Genetic Diversity on the Integrase Region of the pol Gene among HIV Type 1-Infected Patients Naive for Integrase Inhibitors in Sao Paulo City, Brazil

The presence of mutations associated with integrase inhibitor (INI) resistance among INI-naive patients may play an important clinical role in the use of those drugs Samples from 76 HIV-1-infected subjects naive to INIs were submitted to direct sequencing. No differences were found between naive (25%) subjects and subjects on HAART (75%). No primary mutation associated with raltegravir or elvitegravir resistance was found. However, 78% of sequences showed at least one accessory mutation associated with resistance. The analysis of the 76 IN sequences showed a high polymorphic level on this region among Brazilian HIV-1-infected subjects, including a high prevalence of aa substitutions related to INI resistance. The impact of these findings remains unclear and further studies are necessary to address these questions.

Diversity of free-living marine nematodes (Enoplida) from Baja California assessed by integrative taxonomy

We used morphological and molecular approaches to evaluate the diversity of free-living marine nematodes (order Enoplida) at four coastal sites in the Gulf of California and three on the Pacific coast of Baja California, Mexico. We identified 22 morphological species belonging to six families, of which Thoracostomopsidae and Oncholaimidae were the most diverse. The genus Mesacanthion (Thoracostomopsidae) was the most widespread and diverse. Five allopatric species, genetically and morphologically differentiated, were found in two localities in the Gulf of California (M. sp1 and M. sp2) and three in the Pacific coast (M. sp3, M. sp4 and M. sp5). Overall, we produced 19 and 20 sequences for the 18S and 28S genes, respectively. Neither gene displayed intraspecific polymorphisms, which allowed us to establish that some morphological variation was likely either ontogenetic or due to phenotypic plasticity. Although 18S and 28S phylogenies were topologically congruent (incongruence length difference test, P > 0.05), divergences between species were much higher in the 28S gene. Moreover, this gene possessed a stronger phylogenetic signal to resolve relationships involving Rhabdodemania and Bathylaimus. On the other hand, the close relationship of Pareurystomina (Enchilidiidae) with oncholaimids warrants further study. The 28S sequences (D2D3 domain) may be better suited for DNA barcoding of marine nematodes than those from the 18S rDNA, particularly for differentiating closely related or cryptic species. Finally, our results underline the relevance of adopting an integrative approach encompassing morphological and molecular analyses to improve the assessment of marine nematode diversity and advance their taxonomy.

Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove

Mangrove sediments are anaerobic ecosystems rich in organic matter. This environment is optimal for anaerobic microorganisms, such as sulphate-reducing bacteria and methanogenic archaea, which are responsible for nutrient cycling. In this study, the diversity of these two functional guilds was evaluated in a pristine mangrove forest using denaturing gradient gel electrophoresis (DGGE) and clone library sequencing in a 50 cm vertical profile sampled every 5.0 cm. DGGE profiles indicated that both groups presented higher richness in shallow samples (0-30 cm) with a steep decrease in richness beyond that depth. According to redundancy analysis, this alteration significantly correlated with a decrease in the amount of organic matter. Clone library sequencing indicated that depth had a strong effect on the selection of dissimilatory sulphate reductase (dsrB) operational taxonomic units (OTUs), as indicated by the small number of shared OTUs found in shallow (0.0 cm) and deep (40.0 cm) libraries. On the other hand, methyl coenzyme-M reductase (mcrA) libraries indicated that most of the OTUs found in the shallow library were present in the deep library. These results show that these two guilds co-exist in these mangrove sediments and indicate important roles for these organisms in nutrient cycling within this ecosystem.

Economic viability of doses and split-applications of nitrogen fertilization in corn crop in a eutrophic Red Latosol

Nitrogen is the nutrient that is most absorbed by the corn crop, with the most complex management, and has the highest share on the cost of corn production. The objective of this work was to evaluate the economic viability of different rates and split-applications of nitrogen fertilization, as such as urea, in the corn crop in a eutrophic Red Latosol (Oxisol). The study was carried out in the Experimental Station of the Regional Pole of the Sao Paulo Northwest Agribusiness Development (APTA), in Votuporanga, State of Sao Paulo, Brazil. The experimental design was randomized complete blocks with nine treatments and four replications, consisting of five N rates: 0, 55, 95, 135 and 175 kg ha(-1), 15 kg ha-l applied in the seeding and the remainder in top dressing: 40 and 80 kg ha(-1) N at forty days after seeding (DAS), or 1/2 + 1/2 at 20 and 40 DAS; 120 kg ha-1 N split in 1/2 + 1/2 or 1/3 + 1/3 + 1/3 at 20, 40 or 60 DAS; 160 kg ha(-1) N split in 1/4 + 3/8 + 3/8 or 114 + 1/4 + 1/4 + 1/4 at 20, 40, 60 and 80 DAS. The application of 135 kg ha-l of N split in three times provided the best benefit/cost ratio. The non-application of N provided the lowest economic return, proving to be unviable.

The use of contingent valuation for evaluating protected areas in the developing world: Economic valuation of Morro do Diabo State Park, Atlantic Rainforest, Sao Paulo State (Brazil)

The Brazilian Atlantic Rainforest is internationally recognised as one of the most biodiverse and threatened tropical forests in the world [Myers, N., Mittermeier, R.A., Mittermeier, C.G., da Fonseca, G.A.B., Kent, J., 2000. Biodiversity hotspots for conservation priorities. Nature 403, 853-858]. The Seasonal Semi-Deciduous Forest is among the most fragmented and threatened biomes of the Atlantic Rainforest Domain. The largest remnant of this biome (35,000 ha) is protected by the Morro do Diabo State Park (MDSP), situated in the area known as the Pontal do Paranapanema, in Sao Paulo State, Brazil. Despite its environmental importance, the park is under political, economic and demographic pressure. The main aim of our research was to estimate the population`s willingness to pay (WTP) for the conservation of MDSP and for the Atlantic Rainforest`s remnants in Sao Paulo State as a whole, by means of the contingent valuation method (CVM). The results featured a high incidence of null WTP and of protest votes. Nevertheless, the population is willing to pay US$ 2,113,548.00/year (R$ 7,080,385.00/year) for the conservation of the MDSP (use and existence values), or US$ 60.39 ha/year (R$ 202.30/ha/year). The results indicate that the preservation value is strongly associated to the population`s ability to pay, increasing with income levels. Qualitative research questions showed that the population considers protected areas to be very important. Still, the valuation of MDSP revealed a gap between the government budget allotted to the park and the value assigned to the area by the public. (C) 2007 Elsevier B.V. All rights reserved.

Evaluation of the microbial diversity in a horizontal-flow anaerobic immobilized biomass reactor treating linear alkylbenzene sulfonate

The purpose of this work was to assess the degradation of linear alkylbenzene sulfonate (LAS) in a horizontal-flow anaerobic immobilized biomass (HAIB) reactor. The reactor was filled with polyurethane foam where the sludge from a sanitary sewage treatment was immobilized. The hydraulic detention time (HDT) used in the experiments was of 12 h. The reactor was fed with synthetic substrate (410 mg l(-1) of meat extract, 115 mg l(-1) of starch, 80 mg l(-1) of saccharose, 320 mg l(-1) of sodium bicarbonate and 5 ml l(-1)of salt solution) in the following stages of operation: SI-synthetic substrate, SII-synthetic substrate with 7 mg l(-1) of LAS, SIII-synthetic substrate with 14 mg l(-1) of LAS and SIV-synthetic substrate containing yeast extract (substituting meat extract) and 14 mg l(-1) of LAS, without starch. At the end of the experiment (313 days) a degradation of similar to 35% of LAS was achieved. The higher the concentration of LAS, the greater the amount of foam for its adsorption. This is necessary because the isotherm of LAS adsorption in the foam is linear for the studied concentrations (2 to 50 mg l(-1)). Microscopic analyses of the biofilm revealed diverse microbial morphologies, while Denaturing Gradient Gel Eletrophoresis (DGGE) profiling showed variations in the population of total bacteria and sulphate-reducing bacteria (SRB). The 16S rRNA gene sequencing and phylogenetic analyses revealed that the members of the order Clostridiales were the major components of the bacterial community in the last reactor operation step.

Using economic instruments to address emissions from air transport in the European Union

Air transport has become a vital component of the global economy. However, greenhouse-gas emissions from this sector have a significant impact on global climate, being responsible for over 3.5% of all anthropogenic radiative forcing. Also, the accrued visibility of aircraft emissions greatly affects the public image of the industry. In this context, incentive-based regulations, in the form of price or quantity controls, can be envisaged as alternatives to mitigate these emissions. The use of environmental charges in air transport, and the inclusion of the sector in the European Union Emissions Trading Scheme (EU ETS), are considered under a range of scenarios. The impacts of these measures on demand are estimated, and results suggest that they are likely to be minimal-mainly due to the high willingness to pay for air transport. In particular, in the EU ETS scenario currently favoured by the EU, demand reductions are less than 2%. This may not be true in the longer run, for short trips, or if future caps become more stringent. Furthermore, given current estimates of the social Cost Of CO2 as well as typical EU ETS prices, supply-side abatement would be too costly to be encouraged by these policies in the short term. The magnitude of aviation CO2 emissions in the EU is estimated, both in physical and monetary terms; the results are consistent with Eurocontrol estimates and, for the EU-25, the total social cost of these emissions represents only 0.03% of the region`s GDP. It is concluded that the use of multisector policies, such as the EU ETS, is unsuitable for curbing emissions from air transport, and that stringent emission charges or an isolated ETS would be better instruments. However, the inclusion of aviation in the EU ETS has advantages under target-oriented post-2012 scenarios, such as policy-costs dilution, certainty in reductions, and flexibility in abatement allocation. This solution is also attractive to airlines, as it would improve their public image but require virtually no reduction of their own emissions, as they would be fully capable of passing on policy costs to their customers.

Economic design of an X chart for short-run production

The aim of this paper is to present an economical design of an X chart for a short-run production. The process mean starts equal to mu(0) (in-control, State I) and in a random time it shifts to mu(1) > mu(0) (out-of-control, State II). The monitoring procedure consists of inspecting a single item at every m produced ones. If the measurement of the quality characteristic does not meet the control limits, the process is stopped, adjusted, and additional (r - 1) items are inspected retrospectively. The probabilistic model was developed considering only shifts in the process mean. A direct search technique is applied to find the optimum parameters which minimizes the expected cost function. Numerical examples illustrate the proposed procedure. (C) 2009 Elsevier B.V. All rights reserved.

Lepidopteran larva consumption of soybean foliage: basis for developing multiple-species economic thresholds for pest management decisions

BACKGROUND: Defoliation by Anticarsia gemmatalis (Hubner), Pseudoplusia includens (Walker), Spodoptera eridania (Cramer), S. cosmioides (Walker) and S. frugiperda (JE Smith) (Lepidoptera: Noctuidae) was evaluated in four soybean genotypes. A multiple-species economic threshold (ET), based upon the species` feeding capacity, is proposed with the aim of improving growers` management decisions on when to initiate control measures for the species complex. RESULTS: Consumption by A. gemmatalis, S. cosmioides or S. eridania on different genotypes was similar. The highest consumption of P. includens was 92.7 cm(2) on Codetec 219RR; that of S. frugiperda was 118 cm(2) on Codetec 219RR and 115.1 cm(2) on MSoy 8787RR. The insect injury equivalent for S. cosmoides, calculated on the basis of insect consumption, was double the standard consumption by A. gemmatalis, and statistically different from the other species tested, which were similar to each other. CONCLUSIONS: As S. cosmioides always defoliated nearly twice the leaf area of the other species, the injury equivalent would be 2 for this lepidopteran species and 1 for the other species. The recommended multiple-species ET to trigger the beginning of insect control would then be 20 insect equivalents per linear metre. (C) 2010 Society of Chemical Industry

Transmission efficiency of Xylella fastidiosa by sharpshooters (Hemiptera : Cicadellidae) in coffee and citrus

Xylella fastidiosa (Wells, Raju, Hung, Weisburg, Mandelco-Paul, and Brenner) is a bacteria] pathogen transmitted by several Sharpshooters in two tribes of Cicadellinae (Proconiini and Cicadellini). Here, we compared the transmission efficiency of X. fastidiosa in coffee (Coffea arabica L) and citrus [Citrus sinensis (L) Osbeck] by Cicadellini [Bucephalogonia xanthophis (Berg) and Dilobopterus costalimai Young] and Proconiini [Homalodisca ignorata Melichar and Oncometopia facialis (Signoret) I sharpshooters that Occur in both crops. At different seasons, healthy adults of each species were submitted to a 48-h acquisition access period on citrus or coffee source plants infected with X. fastidiosa isolates that cause Citrus variegated chlorosis (CVC) and Coffee leaf scorch (CLS), respectively, and then confined on healthy seedlings of the corresponding host plant for a 48-h inoculation access period. No significant effect of inoculation season was observed when comparing infection rates of citrus or coffee plants inoculated by vectors at different times of the year. In Citrus, the transmission rate by single insects was significantly higher for H. ignorata (30%) in relation to B. xanthophis (5%) and O. facialis (1.1%) but there was no difference among vector species in coffee, whose transmission rates ranged from 1.2 to 7.2%. Comparing host plants, H. ignorata was more effective in transmitting X. fastidiosa to citrus (30%) in relation to coffee (2.2%), whereas the other vectors transmitted the bacterium to both hosts with similar efficiencies. Despite these variations. vector efficiency in coffee and Citrus is lower than that reported in other hosts.

Economic feasibility of cowpea irrigation in Piaui State

The objective of this work was to evaluate the economic feasibility of cowpea irrigation in Piaui State Brazil. Water balances were carried out on a daily basis using the Thornthwaite and Mather (1955) method, for 165 sites, considering twelve sowings dates and available water capacity in the soil of 20, 40 and 60 mm. The net revenues were estimated with a probability of occurrence of 75%, later being spatialized to Piaui State. Cowpea irrigation was shown to economically viable for all sowing dates, irrespective of the available water capacity. Net revenues varied among several regions of the State, in function of the sowing date and available water capacity in the soil. Considering a planning strategy for Piaui State, sowing on February, I was shown to be most favorable, because it enabled higher net revenue values, covering larger areas of the State.

Fauna of plant-parasitic nematodes in natural and cultivated areas of the Amazon forest, Mato Grosso State, Brazil

The aim of this work was to study the diversity of the fauna of plant-parasitic nematodes in preserved areas of the Amazon forest, Mato Grosso state (MT), and to assess the effect of agricultural land use on plant-parasitic nematode communities. Soil and root samples were collected in each location in the late spring during the rainy season of 2005, in two areas of primary vegetation in Nova Maringa (Northwest) and Guaranta do Norte (North) and two adjacent areas planted with teak trees (Tectona grandis) and pasture (Brachiaria brizantha). Four-teen taxa of plant-parasitic nematodes were identified at species level: Discocriconemella degrissei, D. limitanea, Dolichodorus minor, Helicotylenchus erythrinae, H. pseudorobustus, Meloidogyne exigua, M javanica, Mesocriconema ornata, Paratrichodorus minor, Pratylenchus loosi, P zeae, Rotylenchus caudaphasmidius, Xiphinema ensiculiferum and X luci (for the first report of this in Brazil) and five at genus level (Atalodera sp., Hemicriconemoides sp., Meloidogyne sp., Paratylenchus sp., and Trophotylenchulus sp). These taxa, mainly those from primary vegetation, belong to families with different parasitic behavior, probably due to great plant diversity in the Amazon forest. Comparison between the two preserved areas revealed low index of similarity, as a consequence of the endemic flora in the Amazon forest, and no similarity was observed between preserved native vegetation and adjacent cultivated areas, demonstrating the high influence of agricultural activity on the plant-parasitic nematode communities. There is evidence of recent introduction of plant-parasitic nematodes in these cultivated areas; therefore measures should be taken to prevent the loss of economic sustainability in Amazonian soils. Keywords: abundance, Amazonia, diversity, Brachiaria brizantha, plant-parasitic nematode fauna, Tectona grandis.

Molecular and morphological diversity in Japanese rice germplasm

Germplasm molecular and phenotypic characterization is instrumental to its utilization and to genetic variability incorporation into rice breeding programmes. The diversity within 192 Japanese rice accessions was analysed for 22 agro-morphological traits and 24 single sequence repeat markers. A total of 181 alleles were detected, 38 of which were exclusive. The number of alleles/marker ranged from 2 to 16, with an average of 7.54 alleles/locus and the H(e) value ranged from 0.01 to 0.82, with an average of 0.46. The accessions showed diversity at molecular and phenotypic level and few showed also good agronomic performance. Tocher`s method applied on a total-dissimilarity matrix was used to determine cluster formation of 13 diversity groups. Most of the accessions (81%) were clustered within a group, whereas eight accessions (Kyuushuu, Eika Ine, Ishiwari Mochi, Col/Fukui/1965, Ookuma Nishiki, Suzume Shirazu, Iwate Ryoon and Toga) did not cluster with other accessions.

Diversity of endophytic yeasts from sweet orange and their localization by scanning electron microscopy

Endophytes are microorganisms that colonize plant tissues internally without causing harm to the host. Despite the increasing number of studies on sweet orange pathogens and endophytes, yeast has not been described as a sweet orange endophyte. In the present study, endophytic yeasts were isolated from sweet orange plants and identified by sequencing of internal transcribed spacer (ITS) rRNA. Plants sampled from four different sites in the state of Sao Paulo, Brazil exhibited different levels of CVC (citrus variegated chlorosis) development. Three citrus endophytic yeasts (CEYs), chosen as representative examples of the isolates observed, were identified as Rhodotorula mucilaginosa, Pichia guilliermondii and Cryptococcus flavescens. These strains were inoculated into axenic Citrus sinensis seedlings. After 45 days, endophytes were reisolated in populations ranging from 10(6) to 10(9) CFU/g of plant tissue, but, in spite of the high concentrations of yeast cells, no disease symptoms were observed. Colonized plant material was examined by scanning electron microscopy (SEM), and yeast cells were found mainly in the stomata and xylem of plants, reinforcing their endophytic nature. P. guilliermondii was isolated primarily from plants colonized by the causal agent of CVC, Xylella fastidiosa. The supernatant from a culture of P. guilliermondii increased the in vitro growth of X. fastidiosa, suggesting that the yeast could assist in the establishment of this pathogen in its host plant and, therefore, contribute to the development of disease symptoms.

Diversity of endophytic enterobacteria associated with different host plants

Fifty-three endophytic enterobacteria isolates from citrus, cocoa, eucalyptus, soybean, and sugar cane were evaluated for susceptibility to the antibiotics ampicillin and kanamycin, and cellulase production. Susceptibility was found on both tested antibiotics. However, in the case of ampicillin susceptibility changed according to the host plant, while all isolates were susceptible to kanamycin. Cellulase production also changed according to host plants. The diversity of these. isolates was estimated by employing BOX-PCR genomic fingerprints and 16S rDNA sequencing. In total, twenty-three distinct operational taxonomic units (OTUs) were identified by employing a criterion of 60% fingerprint similarity as a surrogate for an OTU. The 23 OTUs belong to the Pantoea and Enterobacter genera, while their high diversity could be an indication of paraphyletic classification. Isolates representing nine different OTUs belong to Pantoea agglomerans, P. ananatis, P, stewartii, Enterobacter sp., and E. homaechei. The results of this study suggest that plant species may select endophytic bacterial genotypes. It has also become apparent that a review of the Pantoea/Enterobacter genera may be necessary.