Expression of P. falciparum var Genes Involves Exchange of the Histone Variant H2A.Z at the Promoter

Plasmodium falciparum employs antigenic variation to evade the human immune response by switching the expression of different variant surface antigens encoded by the var gene family. Epigenetic mechanisms including histone modifications and sub-nuclear compartmentalization contribute to transcriptional regulation in the malaria parasite, in particular to control antigenic variation. Another mechanism of epigenetic control is the exchange of canonical histones with alternative variants to generate functionally specialized chromatin domains. Here we demonstrate that the alternative histone PfH2A.Z is associated with the epigenetic regulation of var genes. In many eukaryotic organisms the histone variant H2A.Z mediates an open chromatin structure at promoters and facilitates diverse levels of regulation, including transcriptional activation. Throughout the asexual, intraerythrocytic lifecycle of P. falciparum we found that the P. falciparum ortholog of H2A.Z (PfH2A.Z) colocalizes with histone modifications that are characteristic of transcriptionally-permissive euchromatin, but not with markers of heterochromatin. Consistent with this finding, antibodies to PfH2A.Z co-precipitate the permissive modification H3K4me3. By chromatin-immunoprecipitation we show that PfH2A.Z is enriched in nucleosomes around the transcription start site (TSS) in both transcriptionally active and silent stage-specific genes. In var genes, however, PfH2A.Z is enriched at the TSS only during active transcription in ring stage parasites. Thus, in contrast to other genes, temporal var gene regulation involves histone variant exchange at promoter nucleosomes. Sir2 histone deacetylases are important for var gene silencing and their yeast ortholog antagonises H2A.Z function in subtelomeric yeast genes. In immature P. falciparum parasites lacking Sir2A or Sir2B high var transcription levels correlate with enrichment of PfH2A.Z at the TSS. As Sir2A knock out parasites mature the var genes are silenced, but PfH2A.Z remains enriched at the TSS of var genes; in contrast, PfH2A.Z is lost from the TSS of de-repressed var genes in mature Sir2B knock out parasites. This result indicates that PfH2A.Z occupancy at the active var promoter is antagonized by PfSir2A during the intraerythrocytic life cycle. We conclude that PfH2A.Z contributes to the nucleosome architecture at promoters and is regulated dynamically in active var genes

Mean-variance and mean-semivariance portfolio selection: A multivariate nonparametric approach

While univariate nonparametric estimation methods have been developed for estimating returns in mean-downside risk portfolio optimization, the problem of handling possible cross-correlations in a vector of asset returns has not been addressed in portfolio selection. We present a novel multivariate nonparametric portfolio optimization procedure using kernel-based estimators of the conditional mean and the conditional median. The method accounts for the covariance structure information from the full set of returns. We also provide two computational algorithms to implement the estimators. Via the analysis of 24 French stock market returns, we evaluate the in- and out-sample performance of both portfolio selection algorithms against optimal portfolios selected by "classical'' and univariate nonparametric methods for three highly different time-periods and different levels of expected return. By allowing for cross-correlations among returns, our results suggest that the proposed multivariate nonparametric method is a useful extension of standard univariate nonparametric portfolio selection approaches

Microbial monitoring by molecular tools of an upflow anaerobic filter treating abattoir wastewaters

The performance of anaerobic digestion of abattoir wastewaters (AW) in an upflow anaerobic filter (UAF) was investigated under mesophilic (37 degrees C) and thermophilic (55 degrees C) conditions. The effects of increasing temperature on the performance of the UAF and on the dynamics of the microbial community of the anaerobic sludge were studied. The results showed that chemical oxygen demand (COD) removal efficiency of 90% was achieved for organic loading rates (OLRs) up to 4.5 g COD L-1 d(-1) in mesophilic conditions, while in thermophilic conditions, the highest OLRs of 9 g COD L-1 d(-1) led to the efficiency of 72%. The use of molecular and microbiological methods to recover microbial populations involved in this process showed that fermentative bacteria were the prominent members of the sludge microbial community. Three novel strains were identified as Macellibacteroides fermentans, Desulfotomaculum peckii and Defluviitalea saccharophila

Exploring by-products generated by the anaerobic degradation process of synthetic wastewater containing indigo dye

This work aims to study the by-products generated by the anaerobic degradation process of synthetic wastewater containing indigo dye. These by-products were analysed and identified by both high performance liquid chromatography (HPLC) and nuclear magnetic resonance (H-1 NMR). HPLC results showed the dependence of the by-products to the operating conditions. The obtained HPLC chromatogram at the end of the experiments (Run 1) reveals different fractions, with at least eight distinguishable by-products. Increasing the hydraulic retention time from 1 to 5days (Run 5) which corresponding to the start up of the bioreactor caused a significant change of the obtained HPLC chromatogram, with the decrease of the number of these by-products to only 3 ones. H-1 NMR analysis was realised with three representative fractions. The results showed that hypothetical structure of the by-products corresponding to aromatic cycles 1,2-disubstituted and possessing an axial symmetry similar to the phthalate groups

Biohydrogen production from hyperthermophilic anaerobic digestion of fruit and vegetable wastes in seawater : simplification of the culture medium of Thermotoga maritima

Biohydrogen production by the hyperthermophilic and halophilic bacterium T. maritima, using fruit and vegetable wastes as the carbon and energy sources was studied. Batch fermentation cultures showed that the use of a culture medium containing natural seawater and fruit and vegetable wastes can replace certain components (CaCl2, MgCl2, Balch's oligo-elements, yeast extract, KH2PO4 and K2HPO4) present in basal medium. However, a source of nitrogen and sulfur remained necessary for biohydrogen production. When fruit and vegetable waste collected from a wholesale market landfill was used, no decreases in total H-2 production (139 mmol L-1) or H-2 yield (3.46 mol mol(-1)) was observed

Application of the bootstrap approach to the choice of dimension and the a parameter in the SIRa method.

International audienceTo reduce the dimensionality of regression problems, sliced inverse regression approaches make it possible to determine linear combinations of a set of explanatory variables X related to the response variable Y in general semiparametric regression context. From a practical point of view, the determination of a suitable dimension (number of the linear combination of X) is important. In the literature, statistical tests based on the nullity of some eigenvalues have been proposed. Another approach is to consider the quality of the estimation of the effective dimension reduction (EDR) space. The square trace correlation between the true EDR space and its estimate can be used as goodness of estimation. In this paper, we focus on the SIR method and propose a na¨ıve bootstrap estimation of the square trace correlation criterion. Moreover, this criterion could also select the parameter in the SIR method. We indicate how it can be used in practice. A simulation study is performed to illustrate the behaviour of this approach

Desulfotomaculum peckii sp nov., a moderately thermophilic member of the genus Desulfotomaculum, isolated from an upflow anaerobic filter treating abattoir wastewaters

A novel anaerobic thermophilic sulfate-reducing bacterium designated strain LINDBHT1(T) was isolated from an anaerobic digester treating abattoir wastewaters in Tunisia. Strain LINDBHT1(T) grew at temperatures between 50 and 65 degrees C (optimum 55-60 degrees C), and at pH between 5.9 and 9.2 (optimum pH 6.0-6.8). Strain LINDBHT1(T) required salt for growth (1-40 g NaCl l(-1)), with an optimum of 20-30 g l(-1). In the presence of sulfate as terminal electron acceptor, strain LINDBHT1(T) used H2/CO2, propanol, butanol and ethanol as carbon and energy sources but fumarate, formate, lactate and pyruvate were not utilized. Butanol was converted to butyrate, while propanol and ethanol were oxidized to propionate and acetate, respectively. Sulfate, sulfite and thiosulfate were utilized as terminal electron acceptors but elemental sulfur, iron (III), fumarate, nitrate and nitrite were not used. The G+C content of the genomic DNA was 44.4 mol%. Phylogenetic analysis of the small-subunit rRNA gene sequence indicated that strain LINDBHT1(T) was affiliated to the genus Desulfotomaculum with the type strains of Desulfotomaculum halophilum and Desulfotomaculum alkaliphilum as its closest phylogenetic relatives (about 89% similarity). This strain represents a novel species of the genus Desulfotomaculum, Desulfotomaculum peckii sp. nov.; the type strain is LINDBHT1(T) (=DSM 23769(T)-JCM 17209(T))

Bacterial ecology of abattoir wastewater treated by an anaerobic digestor

Wastewater from an anaerobic treatment plant at a slaughterhouse was analysed to determine the bacterial biodiversity present. Molecular analysis of the anaerobic sludge obtained from the treatment plant showed significant diversity, as 27 different phyla were identified. Firmicutes, Proteobacteria, Bacteroidetes, Thermotogae, Euryarchaeota (methanogens), and msbl6 (candidate division) were the dominant phyla of the anaerobic treatment plant and represented 21.7%, 18.5%, 11.5%, 9.4%, 8.9%, and 8.8% of the total bacteria identified, respectively. The dominant bacteria isolated were Clostridium, Bacteroides, Desulfobulbus, Desulfomicrobium, Desulfovibrio and Desulfotomaculum. Our results revealed the presence of new species, genera and families of microorganisms. The most interesting strains were characterised. Three new bacteria involved in anaerobic digestion of abattoir wastewater were published