and gene conversion, while maintaining the chromosome haplotype. We conclude that these nonreciprocal recombination events may represent a major source of antigenic diversity in MSP-2 in P falciparum populations with low rates of classical meiotic recombination. (c) 2006 Elsevier B.V. All rights reserved.

Identification of bacteria in endodontic infections by sequence analysis of 16S rDNA clone libraries

A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98 % minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65(.)2 %) belonged to the phylum Firmicutes of the Gram-positive bacteria, followed by Proteobacteria (10(.)9 %), Spirochaetes (4(.)3 %), Bacteroidetes (6(.)5 %), Actinobacteria (2(.)2 %) and Deferribacteres (2(.)2 %). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order Clostridiales, including a putative novel species of Mogibacterium. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa.

Joint rolling-horizon scheduling of materials processing and lot-sizing with sequence-dependent setups

A lot sizing and scheduling problem from a foundry is considered in which key materials are produced and then transformed into many products on a single machine. A mixed integer programming (MIP) model is developed, taking into account sequence-dependent setup costs and times, and then adapted for rolling horizon use. A relax-and-fix (RF) solution heuristic is proposed and computationally tested against a high-performance MIP solver. Three variants of local search are also developed to improve the RF method and tested. Finally the solutions are compared with those currently practiced at the foundry.

Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci

Background: the soil fungus Rhizoctonia solani anastomosis group 3 (AG-3) is an important pathogen of cultivated plants in the family Solanaceae. Isolates of R. solani AG-3 are taxonomically related based on the composition of cellular fatty acids, phylogenetic analysis of nuclear ribosomal DNA (rDNA) and beta-tubulin gene sequences, and somatic hyphal interactions. Despite the close genetic relationship among isolates of R. solani AG-3, field populations from potato and tobacco exhibit comparative differences in their disease biology, dispersal ecology, host specialization, genetic diversity and population structure. However, little information is available on how field populations of R. solani AG-3 on potato and tobacco are shaped by population genetic processes. In this study, two field populations of R. solani AG-3 from potato in North Carolina (NC) and the Northern USA; and two field populations from tobacco in NC and Southern Brazil were examined using sequence analysis of two cloned regions of nuclear DNA (pP42F and pP89).Results: Populations of R. solani AG-3 from potato were genetically diverse with a high frequency of heterozygosity, while limited or no genetic diversity was observed within the highly homozygous tobacco populations from NC and Brazil. Except for one isolate (TBR24), all NC and Brazilian isolates from tobacco shared the same alleles. No alleles were shared between potato and tobacco populations of R. solani AG-3, indicating no gene flow between them. To infer historical events that influenced current geographical patterns observed for populations of R. solani AG-3 from potato, we performed an analysis of molecular variance (AMOVA) and a nested clade analysis (NCA). Population differentiation was detected for locus pP89 (Phi(ST) = 0.257, significant at P < 0.05) but not for locus pP42F (Phi(ST) = 0.034, not significant). Results based on NCA of the pP89 locus suggest that historical restricted gene flow is a plausible explanation for the geographical association of clades. Coalescent-based simulations of genealogical relationships between populations of R. solani AG-3 from potato and tobacco were used to estimate the amount and directionality of historical migration patterns in time, and the ages of mutations of populations. Low rates of historical movement of genes were observed between the potato and tobacco populations of R. solani AG-3.Conclusion: the two sisters populations of the basidiomycete fungus R. solani AG-3 from potato and tobacco represent two genetically distinct and historically divergent lineages that have probably evolved within the range of their particular related Solanaceae hosts as sympatric species.

Synthesis and properties of branched polyethylene/high-density polyethylene blends using a homogeneous binary catalyst system composed of early and late transition metal complexes

Branched polyethylene/high-density polyethylene blends (BPE/HDPE) with a wide range of molecular weights, melt flow indexes (MFI), and intrinsic viscosity were prepared using the homogeneous binary catalyst system composed by Ni(alpha-diimine)Cl-2 (1) (alpha-diimine = 1,4-bis(2,6-diisopropylphenyl)-acenaphthenediimine) and {Tp(Ms*)} TiCl3 (2) (Tp(Ms*)=hydridobis(3-mesitylpyrazol-1-yl)(5-mesityl-pyrazol-1-yl)) activated with MAO and/or TIBA in hexane at two different polymerization temperatures (30 and 55 degreesC) and by varying the nickel loading molar fraction (x(Ni)). At all Temperatures, a non-linear correlation between the x(Ni) and the productivity was observed, suggesting the occurrence of a synergistic effect between the nickel and the titanium catalyst precursors, which is more pronounced at 55 degreesC. The molecular weight of the BPE/HDPE blends considerably decreases with increasing Al/M molar ratio. The melt flow indexes (MFI) and intrinsic viscosities (eta) are strongly affected by x(Ni), but the melting temperatures are nearly constant, 132 +/- 3 degreesC. Dynamic mechanical thermal analysis (DMTA) shows the formation of different polymeric materials where the stiffness vanes according, to the x(Ni) and temperature used in the polymerization reaction. The surface morphology of the BPE/HDPE blends studied by scanning electron microscopy (SEM) revealed a low miscibility between the PE phases resulting in the formation of a sandwich structure after etching with o-xylene.

Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups

Although the retrotransposon copia has been studied in the melanogaster group of Drosophila species, very little is known about copia dynamism and evolution in other groups. We analyzed the occurrence and heterogeneity of the copia 5' LTR-ULR partial sequence and their phylogenetic relationships in 24 species of the repleta group of Drosophila. PCR showed that copia occurs in 18 out of the 24 species evaluated. Sequencing was possible in only eight species. The sequences showed a low nucleotide diversity, which suggests selective constraints maintaining this regulatory region over evolutionary time. on the contrary, the low nucleotide divergence and the phylogenetic relationships between the D. willistoni/Zaprionus tuberculatus/melanogaster species subgroup suggest horizontal transfer. Sixteen transcription factor binding sites were identified in the LTR-ULR repleta and melanogaster consensus sequences. However, these motifs are not homologous, neither according to their position in the LTR-ULR sequences, nor according to their sequences. Taken together, the low motif homologies, the phylogenetic relationship and the great nucleotide divergence between the melanogaster and repleta copia sequences reinforce the hypothesis that there are two copia families.

Fmoc-POAC: [(9-fluorenylmethyloxycarbonyl)-2,2,5,5-tetramethylpyrrolidine-N-oxyl-3-amino-4-carboxylic acid]: A novel protected spin labeled beta-amino acid for peptide and protein chemistry

The stable free radical 2,2,6,6-tetramethylpiperidine-N-oxyl-4-amino-4-carboxylic acid (TOAC) is the only spin labeled amino acid that has been used to date to successfully label peptide sequences for structural studies. However, severe difficulty in coupling the subsequent amino acid has been the most serious shortcoming of this paramagnetic marker. This problem stems from the low nucleophilicity of TOAC's amine group towards the acylation reaction during peptide chain elongation. The present report introduces the alternative beta -amino acid 2,2,5,5-tetramethylpyrrolidine-N-oxyl-3-amino-4-carboxylic acid (POAC), potentially useful in peptide and protein chemistry. Investigations aimed at addressing the stereochemistry of this cyclic molecule through X-ray diffraction measurements of crystalline and bulk samples revealed that it consists only of the trans conformer. The 9-fluorenylmethyloxyearbonyl group (Fmoc) was chosen for temporary protection of the POAC amine function, allowing insertion of the probe at any position in a peptide sequence. The vasoactive octapeptide angiotensin II (AII, DRVYIHPF) was synthesized by replacing Pro(7) with POAC. The reaction of Fmoc-POAC with the peptidyl-resin occurred smoothly, and the coupling of the subsequent amino acid showed a much faster reaction when compared with TOAC. POAC(7)-AII was obtained in good yield, demonstrating that, in addition to TOAC, POAC is a convenient amino acid for the synthesis of spin labeled peptide analogues. The present findings open the possibility of a wide range of chemical and biological applications for this novel beta -amino acid derivative, including structural investigations involving its differentiated bend-inducing characteristics.

Low-temperature synthesis of single-phase Co7Sb2O12

Polycrystalline Co7Sb2O12 compounds have been synthesized by a chemical route, which is based on a modified polymeric precursor method. In order to study the physical properties of the samples, X-ray diffraction (XRD), thermal analyses (TG and DSC), infrared spectroscopy (IR), specific surface area (BET), and magnetization measurements were performed on these materials. Characterization through XRD revealed that the samples are single-phase after a heat-treatment at 1100degreesC for 2h, while the X-ray patterns of the samples heat-treated at lower temperatures revealed the presence of additional Bragg reflections belonging to the Co6Sb2O6 phase. These data were analyzed by means of Rietveld refinement and further analyze showed that Co7Sb2O12 displays an inverse spinel crystalline structure. In this structure, the Co2+ ions occupy the eight tetrahedral positions, and the sixteen octahedral positions are randomly occupied by the Sb5+ and Co2+ ions. IR studies disclosed two strong absorption bands, v(1) and v(2), in the expected spectral range for a spinel-type binary oxide with space group Fd3m. Exploratory studies concerning the magnetic properties indicated that this sample presents a spin-glass transition at T-f similar to 64 K. (C) 2004 Elsevier B.V. All rights reserved.

Numerical study of low-cost alternative orbits around the Moon

In this paper, we have investigated a region of direct stable orbits around the Moon, whose stability is related to the H2 Family of periodic orbits and to the quasi-periodic orbits that oscillate around them. The stability criteria adopted was that the path did not escape from the Moon during an integration period of 1000 days (remaining with negative two-body Moon-probe orbital energy during this period). Considering the three-dimensional four-body Sun-Earth-Moon-probe problem, we investigated the evolution of the size of the stability region, taking into account the eccentricity of the Earth's orbit, the eccentricity and inclination of the Moon's orbit, and the solar radiation pressure on the probe. We also investigated the evolution of the region's size and its location by varying the inclination of the probe's initial osculating orbit relative to the Moon's orbital plane between 0 degrees and 180 degrees. The size of the stability region diminishes; nevertheless, it remains significant for 0 <= i <= 25 degrees and 35 degrees <= i <= 45 degrees. The orbits of this region could be useful for missions by space vehicles that must remain in orbit around the Moon for periods of up to 1000 days, requiring low maintenance costs. (c) 2005 COSPAR. Published by Elsevier Ltd. All rights reserved.

Low genetic diversities of rabies virus populations within different hosts in Brazil

The low rates of nonsynonymous evolution observed in natural rabies virus (RABV) isolates are suggested to have arisen in association with the structural and functional constraints operating on the virus protein and the infection strategies employed by RABV within infected hosts to avoid strong selection by the immune response. In order to investigate the relationship between the genetic characteristics of RABV populations within hosts and the virus evolution, the present study examined the genetic heterogeneities of RABV populations within naturally infected dogs and foxes in Brazil, as well as those of bat RABV populations that were passaged once in suckling mice. Sequence analyses of complete RABV glycoprotein (G) genes showed that RABV populations within infected hosts were genetically highly homogeneous whether they were infected naturally or experimentally (nucleotide diversities of 0-0.95 x 10(-3)). In addition, amino acid mutations were randomly distributed over the entire region of the G protein, and the nonsynonymous/synonymous rate ratios (d(N)/d(S)) for the G protein gene were less than 1. These findings suggest that the low genetic diversities of RABV populations within hosts reflect the stabilizing selection operating on the virus, the infection strategies of the virus, and eventually, the evolutionary patterns of the virus. (C) 2009 Elsevier B.V. All rights reserved.

Genetic Algorithms (Binary and Real Codes) for the Optimisation of a Fermentation Process for Butanol Production

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

Solution approaches for the soft drink integrated production lot sizing and scheduling problem

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

Density functional theory study on the structural and electronic properties of low index rutile surfaces for TiO2/SnO2/TiO2 and SnO2/TiO2/SnO2 composite systems

The present study is concerned with the structural and electronic properties of the TiO2/SnO2/TiO2 and SnO2/TiO2/SnO2 composite systems. Periodic quantum mechanical method with density functional theory at the B3LYP level has been carried out. Relaxed surface energies, structural characteristics and electronic properties of the (I 10), (0 10), (10 1) and (00) low-index rutile surfaces for TiO2/SnO2/TiO2 and SnO2/TiO2/SnO2 models are studied. For, comparison purposes, the bare rutile TiO2 and SnO2 structures are also analyzed and compared with previous theoretical and experimental data. The calculated surface energy for both rutile TiO2 and SnO2 surfaces follows the sequence (110) < (010) < (101) < (001) and the energy increases as (010) < (101) < (110) < (001) and (010) approximate to (110) < (101) < (001) for SnO2/TiO2/SnO2 and TiO2/SnO2/TiO2 composite systems, respectively. SnO2/TiO2/SnO2 presents larger values of surface energy than the individual SnO2 and TiO2 metal oxides and the TiO2/SnO2/TiO2 system renders surface energy values of the same order that the TiO2 and lower than the SnO2. An analysis of the electronic structure of the TiO2/SnO2/TiO2 and SnO2/TiO2/SnO2 systems shows that the main characteristics of the upper part of the valence bands for all the studied surfaces are dominated by the external layers, i.e., by the TiO2 and the SnO2, respectively, and the topology of the lower part of the conduction bands looks like the core layers. There is an energy stabilization of both valence band top and conduction band bottom for (110) and (010) surfaces of the SnO2/TiO2/SnO2 composite system in relation to their core TiO2, whereas an opposite trend is found for the same surfaces of the TiO2/SnO2/TiO2 composite system in relation to the bare SnO2. The present theoretical results may explain the growth of TiO2@SnO2 bimorph composite nanotape.

On a moment problem associated with Chebyshev polynomials

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Using traditional heuristic algorithms on an initial genetic algorithm population applied to the transmission expansion planning problem

This paper analyses the impact of choosing good initial populations for genetic algorithms regarding convergence speed and final solution quality. Test problems were taken from complex electricity distribution network expansion planning. Constructive heuristic algorithms were used to generate good initial populations, particularly those used in resolving transmission network expansion planning. The results were compared to those found by a genetic algorithm with random initial populations. The results showed that an efficiently generated initial population led to better solutions being found in less time when applied to low complexity electricity distribution networks and better quality solutions for highly complex networks when compared to a genetic algorithm using random initial populations.