Geospatial analysis of spatiotemporal patterns of pH, total suspended sediment and chlorophyll-a on the Amazon floodplain

We applied spatial data analysis and geostatistical procedures to pH, total suspended sediment and chlorophyll-a concentration data gathered on an Amazon floodplain lake. Variographic analysis and ordinary kriging interpolation were used to identify and describe spatiotemporal patterns of variability in these parameters, which are relevant to understand the dynamics of water circulation on the floodplain lake. In spite of the complexity of the processes underlying the spatiotemporal patterns, this approach demonstrated that the heterogeneity in the seasonal water composition is forced not only by the Amazon River flood pulse, but also by the lake bottom topography and the wind intensity.     

Eicosapentaenoic and docosahexaenoic acids production by and okara-utilizing potential of thraustochytrids

Nine thraustochytrid strains isolated from subtropical mangroves were screened for their eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) production potential in a glucose yeast extract medium. Their ability to utilize okara (soymilk residue) for growth and EPA and DHA production was also evaluated. EPA yield was low in most strains, while DHA level was high on glucose yeast extract medium, producing 28.1–41.1% of total fatty acids, for all strains, with the exception of Ulkenia sp. KF13. The DHA yield of Schizochytrium mangrovei strains ranged from 747.7 to 2778.9 mg/l after 52 h of fermentation at 25°C. All strains utilized okara as a substrate for growth, but DHA yield was lower when compared with fermentation in a glucose yeast extract medium. Journal of Industrial Microbiology & Biotechnology (2001) 27, 199–202. Received 11 December 2000/ Accepted in revised form 29 June 2001     

The vertical structure of mediterranean scrub in Doñana national park (SW spain)

The vertical structure of pioneer and stabilized mediterranean sand vegetation at Doñana National Park has been compared using a non destructive method based on organ frequency analysis. Vertical distribution of organ frequencies and light intensity through the canopy, leaf chlorophyll content, leaf area index, organ biomass, are also discussed forArtemisia campestris subsp.maritima, Scrophularia frutescens, Halimium halimifolium, andCistus salvifolius.     

Oxidative metabolism and release of myeloperoxidase from polymorphonuclear leukocytes obtained from blood sedimentation in a Ficoll-Hypaque gradient

Polymorphonuclear neutrophils (PMN) have an important role in the host defence response to infection. These cells produce large amounts of reactive oxygen species (O(2).(-), H(2)O(2) and ONOO(-)) with microbicidal activity. PMN are commonly isolated from peripheral blood by sedimentation through a gradient of density (Ficoll-Hypaque gradient and dextran), yielding a highly homogeneous cellular population. However, some cellular activation due to membrane perturbation is also expected. We studied how the production of reactive oxygen species and release of myeloperoxidase (MPO) from blood PMN are affected by the use of the Ficoll-Hypaque density gradient. PMN isolated by spontaneous sedimentation and total blood were used for comparisons. Lucigenin- and luminol-enhanced chemiluminescence was used to estimate the production of reactive oxygen from intact cells and shown to be higher for cells isolated by density gradient both in the absence and presence of added stimuli. The release of MPO, estimated by the chemiluminescence of the luminol/H(2)O(2) reaction in the supernatant of PMN incubated in the absence and presence of stimuli and absence and presence of cytochalasin B, was also higher for PMN isolated by a density gradient. In conclusion, it was shown that the PMN isolation procedure affects reactive oxygen species production and MPO release and in some cases may cause a misinterpretation of results.     

Predicting host tropism of influenza A virus proteins using random forest

Background

Majority of influenza A viruses reside and circulate among animal populations, seldom infecting humans due to host range restriction. Yet when some avian strains do acquire the ability to overcome species barrier, they might become adapted to humans, replicating efficiently and causing diseases, leading to potential pandemic. With the huge influenza A virus reservoir in wild birds, it is a cause for concern when a new influenza strain emerges with the ability to cross host species barrier, as shown in light of the recent H7N9 outbreak in China. Several influenza proteins have been shown to be major determinants in host tropism. Further understanding and determining host tropism would be important in identifying zoonotic influenza virus strains capable of crossing species barrier and infecting humans.

Results

In this study, computational models for 11 influenza proteins have been constructed using the machine learning algorithm random forest for prediction of host tropism. The prediction models were trained on influenza protein sequences isolated from both avian and human samples, which were transformed into amino acid physicochemical properties feature vectors. The results were highly accurate prediction models (ACC>96.57; AUC>0.980; MCC>0.916) capable of determining host tropism of individual influenza proteins. In addition, features from all 11 proteins were used to construct a combined model to predict host tropism of influenza virus strains. This would help assess a novel influenza strain's host range capability.

Conclusions

From the prediction models constructed, all achieved high prediction performance, indicating clear distinctions in both avian and human proteins. When used together as a host tropism prediction system, zoonotic strains could potentially be identified based on different protein prediction results. Understanding and predicting host tropism of influenza proteins lay an important foundation for future work in constructing computation models capable of directly predicting interspecies transmission of influenza viruses. The models are available for prediction at http://fluleap.bic.nus.edu.sg.

     

Human toxocariasis: a seroepidemiological survey in schoolchildren of Sorocaba, Brazil

A seroepidemiological survey for toxocariasis, among 180 schoolchildren of the public schools of Sorocaba City, state of S?o Paulo, Brazil, was carried out from August 2000 to July 2001. ELISA test was performed using excretory and secretory antigens for the detection of IgG anti-Toxocara antibodies. Information regarding the children was obtained from the parents or legal guardians. The results showed that the mean age was 5.4 +/- 1.4 years, the infection coefficient (IC) was 38.3 and the infection risk was higher among the children living in the city outskirts (IC = 47.4) where the socioeconomic conditions were worse than in the central region of the city (IC = 11.1). There was an association between higher frequency of seroreactivity in the ELISA test and the condition of living in a house with a yard and/or unpaved street. The same was observed in relation to a history of enteroparasitism. There was also an association between a seronegative ELISA test and previous treatment of pet dogs and/or cats with vermifuge. Based on these results, the authors propose that public health programs should include anthelmintic for dogs and cats during the antirabies vaccination campaigns, in order to diminish environmental contamination with Toxocara spp. eggs and consequently human infection.     

Downregulation of the Basic Peroxidase Isoenzyme from Zinnia elegans by Gibberellic Acid

Hypocotyl formation during the epigeal germination of seedlings is under strict hormonal regulation. In a 3 d old Zinnia elegans seedling system, gibberellic acid (GA_3) exerts an opposite effect to that exerted by light on hypocotyl photomorphogenesis because GA_3 promotes an etiolated-like growth with an inhibition of radial (secondary) growth. For this reason, the effect of GA_3 on the basic peroxidase isoenzyme from Z. Elegans (ZePrx), an enzyme involved in hypocotyl lignin biosynthesis, was studied. The results showed that GA_3 reduces ZePrx activity, similarly to the way in which it reduces seedling secondary growth. This hormonal response is supported by the analysis of the ZePrx promoter, which contains four types of GA_3-responsive cis-elements: the W Box/O2S; the Pyr Box; the GARE; and the Amy Box. Taken together, these results suggest that ZePrx is directly regulated by GA_3, with this effect matching the inhibitory effect of GA on the hypocotyl secondary growth.     

The suppression of AtPrx52 affects fibers but not xylem lignification in Arabidopsis by altering the proportion of syringyl units

Lignins result from the oxidative polymerization of three hydroxycinnamyl (p‐coumaryl, coniferyl and sinapyl) alcohols in a reaction mediated by peroxidases (EC 1.11.1.7) and laccases (EC 1.10.3.2), yielding H, G and S units, respectively. Although both acidic and basic peroxidases can oxidize p‐coumaryl and coniferyl alcohol, only basic peroxidases are able to oxidize sinapyl alcohol. The AtPrx52 from Arabidopsis is a basic peroxidase that has been reported to be highly homologous to the basic peroxidase of Zinnia elegans, the only peroxidase which has been unequivocally linked to lignin formation. Here, we show how the suppression of AtPrx52 causes a change in lignin composition, mainly at the level of stem interfascicular fibers. Quantification of lignins in two different atprx52 knock‐out mutants revealed a decrease of lignin amount compared with wild type. The S/G ratio, obtained by both nitrobenzene oxidation and thioacidolysis, indicated a decrease in S units in the atprx52 mutants. As deduced from Wiesner and mainly Mäule staining, this reduction in S unit content appears to be restricted to the interfascicular fibers. Moreover, quantitative polymerase chain reaction analysis in atprx52 plants showed a general downregulation of genes involved in lignin biosynthetic pathway, as well as genes related to secondary cell wall. On the other hand, other routes from phenylpropanoid metabolism were induced. Taken together, our results indicate that AtPrx52 is involved in the synthesis of S units in interfascicular fibers at late stages of the lignification process.