Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models

Background: This study describes a bioinformatics approach designed to identify Plasmodium vivax proteins potentially involved in reticulocyte invasion. Specifically, different protein training sets were built and tuned based on different biological parameters, such as experimental evidence of secretion and/or involvement in invasion-related processes. A profile-based sequence method supported by hidden Markov models (HMMs) was then used to build classifiers to search for biologically-related proteins. The transcriptional profile of the P. vivax intra-erythrocyte developmental cycle was then screened using these classifiers. Results: A bioinformatics methodology for identifying potentially secreted P. vivax proteins was designed using sequence redundancy reduction and probabilistic profiles. This methodology led to identifying a set of 45 proteins that are potentially secreted during the P. vivax intra-erythrocyte development cycle and could be involved in cell invasion. Thirteen of the 45 proteins have already been described as vaccine candidates; there is experimental evidence of protein expression for 7 of the 32 remaining ones, while no previous studies of expression, function or immunology have been carried out for the additional 25. Conclusions: The results support the idea that probabilistic techniques like profile HMMs improve similarity searches. Also, different adjustments such as sequence redundancy reduction using Pisces or Cd-Hit allowed data clustering based on rational reproducible measurements. This kind of approach for selecting proteins with specific functions is highly important for supporting large-scale analyses that could aid in the identification of genes encoding potential new target antigens for vaccine development and drug design. The present study has led to targeting 32 proteins for further testing regarding their ability to induce protective immune responses against P. vivax malaria.

Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes

The aim of this study was to examine interrelationships between functional biochemical and microbial indicators of soil quality, and their suitability to differentiate areas under contrasting agricultural management regimes. The study included five 0.8 ha areas on a sandy-loam soil which had received contrasting fertility and cropping regimes over a 5 year period. These were organically managed vegetable, vegetable -cereal and arable rotations, an organically managed grass clover ley, and a conventional cereal rotation. The organic areas had been converted from conventional cereal production 5 years prior to the start of the study. All of the biochemical analyses, including light fraction organic matter (LFOM) C and N, labile organic N (LON), dissolved organic N and water-soluble carbohydrates showed significant differences between the areas, although the nature of the relationships between the areas varied between the different parameters, and were not related to differences in total soil organic matter content. The clearest differences were seen in LFOM C and N and LON, which were higher in the organic arable area relative to the other areas. In the case of the biological parameters, there were differences between the areas for biomass-N, ATP, chitin content, and the ratios of ATP: biomass and basal respiration: biomass. For these parameters, the precise relationships between the areas varied. However, relative to the conventionally managed area, areas under organic management generally had lower biomass-N and higher ATP contents. Arbuscular mycorrhizal fungus colonization potential was extremely low in the conventional area relative to the organic areas. Further, metabolic diversity and microbial community level physiological profiles, determined by analysis of microbial community metabolism using Biolog GN plates and the activities of eight key nutrient cycling enzymes, grouped the organic areas together, but separated them from the conventional area. We conclude that microbial parameters are more effective and consistent indicators of management induced changes to soil quality than biochemical parameters, and that a variety of biochemical and microbial analyses should be used when considering the impact of management on soil quality. (C) 2004 Elsevier Ltd. All rights reserved.

Population performance of collembolans feeding on soil fungi from different ecological niches

The potential reproductive value of arbuscular mycorrhizal fungi (Gloinus intraradices and Glomus invermaium), root pathogenic fungi (Rhizoctonia solani and Fusarium culmorum) and saprotrophic fungi (Penicillium hordei and Trichoderma harzianum) were examined for the collembolans Folsomia candida Willem and Folsomia fimetaria L. Dried baker's yeast (Saccharomyces cerevisiae) was used as a reference standard food in laboratory cultures. Collembolan performance was determined as final size, fecundity and population growth rate after when fed the fungal food sources for 31 days. The mycorrhizal fungi gave the least growth and fecundity compared with the other fungi, but G. intraradices gave good fecundity for F. candida. In terms of growth, Baker's yeast was a high-quality food for both adults and juveniles of both species, but it was a poorer food in terms of fecundity of F. candida. Preference of the fungi in all possible pairwise combinations showed that although F. fimetaria did not perform well on Glomus spp. and F. candida did not grow well on Glomus spp. their preference for these fungi did not reflect this. The highest fecundity was seen with the root pathogen F. culmorum. Different quality indicators such as the C:N ratio of the fungal food sources as well as other biological parameters are discussed in relation to their reproductive value and Collembola preferential feeding. (c) 2007 Elsevier Ltd. All rights reserved.

ONeSAMP: a program to estimate effective population size using approximate Bayesian computation

The estimation of effective population size from one sample of genotypes has been problematic because most estimators have been proven imprecise or biased. We developed a web-based program, ONeSAMP that uses approximate Bayesian computation to estimate effective population size from a sample of microsatellite genotypes. ONeSAMP requires an input file of sampled individuals' microsatellite genotypes along with information about several sampling and biological parameters. ONeSAMP provides an estimate of effective population size, along with 95% credible limits. We illustrate the use of ONeSAMP with an example data set from a re-introduced population of ibex Capra ibex.

Fecal water as a non-invasive biomarker in nutritional intervention: comparison of preparation methods and refinement of different endpoints

The assessment of cellular effects by the aqueous phase of human feces (fecal water, FW) is a useful biomarker approach to study cancer risks and protective activities of food. In order to refine and develop the biomarker, different protocols of preparing FW were compared. Fecal waters were prepared by 3 methods: (A) direct centrifugation; (B) extraction of feces in PBS before centrifugation; and (C) centrifugation of lyophilized and reconstituted feces. Genotoxicity was determined in colon cells using the Comet assay. Selected samples were investigated for additional parameters related to carcinogenesis. Two of 7 FWs obtained by methods A and B were similarly genotoxic. Method B, however, yielded higher volumes of FW, allowing sterile filtration for long-term culture experiments. Four of 7 samples were non-genotoxic when prepared according to all 3 methods. FW from lyophilized feces and from fresh samples were equally genotoxic. FWs modulated cytotoxicity, paracellular permeability, and invasion, independent of their genotoxicity. All 3 methods of FW preparation can be used to assess genotoxicity. The higher volumes of FWobtained by preparation method B greatly enhance the perspectives of measuring different types of biological parameters and using these to disclose activities related to cancer development.

A nutrient increment method for reducing bias in global biogeochemical models

Assimilation of physical variables into coupled physical/biogeochemical models poses considerable difficulties. One problem is that data assimilation can break relationships between physical and biological variables. As a consequence, biological tracers, especially nutrients, are incorrectly displaced in the vertical, resulting in unrealistic biogeochemical fields. To prevent this, we present the idea of applying an increment to the nutrient field within a data assimilating model to ensure that nutrient-potential density relationships are maintained within a water column during assimilation. After correcting the nutrients, it is assumed that other biological variables rapidly adjust to the corrected nutrient fields. We applied this method to a 17 year run of the 2° NEMO ocean-ice model coupled to the PlankTOM5 ecosystem model. Results were compared with a control with no assimilation, and with a model with physical assimilation but no nutrient increment. In the nutrient incrementing experiment, phosphate distributions were improved both at high latitudes and at the equator. At midlatitudes, assimilation generated unrealistic advective upwelling of nutrients within the boundary currents, which spread into the subtropical gyres resulting in more biased nutrient fields. This result was largely unaffected by the nutrient increment and is probably due to boundary currents being poorly resolved in a 2° model. Changes to nutrient distributions fed through into other biological parameters altering primary production, air-sea CO2 flux, and chlorophyll distributions. These secondary changes were most pronounced in the subtropical gyres and at the equator, which are more nutrient limited than high latitudes.

Increased levels of microparticles originating from endothelial cells, platelets and erythrocytes in subjects with metabolic syndrome: relationship with oxidative stress

Background and aims The Metabolic Syndrome (MetS) is associated with increased cardiovascular risk. Circulating microparticles (MP) are involved in the pathogenesis of atherothrombotic disorders and are raised in individual with CVD. We measured their level and cellular origin in subjects with MetS and analyzed their associations with 1/anthropometric and biological parameters of MetS, 2/inflammation and oxidative stress markers. Methods and results Eighty-eight subjects with the MetS according to the NCEP-ATPIII definition were enrolled in a bicentric study and compared to 27 healthy controls. AnnexinV-positive MP (TMP), MP derived from platelets (PMP), erythrocytes (ErMP), endothelial cells (EMP), leukocytes (LMP) and granulocytes (PNMP) were determined by flow cytometry. MetS subjects had significantly higher counts/μl of TMP (730.6 ± 49.7 vs 352.8 ± 35.6), PMP (416.0 ± 43.8 vs 250.5 ± 23.5), ErMP (243.8 ± 22.1 vs 73.6 ± 19.6) and EMP (7.8 ± 0.8 vs 4.0 ± 1.0) compared with controls. LMP and PNMP were not statistically different between groups. Multivariate analysis demonstrated that each criterion for the MetS influenced the number of TMP. Waist girth was a significant determinant of PMP and EMP level and blood pressure was correlated with EMP level. Glycemia positively correlated with PMP level whereas dyslipidemia influenced EMP and ErMP levels. Interestingly, the oxidative stress markers, plasma glutathione peroxydase and urinary 8-iso-prostaglandin F2 α, independently influenced TMP and PMP levels whereas inflammatory markers did not, irrespective of MP type. Conclusion Increased levels of TMP, PMP, ErMP and EMP are associated with individual metabolic abnormalities of MetS and oxidative stress. Whether MP assessment may represent a marker for risk stratification or a target for pharmacological intervention deserves further investigation.

Sequential variations of phytoplankton growth and mortality in an NPZ model: a remote-sensing-based assessment

Radiometric data in the visible domain acquired by satellite remote sensing have proven to be powerful for monitoring the states of the ocean, both physical and biological. With the help of these data it is possible to understand certain variations in biological responses of marine phytoplankton on ecological time scales. Here, we implement a sequential data-assimilation technique to estimate from a conventional nutrient–phytoplankton–zooplankton (NPZ) model the time variations of observed and unobserved variables. In addition, we estimate the time evolution of two biological parameters, namely, the specific growth rate and specific mortality of phytoplankton. Our study demonstrates that: (i) the series of time-varying estimates of specific growth rate obtained by sequential data assimilation improves the fitting of the NPZ model to the satellite-derived time series: the model trajectories are closer to the observations than those obtained by implementing static values of the parameter; (ii) the estimates of unobserved variables, i.e., nutrient and zooplankton, obtained from an NPZ model by implementation of a pre-defined parameter evolution can be different from those obtained on applying the sequences of parameters estimated by assimilation; and (iii) the maximum estimated specific growth rate of phytoplankton in the study area is more sensitive to the sea-surface temperature than would be predicted by temperature-dependent functions reported previously. The overall results of the study are potentially useful for enhancing our understanding of the biological response of phytoplankton in a changing environment.

Modelos dinâmicos não lineares e aplicações de quadratura gaussiana

We propose mo deIs to analyze animal growlh data wilh lhe aim of eslimating and predicting quanlities of Liological and economical interest such as the maturing rate and asymptotic weight. lt is also studied lhe effect of environmenlal facLors of relevant influence in the growlh processo The models considered in this paper are based on an extension and specialization of the dynamic hierarchical model (Gamerman " Migon, 1993) lo a non-Iinear growlh curve sdLillg, where some of the growth curve parameters are considered cxchangeable among lhe unils. The inferencc for thcse models are appruximale conjugale analysis Lascd on Taylor series cxpallsiulIs aliei linear Bayes procedures.

Retrievals of a size parameter for phytoplankton and spectral light absorption by colored detrital matter from water-leaving radiances at SeaWiFS channels in a continental shelf region off Brazil

Many efforts are currently oriented toward extracting more information from ocean color than the chlorophyll a concentration. Among biological parameters potentially accessible from space, estimates of phytoplankton cell size and light absorption by colored detrital matter (CDM) would lead to an indirect assessment of major components of the organic carbon pool in the ocean, which would benefit oceanic carbon budget models. We present here 2 procedures to retrieve simultaneously from ocean color measurements in a limited number of bands, magnitudes, and spectral shapes for both light absorption by CDM and phytoplankton, along with a size parameter for phytoplankton. The performance of the 2 procedures was evaluated using different data sets that correspond to increasing uncertainties: ( 1) measured absorption coefficients of phytoplankton, particulate detritus, and colored dissolved organic matter ( CDOM) and measured chlorophyll a concentrations and ( 2) SeaWiFS upwelling radiance measurements and chlorophyll a concentrations estimated from global algorithms. In situ data were acquired during 3 cruises, differing by their relative proportions in CDM and phytoplankton, over a continental shelf off Brazil. No local information was introduced in either procedure, to make them more generally applicable. Over the study area, the absorption coefficient of CDM at 443 nm was retrieved from SeaWiFS radiances with a relative root mean square error (RMSE) of 33%, and phytoplankton light absorption coefficients in SeaWiFS bands ( from 412 to 510 nm) were retrieved with RMSEs between 28% and 33%. These results are comparable to or better than those obtained by 3 published models. In addition, a size parameter of phytoplankton and the spectral slope of CDM absorption were retrieved with RMSEs of 17% and 22%, respectively. If these methods are applied at a regional scale, the performances could be substantially improved by locally tuning some empirical relationships.

Qualidade da água e composição fitoplanctônica de um viveiro de piscicultura utilizado para fins de pesca esportiva e irrigação

Water quality of a fish pond used by UNESP, at Jaboticabal, SP, Brazil, for both fishing and irrigation has been evaluated according to certain limnological parameters and to its phytoplankton composition. During the year, four sampling sites were assigned at the pond: P(1)=inlet water in the pond; P(2)=inlet water from a shrimp pond; P(3)=irrigation spot; and P(4)=outlet water (water flowing directly into another pond). The collected data show a water pond with high concentration of nutrients and chlorophyll-a, and high values of electrical conductivity, total hardness and total dissolved solids, proceeding from the above pond. These factors affected substantially some biological parameters, such as chlorophyll-a and phytoplankton. In P(3), whereas class Zygnematophyceae showed the highest specimens richness, with 34.01%, the Chlorophyceae, that had the highest number of genera, comprehended 33.52% of the total number of individuals. The use of the water fish pond for irrigation must be re-evaluated, due to eutrophic conditions of the water, the presence of potentially toxic cyanobacteria, so as the proper management employed.

Efeitos das variáveis ambientais locais sobre a abundância, a riqueza e a biomassa da macrofauna de solo em um ecossistema semiárido no estado do rio grande do norte, nordeste do brasil

The soil macrofauna is influenced to several biotic and abiotic environmental factors, from changes in the physical environment to a variety of interactions among the species involved, affecting the patterns of biodiversity of soil fauna. The power and specificity of the mechanisms that act on soil organisms vary greatly depending on environmental conditions at different scales of space and time. The Caatinga has great spatial heterogeneity of vegetation, climate and soil, so the soil macrofauna would follow this local spatial variation in the environment? This study aimed to investigate the effects of local environmental variables on biological parameters (taxa richness, total abundance and biomass) of soil macrofauna in a fragment of caatinga in João Câmara, Rio Grande Norte, Northeast Brazil. The study was conducted in the Cauaçu farm, where a grid of 2000m x 500m was drawn, and later, 30 sampling points were randomly selected. The methodology used to collect the macrofauna was the TSBF method. We tested the effects of 10 environmental variables on macrofauna across the plots and across the layers of soil. The hypothesis that macrofauna soil responds to changes in the environment was not supported throughout the plots, but was confirmed to soil layers. The soil macrofauna shows a pattern of concentration in the surface layer and decreases considerably in the deeper layers. This pattern had significant and positive relationship with the aerial plant biomass and fine root stock. The aerial plant biomass releases plant necromass that accumulates in the surface layer, providing an important source of resource and shelter for soil macrofauna, explaining their greater abundance in this layer. The roots are used as a means for the arrival of nutrients to the soil from the primary production, thus a greater amount of root conditions higher food intake for macrofauna, especially the herbivores

Capacidade reprodutiva e preferência da traça-das-crucíferas para diferentes brassicáceas

O objetivo desta pesquisa foi comparar diferentes cultivares de brassicáceas em relação à capacidade reprodutiva e preferência para alimentação e oviposição da traça-das-crucíferas. Os experimentos foram realizados utilizando-se as cultivares de repolho Midori, Chato-de-Quintal, híbridos da Top Seed® - Agristar (TPC 308, TPC 681 e TPC 668), couve-flor Bola de Neve, couve brócolis Ramoso Piracicaba Precoce e couve Manteiga da Geórgia, sendo esta última utilizada como padrão de suscetibilidade. Por meio dos dados biológicos de P. xylostella foram estimados os parâmetros necessários para a construção de tabela de vida de fertilidade, para comparação das cultivares testadas em relação à capacidade reprodutiva da praga. em gaiolas de criação da traça-das-crucíferas foram colocados quatro quartos de folha, dois a dois, que justapostos formavam um círculo de 8 cm de diâmetro, confrontando-se os materiais dois a dois. As partes foram dispostas equidistantemente, para realização do teste de dupla chance de escolha (preferência para alimentação e oviposição) e de múltipla chance de escolha, confrontando todos os substratos (preferência para alimentação). As cultivares que proporcionaram melhor desenvolvimento e reprodução para a traça-das-crucíferas foram couve Manteiga da Geórgia e couve brócolis. Para preferência alimentar constatou-se alta suscetibilidade em couve Manteiga e TPC 681 e para preferência de oviposição alta preferência para couve-flor Bola de Neve. Com isso, sugere-se a divisão das cultivares estudadas em quatro classes distintas: repolho Midori como moderadamente resistente (MR); couve-flor Bola de Neve e repolho Chato-de-Quintal como suscetíveis (S); couve brócolis, TPC308, TPC681 e TPC668 como moderadamente suscetíveis (MS); e couve Manteiga como altamente suscetível (AS).

Temperatura no desenvolvimento e na reprodução de cochonilhas criadas sobre abóboras

O desenvolvimento de insetos é dependente da temperatura. Nesta pesquisa, foi verificada a influência da temperatura no desenvolvimento e na reprodução de Chrysomphalus aonidum (L.) em câmaras climatizadas com UR do ar 70±10%, fotofase de 12h e temperaturas constantes de 17, 19, 21, 23, 25 e 27 ± 1°C, tendo como substrato abóboras cabotiá (Curcubita maxima x Curcubita moschata var. Tetsukabuto). Foi observada a influência da temperatura nos parâmetros biológicos da cochonilha, sendo que temperaturas entre 23 e 27°C foram as mais adequadas ao inseto, propiciando menor duração do período ninfal e maior produção diária de ninfas por fêmea. Temperaturas entre 17 e 19°C provocam maior duração na fase ninfal, maior longevidade das fêmeas e menor produção diária de ninfas por fêmea.

Biology of Plutella xylostella L. (Lepidoptera: Plutellidade) Reared on Cauliflower Genotypes

This work was conducted to evaluate biological parameters of Plutella xylostella L. reared on leaves of several cauliflower genotypes under laboratory conditions. The experiment was set in a randomized block design and arranged in a 6 x 2 factorial (genotypes x generations). Leaf disks of the cultivars Barcelona, Verona, Piracicaba Precoce, Sharon, Silver Streak, and Teresopolis Gigante were placed in Petri dishes with 12 newly-hatched larvae. Leaf disks were initially changed after the fourth day, but daily afterwards until the larvae reached the pupal stage. The same procedure was adopted for the second generation. Twenty adults of each sex were separated from each genotype to evaluate their longevity, and I 0 couples from each treatment were used to assess female fecundity. The lowest larval survival was obtained on the 'Silver Streak' (78.9%) and highest on 'Verona' (97.1%). The 'Silver Streak' and `Teresopolis Gigante' showed the lowest pupal weights (4.83 mg and 5.11 mg, respectively), as well as the lowest fecundity, 119.4 and 123.0 eggs/female, respectively, while 'Piracicaba Precoce' the highest (167.7 eggs/female). Males obtained from larvae reared on `Teresopolis Gigante' and 'Silver Streak' lived shorter (5.1 days), while the short-lived females were obtained from larvae reared on 'Barcelona' and 'Verona' (4.9 and 5.0 days). Insect development was prolonged in the second generation in all tested genotypes.