Taxonomic and Nomenclatural Changes in the Ocotea indecora Group (Lauraceae)

Following a recent revision of the Ocotea indecora (Schott) Meisn. ex Mez group (Lauraceae), some taxonomic and nomenclatural changes have been made. We present here the resulting synonyms, together with typifications, and one new combination. Seven new synonyms are proposed. The following seven names are lectotypified: Mespilodaphne indecora (Schott) Meisn. var. cannella Meisn.. M. indecora var. intermedia Meisn., M. indecora var. laxa Meisn., indecora var. stricta Meisn., O. complicata (Meisn.) Maz, O. elegans Mez, and O. fasciculata (Nees) Mez. Mespilodaphne leucophloea Nees & Mart, is transferred as O. leacophloea (Nees & Mart.) L. C. S. Assis & Mello-Silva.

Group I introns and associated homing endonuclease genes reveals a clinal structure for Porphyra spiralis var. amplifolia (Bangiales, Rhodophyta) along the Eastern coast of South America

Background: Group I introns are found in the nuclear small subunit ribosomal RNA gene (SSU rDNA) of some species of the genus Porphyra (Bangiales, Rhodophyta). Size polymorphisms in group I introns has been interpreted as the result of the degeneration of homing endonuclease genes (HEG) inserted in peripheral loops of intron paired elements. In this study, intron size polymorphisms were characterized for different Porphyra spiralis var. amplifolia (PSA) populations on the Southern Brazilian coast, and were used to infer genetic relationships and genetic structure of these PSA populations, in addition to cox2-3 and rbcL-S regions. Introns of different sizes were tested qualitatively for in vitro self-splicing. Results: Five intron size polymorphisms within 17 haplotypes were obtained from 80 individuals representing eight localities along the distribution of PSA in the Eastern coast of South America. In order to infer genetic structure and genetic relationships of PSA, these polymorphisms and haplotypes were used as markers for pairwise Fst analyses, Mantel's test and median joining network. The five cox2-3 haplotypes and the unique rbcL-S haplotype were used as markers for summary statistics, neutrality tests Tajima's D and Fu's Fs and for median joining network analyses. An event of demographic expansion from a population with low effective number, followed by a pattern of isolation by distance was obtained for PSA populations with the three analyses. In vitro experiments have shown that introns of different lengths were able to self-splice from pre-RNA transcripts. Conclusion: The findings indicated that degenerated HEGs are reminiscent of the presence of a full-length and functional HEG, once fixed for PSA populations. The cline of HEG degeneration determined the pattern of isolation by distance. Analyses with the other markers indicated an event of demographic expansion from a population with low effective number. The different degrees of degeneration of the HEG do not refrain intron self-splicing. To our knowledge, this was the first study to address intraspecific evolutionary history of a nuclear group I intron; to use nuclear, mitochondrial and chloroplast DNA for population level analyses of Porphyra; and intron size polymorphism as a marker for population genetics.

Systematic Revision of the granulatus Group of Urophonius Pocock, 1893 (Scorpiones, Bothriuridae), with Description of a New Species from Central Chile

A systematic revision of the granulatus group of the bothriurid scorpion genus Urophonius Pocock, 1893 is presented. Urophonius pizarroi, n. sp., a new species from central Chile, is described. Urophonius granulatus Pocock, 1898, Urophonius somuncura Acosta, 2003, and Urophonius tregualemuensis Cekalovic, 1981, are redescribed using modern standards. The adult males of U. somuncura and U. tregualemuensis are described for the first time. A distribution map and key to the species of the granulatus group are provided, along with a discussion of their phenology.

Genetic variability and natural selection at the ligand domain of the Duffy binding protein in brazilian Plasmodium vivax populations

Background: Plasmodium vivax malaria is a major public health challenge in Latin America, Asia and Oceania, with 130-435 million clinical cases per year worldwide. Invasion of host blood cells by P. vivax mainly depends on a type I membrane protein called Duffy binding protein (PvDBP). The erythrocyte-binding motif of PvDBP is a 170 amino-acid stretch located in its cysteine-rich region II (PvDBP(II)), which is the most variable segment of the protein. Methods: To test whether diversifying natural selection has shaped the nucleotide diversity of PvDBP(II) in Brazilian populations, this region was sequenced in 122 isolates from six different geographic areas. A Bayesian method was applied to test for the action of natural selection under a population genetic model that incorporates recombination. The analysis was integrated with a structural model of PvDBP(II), and T-and B-cell epitopes were localized on the 3-D structure. Results: The results suggest that: (i) recombination plays an important role in determining the haplotype structure of PvDBP(II), and (ii) PvDBP(II) appears to contain neutrally evolving codons as well as codons evolving under natural selection. Diversifying selection preferentially acts on sites identified as epitopes, particularly on amino acid residues 417, 419, and 424, which show strong linkage disequilibrium. Conclusions: This study shows that some polymorphisms of PvDBP(II) are present near the erythrocyte-binding domain and might serve to elude antibodies that inhibit cell invasion. Therefore, these polymorphisms should be taken into account when designing vaccines aimed at eliciting antibodies to inhibit erythrocyte invasion.

Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies

Background: The ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized. Results: We examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for similar to 40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance. Conclusion: These findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.

Flat tori, lattices and bounds for commutative group codes

We show that commutative group spherical codes in R(n), as introduced by D. Slepian, are directly related to flat tori and quotients of lattices. As consequence of this view, we derive new results on the geometry of these codes and an upper bound for their cardinality in terms of minimum distance and the maximum center density of lattices and general spherical packings in the half dimension of the code. This bound is tight in the sense it can be arbitrarily approached in any dimension. Examples of this approach and a comparison of this bound with Union and Rankin bounds for general spherical codes is also presented.

A flexible consensus scheme for multicriteria group decision making under linguistic assessments

The present paper proposes a flexible consensus scheme for group decision making, which allows one to obtain a consistent collective opinion, from information provided by each expert in terms of multigranular fuzzy estimates. It is based on a linguistic hierarchical model with multigranular sets of linguistic terms, and the choice of the most suitable set is a prerogative of each expert. From the human viewpoint, using such model is advantageous, since it permits each expert to utilize linguistic terms that reflect more adequately the level of uncertainty intrinsic to his evaluation. From the operational viewpoint, the advantage of using such model lies in the fact that it allows one to express the linguistic information in a unique domain, without losses of information, during the discussion process. The proposed consensus scheme supposes that the moderator can interfere in the discussion process in different ways. The intervention can be a request to any expert to update his opinion or can be the adjustment of the weight of each expert`s opinion. An optimal adjustment can be achieved through the execution of an optimization procedure that searches for the weights that maximize a corresponding soft consensus index. In order to demonstrate the usefulness of the presented consensus scheme, a technique for multicriteria analysis, based on fuzzy preference relation modeling, is utilized for solving a hypothetical enterprise strategy planning problem, generated with the use of the Balanced Scorecard methodology. (C) 2009 Elsevier Inc. All rights reserved.

Design and Characterization of a Biomimetic Piezoelectric Pump Inspired on Group Fish Swimming Effect

Flow pumps are important tools in several engineering areas, such as in the fields of bioengineering and thermal management solutions for electronic devices. Nowadays, many of the new flow pump principles are based on the use of piezoelectric actuators, which present some advantages such as miniaturization potential and lower noise generation. In previous work, authors presented a study of a novel pump configuration based on placing an oscillating bimorph piezoelectric actuator in water to generate flow. It was concluded that this oscillatory behavior (such as fish swimming) yields vortex interaction, generating flow rate due to the action and reaction principle. Thus, following this idea the objective of this work is to explore this oscillatory principle by studying the interaction among generated vortex from two bimorph piezoelectric actuators oscillating inside the same pump channel, which is similar to the interaction of vortex generated by frontal fish and posterior ones when they swim together in a group formation. It is shown that parallel-series configurations of bimorph piezoelectric actuators inside the same pump channel provide higher flow rates and pressure for liquid pumping than simple parallel-series arrangements of corresponding single piezoelectric pumps, respectively. The scope of this work includes structural simulations of bimorph piezoelectric actuators, fluid flow simulations, and prototype construction for result validation.

Molecular Identification and Phylogenetic Analysis of a Group 16SrI-B Phytoplasma Associated with Sugarcane Yellow Leaf Syndrome in Brazil

Yellow leaf syndrome was a serious problem in the beginning of the 1990s in Brazil, when yield losses were estimated to be around 50%. The disease is currently endemic, but it is considered potentially important. Previous studies have revealed only the presence of a luteovirus associated with the disease in Brazil. We report that a phytoplasma of 16SrI-B is also associated with this disease. This is the first demonstration of the presence of a group 16SrI-B phytoplasma in association with sugarcane yellow leaf in Brazil.

Summer squash: a new host of phytoplasm belonging to the 16SrIII group

Summer squash: a new host of phytoplasm belonging to the 16SrIII group In a commercial field located in the Vale do Ribeira, in the State of Sao Paulo, Brazil, plants of summer squash (Cucurbita pepo L.) exhibiting witches` broom and leaf deformation were observed. PCR assays demonstrated the presence of phytoplasma associated with diseased tissues. A phytoplasma belonging to the 16SrIII group was identified by PCR and RFLP analysis performed with five restriction enzymes. The present note is the first report of the presence of phytoplasma representative of the 16SrIII group in summer squash in Brazil.

An integrated molecular map of yellow passion fruit based on simultaneous maximum-likelihood estimation of linkage and linkage phases

The development of genetic maps for auto-incompatible species, such as the yellow passion fruit (Passiflora edulis Sims f.flavicarpa Deg.) is restricted due to the unfeasibility of obtaining traditional mapping populations based on inbred lines. For this reason, yellow passion fruit linkage maps were generally constructed using a strategy known as two-way pseudo-testeross, based on monoparental dominant markers segregating in a 1:1 fashion. Due to the lack of information from these markers in one of the parents, two individual (parental) maps were obtained. However, integration of these maps is essential, and biparental markers can be used for such an operation. The objective of our study was to construct an integrated molecular map for a full-sib population of yellow passion fruit combining different loci configuration generated from amplified fragment length polymorphisms (AFLPs) and microsatellite markers and using a novel approach based on simultaneous maximum-likelihood estimation of linkage and linkage phases, specially designed for outcrossing species. Of the total number of loci, approximate to 76%, 21%, 0.7%, and 2.3% did segregate in 1:1, 3:1, 1:2:1, and 1:1:1:1 ratios, respectively. Ten linkage groups (LGs) were established with a logarithm of the odds (LOD) score >= 5.0 assuming a recombination fraction : <= 0.35. On average, 24 markers were assigned per LG, representing a total map length of 1687 cM, with a marker density of 6.9 cM. No markers were placed as accessories on the map as was done with previously constructed individual maps.

Inheritance of growth habit detected by genetic linkage analysis using microsatellites in the common bean (Phaseolus vulgaris L.)

The genetic linkage map for the common bean (Phaseolus vulgaris L.) is a valuable tool for breeding programs. Breeders provide new cultivars that meet the requirements of farmers and consumers, such as seed color, seed size, maturity, and growth habit. A genetic study was conducted to examine the genetics behind certain qualitative traits. Growth habit is usually described as a recessive trait inherited by a single gene, and there is no consensus about the position of the locus. The aim of this study was to develop a new genetic linkage map using genic and genomic microsatellite markers and three morphological traits: growth habit, flower color, and pod tip shape. A mapping population consisting of 380 recombinant F10 lines was generated from IAC-UNA x CAL143. A total of 871 microsatellites were screened for polymorphisms among the parents, and a linkage map was obtained with 198 mapped microsatellites. The total map length was 1865.9 cM, and the average distance between markers was 9.4 cM. Flower color and pod tip shape were mapped and segregated at Mendelian ratios, as expected. The segregation ratio and linkage data analyses indicated that the determinacy growth habit was inherited as two independent and dominant genes, and a genetic model is proposed for this trait.

Genetic Diversity and a PCR-Based Method for Xanthomonas axonopodis Detection in Passion Fruit

Xanthomonas axonopodis pv. passiflorae causes bacterial spot in passion fruit. It attacks the purple and yellow passion fruit as well as the sweet passion fruit. The diversity of 87 isolates of pv. passiflorae collected from across 22 fruit orchards in Brazil was evaluated using molecular profiles and statistical procedures, including an unweighted pair-group method with arithmetical averages-based dendrogram, analysis of molecular variance (AMOVA), and an assigning test that provides information on genetic structure at the population level. Isolates from another eight pathovars were included in the molecular analyses and all were shown to have a distinct repetitive sequence-based polymerase chain reaction profile. Amplified fragment length polymorphism technique revealed considerable diversity among isolates of pv. passiflorae, and AMOVA showed that most of the variance (49.4%) was due to differences between localities. Cluster analysis revealed that most genotypic clusters were homogeneous and that variance was associated primarily with geographic origin. The disease adversely affects fruit production and may kill infected plants. A method for rapid diagnosis of the pathogen, even before the disease symptoms become evident, has value for producers. Here, a set of primers (Xapas) was designed by exploiting a single-nucleotide polymorphism between the sequences of the intergenic 16S-23S rRNA spacer region of the pathovars. Xapas was shown to effectively detect all pv. passiflorae isolates and is recommended for disease diagnosis in passion fruit orchards.

Mendelian inheritance, linkage and linkage disequilibrium in microsatellite loci of Copaifera langsdorffii Desf.

Copaifera langsdorffii is a Neotropical tree with wide distribution in the Brazilian Atlantic rain forest and savanna. Although eight microsatellite loci (SSR) were developed in 2000 and have been widely used since then, there is yet no information about their inheritance, linkage and linkage disequilibrium (LD). Through the analysis of 28 open-pollinated (OP) progenies, the SSR loci revealed Mendelian inheritance and independent assortment. Using these progenies, young and adult trees LD was mainly detected in OP progenies. Our results show clear evidence that the eight SSR loci can be used without restriction in genetic diversity, mating system and parentage analysis.

An unusual dimeric guaianolide with antiprotozoal activity and further sesquiterpene lactones from Eupatorium perfoliatum

The CH(2)Cl(2) extract of aerial parts of Eupatorium perfoliatum L. exhibits antiprotozoal activity under in vitro conditions, especially against Plasmodium falciparum (IC(50)=2.7 mu g/ml). The search for active compounds yielded seven sesquiterpene lactones: Four structurally similar guaianolides, one dimeric guaianolide, and two germacranolides. The guaianolides differ in the degree of oxidation at C-14, ranging from a hydroxyl group up to a free carboxylic acid. The dimeric guaianolide, structurally closely related to the monomers, displays an unusual type of interguaianolide linkage between C-14 and C-4. Except for the germacranolide euperfolitin, all STLs described here were hitherto unknown. Furthermore, the flavonoid aglycones eupafolin, hispidulin, patuletin, and kaempferol were identified in the extract, which, except for kaempferol, have not been described as constituents of E. perfoliatum before. The dimeric guaianolide was shown to be the most active constituent against Plasmodium falciparum (IC(50) = 2.0 mu M) and was less cytotoxic against rat skeletal myoblasts (IC(50) = 16.2 mu M, selectivity index of about 8). (C) 2011 Elsevier Ltd. All rights reserved.