Contrasting intra versus interspecies DNA sequence variation for representatives of the Batrachospermales (Rhodophyta): Insights from a DNA barcoding approach

Sixty-five accessions of the species-rich freshwater red algal order Batrachospermales were characterized through DNA sequencing of two regions: the mitochondrial cox1 gene (664 bp), which is proposed as the DNA barcode for red algae, and the UPA (universal plastid amplicon) marker (370 bp), which has been recently identified as a universally amplifying region of the plastid genome. upgma phenograms of both markers were consistent in their species-level relationships, although levels of sequence divergence were very different. Intraspecific variation of morphologically identified accessions for the cox1 gene ranged from 0 to 67 bp (divergences were highest for the two taxa with the greatest number of accessions; Batrachospermum helminthosum and Batrachospermum macrosporum); while in contrast, the more conserved universal plastid amplicon exhibited much lower intraspecific variation (generally 0-3 bp). Comparisons to previously published mitochondrial cox2-3 spacer sequences for B. helminthosum indicated that the cox1 gene and cox2-3 spacer were characterized by similar levels of sequence divergence, and phylogeographic patterns based on these two markers were consistent. The two taxa represented by the largest numbers of specimens (B. helminthosum and B. macrosporum) have cox1 intraspecific divergence values that are substantially higher than previously reported, but no morphological differences can be discerned at this time among the intraspecific groups revealed in the analyses. DNA barcode data, which are based on a short fragment of an organellar genome, need to be interpreted in conjunction with other taxonomic characters, and additional batrachospermalean taxa need to be analyzed in detail to be able to draw generalities regarding intraspecific variation in this order. Nevertheless, these analyses reveal a number of batrachospermalean taxa worthy of more detailed DNA barcode study, and it is predicted that such research will have a substantial effect on the taxonomy of species within the Batrachospermales in the future.

Expressed sequence tags from Atta laevigata and identification of candidate genes for the control of pest leaf-cutting ants.

Leafcutters are the highest evolved within Neotropical ants in the tribe Attini and model systems for studying caste formation, labor division and symbiosis with microorganisms. Some species of leafcutters are agricultural pests controlled by chemicals which affect other animals and accumulate in the environment. Aiming to provide genetic basis for the study of leafcutters and for the development of more specific and environmentally friendly methods for the control of pest leafcutters, we generated expressed sequence tag data from Atta laevigata, one of the pest ants with broad geographic distribution in South America. Results: The analysis of the expressed sequence tags allowed us to characterize 2,006 unique sequences in Atta laevigata. Sixteen of these genes had a high number of transcripts and are likely positively selected for high level of gene expression, being responsible for three basic biological functions: energy conservation through redox reactions in mitochondria; cytoskeleton and muscle structuring; regulation of gene expression and metabolism. Based on leafcutters lifestyle and reports of genes involved in key processes of other social insects, we identified 146 sequences potential targets for controlling pest leafcutters. The targets are responsible for antixenobiosis, development and longevity, immunity, resistance to pathogens, pheromone function, cell signaling, behavior, polysaccharide metabolism and arginine kynase activity. Conclusion: The generation and analysis of expressed sequence tags from Atta laevigata have provided important genetic basis for future studies on the biology of leaf-cutting ants and may contribute to the development of a more specific and environmentally friendly method for the control of agricultural pest leafcutters.

Alteration of soil properties through a weathering sequence as evaluated by spectral reflectance

In the study of physical, chemical, and mineralogical data related to the weathering of soils and the quantification of their properties, remote sensing constitutes an important technique that, in addition to conventional analyses, can contribute to soil survey. The objectives of this research were to characterize and differentiate soils developed from basaltic rocks that occur in the Parana state, Brazil and to quantify soil properties based on their spectral reflectance. These observations were used to verify the relationship between the soils and reflectance with regard to weathering, organic matter (OM), and forms of Fe. From the least to the most weathered soil, we used a Typic Argiudoll (Reddish Brunizem), Rhodudalf (Terra Roxa Estruturada), and Rhodic Hapludox (Very Dark Red Latosol). The spectral reflectances between 400 and 2500 nm were obtained in the laboratory from soil samples collected at two depth increments, 0- to 20- and 40- to 60-cm, using an Infra Red Intelligent Spectroradiometer (IRIS). Correlation, regression, and discriminant estimates were used in analyzing the soil and spectral data. Results of this study indicated that soils could be separated at the soil-type level based on reflectance intensity in various absorption bands. Soil collected in the 40- to 60-cm depth appeared to have higher reflectance intensities than those from the 0- to 20-cm depth. Removal of OM from soil samples promoted higher reflectance intensity in the entire spectrum. Amorphous and crystalline Fe influenced reflectance differently. Weathering of basaltic soils was correlated with alterations in the reflectance intensities and absorption features of the spectral curves. Multivariate analysis demonstrated that this technique was efficient in the estimation of clay, silt, kaolinite, crystalline Fe, amorphous Fe, and Mg through the use of reflected energy of the soils.

Influence of nearest-neighbor Coulomb interactions on the phase diagram of the ferromagnetic Kondo model

The influence of a nearest-neighbor Coulomb repulsion of strength V on the properties of the ferromagnetic Kondo model is analyzed using computational techniques. The Hamiltonian studied here is defined on a chain using localized S = 1/2 spins, and one orbital per site. Special emphasis is given to the influence of the Coulomb repulsion on the regions of phase separation recently discovered in this family of models, as well as on the double-exchange-induced ferromagnetic ground state. When phase separation dominates at V= 0, the Coulomb interaction breaks the large domains of the two competing phases into small islands of one phase embedded into the other. This is in agreement with several experimental results, as discussed in the text. Vestiges of the original phase separation regime are found in the spin structure factor as incommensurate peaks, even at large values of V. In the ferromagnetic regime close to density n = 0.5, the Coulomb interaction induces tendencies to charge ordering without altering the fully polarized character of the state. This regime of charge-ordered ferromagnetism may be related with experimental observations of a similar phase by Chen and Cheong [Phys. Rev. Lett. 76, 4042 (1996)]. Our results reinforce the recently introduced notion [see, e.g., S. Yunoki et al., Phys. Rev. Lett. 80, 845 (1998)] that in realistic models for manganites analyzed with unbiased many-body techniques, the ground state properties arise from a competition between ferromagnetism and phase-separation - charge-ordering tendencies. ©1999 The American Physical Society.

Nucleotide sequence of 5S rDNA and localization of the ribosomal RNA genes to metaphase chromosomes of the Tilapiine cichlid fish, Oreochromis niloticus

In this study, we report the cloning and nucleotide sequence of PCR-generated 5S rDNA from the Tilapiine cichlid fish, Oreochromis niloticus. Two types of 5S rDNA were detected that differed by insertions and/or deletions and base substitutions within the non-transcribed spacer (NTS). Two 5S rDNA loci were observed by fluorescent in situ hybridization (FISH) in metaphase spreads of tilapia chromosomes. FISH using an 18S rDNA probe and silver nitrate sequential staining of 5S-FISH slides showed three 18S rDNA loci that are not syntenic to the 5S rDNA loci.

Short-chain di-ureasil ormolytes doped with potassium triflate: Phase diagram and conductivity behavior

Di-urea cross-linked poly(oxyethylene)/siloxane hybrids, synthesized by the sol-gel process and containing a wide concentration range of potassium triflate, KCF3SO3, have been analyzed by x-ray diffraction and differential scanning calorimetry. The pseudo-phase diagram proposed has been taken into account in the interpretation of the complex impedance measurements. The xerogels prepared are obtained as transparent, thin monoliths. At room temperature the highest conductivity found was 2 × 10-6 Ω-1 cm-1.

Affinities of the Saw-billed Hermit (Ramphodon naevius) determined by cytochrome-b sequence data

We sequenced 912 bp of the cytochrome-b gene to examine phylogenetic relationships of the enigmatic Saw-billed Hermit (Ramphodon naevius), a large and distinctive hummingbird endemic to tropical forests of southeastern Brazil. Bootstrapped maximum parsimony and maximum likelihood analyses of sequence data from 11 hummingbirds and several outgroups (two swifts, one goatsucker) support: (a) monophyly of the traditional hermit (Phaethornithinae) and nonhermit (Trochilinae) subfamilies, (b) placement of Ramphodon among hermits, and (c) a sister relationship between Ramphodon and an exemplar of the widespread polytypic hermit genus Glaucis. The association of Ramphodon with derived hermit lineages is concordant with subfamilial patterns of wing anatomy and nest architecture. However, the unusual plumages (striped underparts) and male bills (long, serrated, hooked) shared by Ramphodon and the Tooth-billed Hummingbird (Androdon aequatorialis) appear to have evolved within separate hermit and nonhermit tooth-billed clades. Distal placement of the Ramphodon-Glaucis clade within hermits implies that even distinctive Brazilian endemics such as Ramphodon are derived forms that evolved relatively recently.

The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) ≈500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) wide-spread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications.

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.

Study of a hybrid solid oxide fuel cell: Energetic analysis and sankey diagram

In this paper a hybrid solid oxide fuel cell (SOFC) system is analyzed. This system applies a combined cycle utilizing gas turbine associated to a SOFC for rational decentralized energy production. Initially the relative concepts about the fuel cell are presented, followed by some chemical and technical informations such as the change of Gibbs free energy in isothermal fuel oxidation (or combustion) directly into electricity. This represents a very high fraction of the lower heating value (LHV) of a hydrocarbon fuel. In the next step a methodology for the study of SOFC associated with a gas turbine system is developed, considering the electricity and steam production for a hospital, as regard to the Brazilian conditions. This methodology is applied to energetic analysis. Natural gas is considered as a fuel. In conclusion, it is shown by a Sankey Diagram that the hybrid SOFC system may be an excellent opportunity to strengthen the decentralized energy production in Brazil. It is necessary to consider that the cogeneration in this version also is a sensible alternative from the technical point of view, demanding special methods of design, equipment selection and mainly of the contractual deals associated to electricity and fuel supply.

Frequency-adjustable positive sequence detector for power conditioning applications

This paper proposes a novel and simple positive sequence detector (PSD), which is inherently self-adjustable to fundamental frequency deviations by means of a software-based PLL (Phase Locked Loop). Since the proposed positive sequence detector is not based on Fortescue's classical decomposition and no special input filtering is needed, its dynamic response may be as fast as one fundamental cycle. The digital PLL ensures that the positive sequence components can be calculated even under distorted waveform conditions and fundamental frequency deviations. For the purpose of validating the proposed models, the positive sequence detector has been implemented in a PC-based Power Quality Monitor and experimental results illustrate its good performance. The PSD algorithm has also been evaluated in the control loop of a Series Active Filter and simulation results demonstrate its effectiveness in a closed-loop system. Moreover, considering single-phase applications, this paper also proposes a general single-phase PLL and a Fundamental Wave Detector (FWD) immune to frequency variations and waveform distortions. © 2005 IEEE.

Sorption isotherm, glass transitions and state diagram for freeze-dried plum skin and pulp

Differential scanning calorimetry (DSC) was used to determine phase transitions of freeze-dried plums. Samples at low and intermediate moisture contents, were conditioned by adsorption at various water activities (0.11≤a w≤0.90) at 25°C, whereas in the high moisture content region (a w>0.90) samples were obtained by direct water addition, with the resulting sorption isotherm being well described by the Guggenheim-Anderson-deBoer (GAB) model. Freeze-dried samples of separated plum skin and pulp were also analysed. At a w≤0.75, two glass transitions were visible, with the glass transition temperature (T g) decreasing with increasing a w due to the water plasticising effect. The first T g was attributed to the matrix formed by sugars and water. The second one, less visible and less plasticised by water, was probably due to macromolecules of the fruit pulp. The Gordon-Taylor model represented satisfactorily the matrix glass transition curve for a w≤0.90. In the higher moisture content range T g remained practically constant around T g′ (-57.5°C). Analysis of the glass transition curve and the sorption isotherm indicated that stability at a temperature of 25°C, would be attained by freeze dried plum at a water activity of 0.04, corresponding to a moisture content of 12.9% (dry basis). © 2006 SAGE Publications.

Taenia solium and Taenia saginata: Identification of sequence characterized amplified region (SCAR) markers

Cysticercosis is one of the most important zoonosis, not only because of the effects on animal health and its economic consequences, but also due to the serious danger it poses to humans. The two main parasites involved in the taeniasis-cysticercosis complex in Brazil are Taenia saginata and Taenia solium. Differentiating between these two parasites is important both for disease control and for epidemiological studies. The purpose of this work was to identify genetic markers that could be used to differentiate these parasites. Out of 120 oligonucleotide decamers tested in random amplified polymorphic DNA (RAPD) assays, 107 were shown to discriminate between the two species of Taenia. Twenty-one DNA fragments that were specific for each species of Taenia were chosen for DNA cloning and sequencing. Seven RAPD markers were converted into sequence characterized amplified region (SCAR) markers with two specific for T. saginata and five specific for T. solium as shown by agarose gel electrophoresis. These markers were developed as potential tools to differentiate T. solium from T. saginata in epidemiological studies. © 2007 Elsevier Inc. All rights reserved.

Mitochondrial genome sequence of the Brazilian luminescent click beetle Pyrophorus divergens (Coleoptera: Elateridae): Mitochondrial genes utility to investigate the evolutionary history of Coleoptera and its bioluminescence

The Coleoptera order is the richest group among Metazoa, but its phylogenetics remains incompletely understood. Among Coleoptera, bioluminescence is found within the Elateroidea, but the evolution of this character remains a mystery. Mitochondrial DNA has been used extensively to reconstruct phylogenetic relationships, however, the evolution of a single gene does not always correspond to the species evolutionary history and the molecular marker choice is a key step in this type of analysis. To create a solid basis to better understand the evolutionary history of Coleoptera and its bioluminescence, we sequenced and comparatively analyzed the mitochondrial genome of the Brazilian luminescent click beetle Pyrophorus divergens (Coleoptera: Elateridae). © 2007 Elsevier B.V. All rights reserved.