Evidence for conformational changes in the yeast deoxyhypusine hydroxylase Lia1 upon iron displacement from its active site

The unique amino acid hypusine is formed exclusively in eIF5A by the successive action of deoxyhypusine synthase and deoxyhypusine hydroxylase (yeast Lia1, human DOHH). Although the first enzyme has been extensively studied, both Lia1 structure and the mechanism of action remain unclear. Hence, a multi-approach was used to evaluate Lia1 catalysis, metal/substrate binding, structural conformation and stability. Mutational analyses of Lia1 revealed fine differences in the mode of substrate binding between the human and yeast counterparts. Like human DOHH, recombinant Lia1 is an iron metalloenzyme. Iron is essential for enzyme activity since its loss renders the enzyme totally inactive. The separation of iron-free and iron-bound forms by gel filtration and native electrophoresis suggests differences in Lia1 tertiary structure related to the iron binding. The ability of Lia1 to undergo conformational changes prompted us to use a set of complementary spectroscopic approaches and SAXS to obtain detailed information on the processes underlying dissociation of iron from Lia1 at different levels of the protein organization. The additive effect of weak interactions, especially within the metal center, resulted in an active enzyme in a stabilized and compact three-dimensional fold. Loss of tertiary contacts upon iron displacement led to an elongated conformation of Lia1, in which the N- and C-terminal domains are no longer in close proximity to guarantee the proper orientation of the active groups within the active site pocket. Our results demonstrate an essential structural role for iron binding in addition to its contribution to the catalysis of hypusine formation in the eIF-5A precursor.     

Protein structure calculation with data imputation: the use of substitute restraints

The amount of experimental restraints e.g., NOEs is often too small for calculating high quality three-dimensional structures by restrained molecular dynamics. Considering this as a typical missing value problem we propose here a model based data imputation technique that should lead to an improved estimation of the correct structure. The novel automated method implemented in AUREMOL makes a more efficient use of the experimental information to obtain NMR structures with higher accuracy. It creates a large set of substitute restraints that are used either alone or together with the experimental restraints. The new approach was successfully tested on three examples: firstly, the Ras-binding domain of Byr2 from Schizosaccharomyces pombe, the mutant HPr (H15A) from Staphylococcus aureus, and a X-ray structure of human ubiquitin. In all three examples, the quality of the resulting final bundles was improved considerably by the use of additional substitute restraints, as assessed quantitatively by the calculation of RMSD values to the “true” structure and NMR R-factors directly calculated from the original NOESY spectra or the published diffraction data.     

Topological control of the spin coupling in dinuclear copper(II) complexes with meta- and para-phenylenediamine bridging ligands

A novel series of copper(II) complexes of formula [Cu(tren)(mpda)](ClO₄)₂ · 1/2H₂O (1), [Cu₂(tren)₂(mpda)](ClO₄)₄ · 2H₂O (2), and [Cu₂(tren)₂(ppda)](ClO₄)₄ · 2H₂O (3) containing the tetradentate tris(2-aminoethyl)amine (tren) terminal ligand and the potentially bridging 1,n-phenylenediamine [n = 3 (mpda) and 4 (ppda)] ligand have been prepared and spectroscopically characterized. X-ray diffraction on single crystals of 1 and 3 show the presence of mono- (1) and dinuclear (3) copper(II) units where the mpda (1) and ppda (3) ligands adopt terminal monodentate (1) and bridging bis(monodentate) (3) coordination modes toward [Cu(tren)]²⁺ cations with an overall non-planar, orthogonal disposition of the phenylene group and the N-Cu-N threefold axis of the trigonal bipyramid of each copper(II) ion [values of the Cu-N-C-C torsion angle (?) in the range of 50.8(3)-79.2(2) (1) and 80.9(2)-86.5(2)° (3)]. Variable-temperature magnetic susceptibility measurements on the dinuclear complexes 2 and 3 show the occurrence of moderate ferromagnetic (J = +8.3 cm⁻¹, 2) and strong antiferromagnetic (J = −51.4 cm⁻¹, 3) couplings between the two copper(II) ions across the meta- and para-phenylenediamine bridges, leading to S = 1 (2) and S = 0 (3) ground spin states [H = −JS₁ · S₂ with S₁ = S₂ = S_Cu = 1/2]. Density functional theory (DFT) calculations on the triplet (2) and broken-symmetry (BS) singlet (3) ground spin states, support the occurrence of a spin polarization mechanism for the propagation of the exchange interaction through the predominantly π-type orbital pathway of the 1,n-phenylenediamine bridge. Finally, a new magneto-structural correlation between the magnitude of the magnetic coupling (J) and the Cu-N-C-C torsion angle (?) has been found which reveals the role of σ- versus π-type orbital pathways in the modulation of the magnetic coupling for m- and p-phenylenediamine-bridged dicopper(II) complexes.     

A preliminary study of the occurrence of actidione-resistant fungi in sediments of Catalonian river mouths (Spain). I. Keratinolytic fungi and related Onygenales

Sediments from eight river mouths along the Catalonian coast (Spain) were surveyed for keratinolytic fungi and related Onygenales. The actidione plating technique was employed. Of 532 actidione-treated sediment samples, 268 (50.3%) were positive for the fungi. Altogether, 384 fungal strains from 35 species were isolated from the samples. Narasimhella marginospora, Aphanoascus fulvescens, Neoarachnotheca keratinophila with its anamorph Myriodontium keratinophilum, Narasimhella hyalinospora, Beauveria alba, Sporothrix schenckii, Chrysosporium lobatum and Gymnoascus littoralis were the predominant species in sediments. Abundance of N. marginospora was clearly correlated with the degree of water pollution with sewage. This revised version was published online in June 2006 with corrections to the Cover Date.     

Influence of recirculation over COD and N-NH4 removals from landfill leachate by horizontal flow constructed treatment wetland

Abstract

Treatment of landfill leachate is a challenge due to its complex chemical composition and high recalcitrance and because of high costs for conventional wastewater treatment. In our study, leachate from the Quitaúna Landfill, Sao Paulo Metropolitan Region, Brazil, was treated at a laboratory scale with a horizontal subsurface flow constructed treatment wetland (HF-CTW) operating under a recirculation regime. Two units planted with Heliconia psittacorum (HP) and Cyperus papyrus (CP), and one unplanted control unit were assessed. With a recirculation regime over 21?days, the planted units removed 40% of chemical oxygen demand (COD) while the control unit removed only 29%. True color removal efficiencies were 2, 22, and 23% for the control, HP, and CP HF-CTWs, respectively. The ammonium nitrogen removal efficiencies for a 21-day hydraulic retention time (HRT) were 63–81% for planted units and 72% for the control. The increase of the HRT from 7 to 21?days led to the enhancement of ammonium nitrogen removal but did not affect the COD and total nitrogen removals. This phenomenon is a consequence of leachate’s low biodegradability. The present study shows the importance of the HRT and plant presence for landfill leachate treatment using HF-CTWs.     

Influence of peroxides, ascorbate and glutathione on germination and growth in Lupinus albus L.

Lupinus albus L. seeds were treated with different concentrations (from 10 μM to 50 mM) of H2O2, m-chloroperoxybenzoic acid (mCPBA), ascorbate (ASC) and glutathione (GSH). The efficiency as inhibitors on germination and on the subsequent growth of the hypocotyl was mCPBA > GSH > ASC = H2O2, which suggest that inhibitory efficiency was dependent on the compound per se rather than on its redox nature. This revised version was published online in July 2006 with corrections to the Cover Date.     

Resilience to fire of phylogenetic diversity across biological domains

Fire alters the structure and composition of above‐ and belowground communities with concurrent shifts in phylogenetic diversity. The inspection of postfire trends in the diversity of ecological communities incorporating phylogenetic information allows to better understand the mechanisms driving fire resilience. While fire reduces plant phylogenetic diversity based on the recruitment of evolutionarily related species with postfire seed persistence, it increases that of soil microbes by limiting soil resources and changing the dominance of competing microbes. Thus, during postfire community reassembly, plant and soil microbes might experience opposing temporal trends in their phylogenetic diversity that are linked through changes in the soil conditions. We tested this hypothesis by investigating the postfire evolution of plant and soil microbial (fungi, bacteria and archaea) communities across three 20‐year chronosequences. Plant phylogenetic diversity increased with time since fire as pioneer seeders facilitate the establishment of distantly related late‐successional shrubs. The postfire increase in plant phylogenetic diversity fostered plant productivity, eventually recovering soil organic matter. These shifts over time in the soil conditions explained the postfire restoration of fungal and bacterial phylogenetic diversity, which decreased to prefire levels, suggesting that evolutionarily related taxa with high relative fitness recover their competitive superiority during community reassembly. The resilience to fire of phylogenetic diversity across biological domains helps preserve the evolutionary history stored in our ecosystems.     

Evaluation of antibody serology to determine current helminth and Plasmodium falciparum infections in a co-endemic area in Southern Mozambique

BackgroundSoil-transmitted helminths (STH), Schistosoma spp. and Plasmodium falciparum are parasites of major public health importance and co-endemic in many sub-Saharan African countries. Management of these infections requires detection and treatment of infected people and evaluation of large-scale measures implemented. Diagnostic tools are available but their low sensitivity, especially for low intensity helminth infections, leaves room for improvement. Antibody serology could be a useful approach thanks to its potential to detect both current infection and past exposure.MethodologyWe evaluated total IgE responses and specific-IgG levels to 9 antigens from STH, 2 from Schistosoma spp., and 16 from P. falciparum, as potential markers of current infection in a population of children and adults from Southern Mozambique (N = 715). Antibody responses were measured by quantitative suspension array Luminex technology and their performance was evaluated by ROC curve analysis using microscopic and molecular detection of infections as reference.Principal findingsIgG against the combination of EXP1, AMA1 and MSP2 (P. falciparum) in children and NIE (Strongyloides stercoralis) in adults and children had the highest accuracies (AUC = 0.942 and AUC = 0.872, respectively) as markers of current infection. IgG against the combination of MEA and Sm25 (Schistosoma spp.) were also reliable markers of current infection (AUC = 0.779). In addition, IgG seropositivity against 20 out of the 27 antigens in the panel differentiated the seropositive endemic population from the non-endemic population, suggesting a possible role as markers of exposure although sensitivity could not be assessed.ConclusionsWe provided evidence for the utility of antibody serology to detect current infection with parasites causing tropical diseases in endemic populations. In addition, most of the markers have potential good specificity as markers of exposure. We also showed the feasibility of measuring antibody serology with a platform that allows the integration of control and elimination programs for different pathogens.     

Study of seasonal and daily variations in airborneOlea europaea L. pollen in Jaén (Spain), 1993–1995

A study is made of the seasonal and daily variations in the concentrations of pollen ofOlea europaea L. over three consecutive years (1993–1995) in the atmosphere of Jaén (southern Spain). A Burkard volumetric spore trap was used for sampling. The results show that the highest concentrations of airborne olive pollen occur during May and the first 2 weeks of June, when levels often exceed 500 grains/m³ and occasionally reach nearly 5000 grains/m³ (the levels of allergenic pollen in the atmosphere of Jaén are among the highest in Europe). Over the 3-year study period a significant seasonal variation was detected, not only in the development of the principal pollination period, but also in the value of the maximum pollen concentrations recorded.     

Molecular phylogenetic diversity of the emerging mucoralean fungus Apophysomyces: Proposal of three new species

BackgroundApophysomyces is a monotypic genus belonging to the order Mucorales. The species Apophysomyces elegans has been reported to cause severe infections in immunocompromised and immunocompetent people. In a previous study of Álvarez et al.³ [J Clin Microbiol 2009;47:1650–6], we demonstrated a high variability among the 5.8S rRNA gene sequences of clinical strains of A. elegans.Material and methodsWe performed a polyphasic study based on the analysis of the sequences of the histone 3 gene, the internal transcribed spacer region of the rDNA gene, and domains D1 and D2 of the 28S rRNA gene, as well as by evaluation of some relevant morphological and physiological characteristics of a set of clinical and environmental strains of A. elegans.Results and conclusionsWe have demonstrated that A. elegans is a complex of species. We propose as new species Apophysomyces ossiformis, characterised by bone-shaped sporangiospores, Apophysomyces trapeziformis, with trapezoid-shaped sporangiospores, and Apophysomyces variabilis, with variable-shaped sporangiospores. These species failed to assimilate esculin, whereas A. elegans was able to assimilate that glycoside. Amphotericin B and posaconazole are the most active in vitro drugs against Apophysomyces.