The soil C pool in different agroecosystems derived from the dry tropical forest of Guanacaste, Costa Rica

Inventories of soil C pools are still lacking from tropical sites. Our objective was to assess total C and N concentrations in the different mineral soil fractions down to 50 cm depth in relation to selected physical and chemical properties of 5 ecosystems at La Flor Sustainable Center in Guanacaste, Costa Rica. The ecosystems studied were a derived savanna with scattered trees, a gallery forest, an abandoned Mango indigofera L. plantation, a Citrus sp. plantation, and a Saccharum officinarum L. (sugarcane) plantation. Significant differences were found for the main fixed factor ecosystem for all variables analyzed (ANOVA). The TSC concentration was significantly higher in the sugarcane plantation compared to the rest of land use systems. The TSC concentration decreased significantly with increase in depth in all ecosystems and ranged from 20.3–38.3 to 4.3–20.9 g kg⁻¹ in the 0–10 and 40–50 cm depth, respectively. In all cases, the clay + silt fraction (<50 μm) contained the highest C concentration. N concentration (0–10 cm depth) at La Flor ranged from 0.32 to 0.19%, and decreased in the order sugarcane > Curatella savanna > Mango and Citrus plantations > gallery forest. A principal component analysis (PCA) performed with all variables studied showed that the ordination of land uses (ecosystems) in the factorial plane defined by the first two axes was significant (Monte Carlo permutation test, P < 0.0001). The highest TSC pool down to 50 cm depth was obtained in the sugarcane plantation (160 Mg C ha⁻¹) while less C was found in the rest of ecosystems, i.e. from 66 (gallery forest) to 80 Mg C ha⁻¹ (Curatella savanna). The TSC concentration obtained in the sugarcane plot is likely the result of the incorporation of surface residues into the soil that would have otherwise been lost through burning, which is the current practice in the region. Further studies on C stabilization in the clay fraction are thus needed to test the hypothesis of soil C enrichment due to residue management. Finally, trade-offs are to be considered for both preservation of the fragile dTf and the productivity of derived land uses that increases soil C at the same time.     

Different duplex/quadruplex junctions determine the properties of anti-thrombin aptamers with mixed folding

Mixed duplex/quadruplex oligonucleotides have attracted great interest as therapeutic targets as well as effective biomedical aptamers. In the case of thrombin-binding aptamer (TBA), the addition of a duplex motif to the G-quadruplex module improves the aptamer resistance to biodegradation and the affinity for thrombin. In particular, the mixed oligonucleotide RE31 is significantly more effective than TBA in anticoagulation experiments and shows a slower disappearance rate in human plasma and blood. In the crystal structure of the complex with thrombin, RE31 adopts an elongated structure in which the duplex and quadruplex regions are perfectly stacked on top of each other, firmly connected by a well-structured junction. The lock-and-key shape complementarity between the TT loops of the G-quadruplex and the protein exosite I gives rise to the basic interaction that stabilizes the complex. However, our data suggest that the duplex motif may have an active role in determining the greater anti-thrombin activity in biological fluids with respect to TBA. This work gives new information on mixed oligonucleotides and highlights the importance of structural data on duplex/quadruplex junctions, which appear to be varied, unpredictable, and fundamental in determining the aptamer functional properties.     

Zinc to cadmium replacement in the A. thaliana SUPERMAN Cys₂ His₂ zinc finger induces structural rearrangements of typical DNA base determinant positions

Among heavy metals, whose toxicity cause a steadily increasing of environmental pollution, cadmium is of special concern due to its relatively high mobility in soils and potential toxicity at low concentrations. Given their ubiquitous role, zinc fingers domains have been proposed as mediators for the toxic and carcinogenic effects exerted by xenobiotic metals. To verify the structural effects of zinc replacement by cadmium in zinc fingers, we have determined the high resolution structure of the single Cys₂His₂ zinc finger of the Arabidopsis thaliana SUPERMAN protein (SUP37) complexed to the cadmium ion by means of UV–vis and NMR techniques. SUP37 is able to bind Cd(II), though with a dissociation constant higher than that measured for Zn(II). Cd‐SUP37 retains the ββα fold but experiences a global structural rearrangement affecting both the relative orientation of the secondary structure elements and the position of side chains involved in DNA recognition: among them Ser17 side chain, which we show to be essential for DNA binding, experiences the largest displacement. © 2011 Wiley Periodicals, Inc. Biopolymers 95: 801‐810, 2011.     

Palytoxin Induces Functional Changes of Anion Transport in Red Blood Cells: Metabolic Impact

Palytoxin (PTX) is classified as one of the most powerful marine biotoxins (of high molecular weight and no protein origin) because it is able to interact strongly with important cellular structures influencing their function in different biological processes. This study of the effects of PTX on red blood cells (RBC) extends the knowledge about its toxicity, which concerns not only the well-known action on Na(+)/K(+)-ATPase but also band 3 protein (B3 or AE1), the role of which is essential for anion transport and for the structure, function, and metabolic integrity of the erythrocyte. The effects of PTX on RBC can be summarized as follows: it alters the anionic flux and seriously compromises not only CO(2) transport but also the metabolic modulation centered on the oxy-deoxy cycle of hemoglobin; it stabilizes the plasma membrane by preventing lipid peroxidation; and its effect does not lead to activation of caspases 3 and 8. From what is reported in steps 2 and 3, and on the basis of the results obtained on hemolysis, methemoglobin levels, and phosphatase activity, an increase of the reducing power of the erythrocytes (RBC) in the presence of PTX clearly emerges. The results have enabled us to outline some metabolic adaptations induced in the RBC by PTX.     

Carbonate facies dominated by syndepositional cements: a key component of Middle Triassic platforms. The Marmolada case history (Dolomites, Italy)

Summary This article deals with the discussion of the role of the syndepositional cementation for the growth of the Middle Triassic pre-volcanic carbonate platforms of the Dolomites (Southern Alps, Northern Italy). The study is concentrated on the Marmolada Buildup, which escaped the facies destroying dolomitization which affected many surrounding platforms. The investigations took place within an almost isochronous uppermost Anisian palcogeographic transect, ranging from the platform-top to the margin and the upper slope. Methods used include geological mapping, sedimentological and paleontological studies, evaluation of the microfacies, as well as SEM and EDS epifluorescence analyses. The well bedded platform-top succession consists of intra-bioclast calcarenites and calcirudites, interbedded with subordinate boundstones, and organized in shallowing upward, meter scale depositional cycles, sometimes capped by subaerial surfaces. The platform margin belt is rich in boundstones and lacks a primary framework formed by organisms; metazoan skeletons form less then 5% of the rock volume. The outer margin and the uppermost slope are characterized by decimeter-scale boundstone blocks, coated and linked to each other by huge amounts of radiaxial fibrous calcite cements, arranged in concentric crusts. These cements (“evinospongiac”) represent the main component of the margin and upper slope facies. Epifluorescence analyses suggest the existence of abundant organic residual matter associated not only with the bioclasts and peloids, but also with the syndepositional cements. Organic matter likely played a significant role in carbonate cementation and was a key factor for the early lithification of the platform as well as for the sediment production. Minor element microanalyses reveal an uniform Mg content in different calcite types (2–4 Mole % MgCO₃), independently from the primary nature of the components. Late diagenetic sparry calcites exhibit similar Mg values but no iron. These data point to a homogenization of minor element distribution, probably associated with a slow but long-lasting semi-closed fluid circulation, possibly related with the Neogene uplifting of the Dolomite Mountains.     

Diversification of the Genus Anopheles and a Neotropical Clade from the Late Cretaceous

The Anopheles genus is a member of the Culicidae family and consists of approximately 460 recognized species. The genus is composed of 7 subgenera with diverse geographical distributions. Despite its huge medical importance, a consensus has not been reached on the phylogenetic relationships among Anopheles subgenera. We assembled a comprehensive dataset comprising the COI, COII and 5.8S rRNA genes and used maximum likelihood and Bayesian inference to estimate the phylogeny and divergence times of six out of the seven Anopheles subgenera. Our analysis reveals a monophyletic group composed of the three exclusively Neotropical subgenera, Stethomyia, Kerteszia and Nyssorhynchus, which began to diversify in the Late Cretaceous, at approximately 90 Ma. The inferred age of the last common ancestor of the Anopheles genus was ca. 110 Ma. The monophyly of all Anopheles subgenera was supported, although we failed to recover a significant level of statistical support for the monophyly of the Anopheles genus. The ages of the last common ancestors of the Neotropical clade and the Anopheles and Cellia subgenera were inferred to be at the Late Cretaceous (ca. 90 Ma). Our analysis failed to statistically support the monophyly of the Anopheles genus because of an unresolved polytomy between Bironella and A. squamifemur.     

Foods and liver health

Chronic liver damage is a worldwide common pathology, characterised by an inflammatory and fibrotic process that leads to a progressive evolution from chronic hepatitis to cirrhosis and hepatocellular carcinoma (HCC). A major role for fats and oxidative stress has been recently demonstrated in the pathogenesis of liver diseases. In the clinical practice, dietary recommendations in the management of chronic diseases often rely on denying patients certain foods, which results in a severe reduction of quality of life. In this paper a new perspective based on the development of Food intended for Specific Medical Purposes (FSMP) containing highly bioavailable antioxidant compounds or polyunsaturated-fatty acids, has been highlighted as a tool for preventive and curative medicine, to be associated to pharmacological treatments.     

A partial proteome reference map of the wine lactic acid bacterium Oenococcus oeni ATCC BAA-1163

Oenococcus oeni is the main lactic acid bacterium that carries out the malolactic fermentation in virtually all red wines and in some white and sparkling wines. Oenococcus oeni possesses an array of metabolic activities that can modify the taste and aromatic properties of wine. There is, therefore, industrial interest in the proteins involved in these metabolic pathways and related transport systems of this bacterium. In this work, we report the characterization of the O. oeni ATCC BAA-1163 proteome. Total and membrane protein preparations from O. oeni were standardized and analysed by two-dimensional gel electrophoresis. Using tandem mass spectrometry, we identified 224 different spots corresponding to 152 unique proteins, which have been classified by their putative function and subjected to bioinformatics analysis.