MB-MDR: Model-Based Multifactor Dimensionality Reduction for detecting interactions in high-dimensional genomic data

L’anàlisi de l’efecte dels gens i els factors ambientals en el desenvolupament de malalties complexes és un gran repte estadístic i computacional. Entre les diverses metodologies de mineria de dades que s’han proposat per a l’anàlisi d’interaccions una de les més populars és el mètode Multifactor Dimensionality Reduction, MDR, (Ritchie i al. 2001). L’estratègia d’aquest mètode és reduir la dimensió multifactorial a u mitjançant l’agrupació dels diferents genotips en dos grups de risc: alt i baix. Tot i la seva utilitat demostrada, el mètode MDR té alguns inconvenients entre els quals l’agrupació excessiva de genotips pot fer que algunes interaccions importants no siguin detectades i que no permet ajustar per efectes principals ni per variables confusores. En aquest article il•lustrem les limitacions de l’estratègia MDR i d’altres aproximacions no paramètriques i demostrem la conveniència d’utilitzar metodologies parametriques per analitzar interaccions en estudis cas-control on es requereix l’ajust per variables confusores i per efectes principals. Proposem una nova metodologia, una versió paramètrica del mètode MDR, que anomenem Model-Based Multifactor Dimensionality Reduction (MB-MDR). La metodologia proposada té com a objectiu la identificació de genotips específics que estiguin associats a la malaltia i permet ajustar per efectes marginals i variables confusores. La nova metodologia s’il•lustra amb dades de l’Estudi Espanyol de Cancer de Bufeta.

Competitive interactions between species of fresh-water snails: I. Laboratory. IC. Comparative survival of Biomphalaria glabrata and B. Straminea kept out of water

Biomphalaria glabrata and B. straminea were submitted to an out-door laboratory experiment for testing their comparative ability to resist desiccation. Results have shown that B. straminea is significantly higher resistant than B. glabrata. After five months under such distressing condition the survival ratios were: B. glabrata 8.1 per cent and B. straminea 18.4 per cent.

Molluscicide activity of the "Avelós" plant (Euphorbia tirucalli, L. ) on Biomphalaria glabrata, the mollusc vector of schistosomiasis

An aqueous solution of the latex of Euphorbia tirucalli collected at sites receiving large amounts of sunlight showed molluscicide action on Biomphalaria glabrata, with LD50 obtained at the concentration of 28,0 ppm and LD90 at the concentration of 85,0 ppm. The toxicity of the product for fish was similar to that of Bayluscide and of copper sulfate used for comparison. However, the wide distribution of the plant, its easy propagation and the simple procedure for extraction of the active substance, which is biodegradable, favor "avelós" as a promising agent in the control of schistosomiasis.

Species distribution models reveal apparent competitive and facilitative effects of a dominant species on the distribution of tundra plants

Abiotic factors are considered strong drivers of species distribution and assemblages. Yet these spatial patterns are also influenced by biotic interactions. Accounting for competitors or facilitators may improve both the fit and the predictive power of species distribution models (SDMs). We investigated the influence of a dominant species, Empetrum nigrum ssp. hermaphroditum, on the distribution of 34 subordinate species in the tundra of northern Norway. We related SDM parameters of those subordinate species to their functional traits and their co-occurrence patterns with E. hermaphroditum across three spatial scales. By combining both approaches, we sought to understand whether these species may be limited by competitive interactions and/or benefit from habitat conditions created by the dominant species. The model fit and predictive power increased for most species when the frequency of occurrence of E. hermaphroditum was included in the SDMs as a predictor. The largest increase was found for species that 1) co-occur most of the time with E. hermaphroditum, both at large (i.e. 750 m) and small spatial scale (i.e. 2 m) or co-occur with E. hermaphroditum at large scale but not at small scale and 2) have particularly low or high leaf dry matter content (LDMC). Species that do not co-occur with E. hermaphroditum at the smallest scale are generally palatable herbaceous species with low LDMC, thus showing a weak ability to tolerate resource depletion that is directly or indirectly induced by E. hermaphroditum. Species with high LDMC, showing a better aptitude to face resource depletion and grazing, are often found in the proximity of E. hermaphroditum. Our results are consistent with previous findings that both competition and facilitation structure plant distribution and assemblages in the Arctic tundra. The functional and co-occurrence approaches used were complementary and provided a deeper understanding of the observed patterns by refinement of the pool of potential direct and indirect ecological effects of E. hermaphroditum on the distribution of subordinate species. Our correlative study would benefit being complemented by experimental approaches.

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis.

The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.

Using life strategies to explore the vulnerability of ecosystem services to invasion by alien plants

Invasive plants can have different effects of ecosystem functioning and on the provision of ecosystem services, from strongly deleterious impacts to positive effects. The nature and intensity of such effects will depend on the service and ecosystem being considered, but also on features of life strategies of invaders that influence their invasiveness as well as their influence of key processes of receiving ecosystems. To address the combined effect of these various factors we developed a robust and efficient methodological framework that allows to identify areas of possible conflict between ecosystem services and alien invasive plants, considering interactions between landscape invasibility and species invasiveness. Our framework combines the statistical robustness of multi-model inference, efficient techniques to map ecosystem services, and life strategies as a functional link between invasion, functional changes and potential provision of services by invaded ecosystems. The framework was applied to a test region in Portugal, for which we could successfully predict the current patterns of plant invasion, of ecosystem service provision, and finally of probable conflict (expressing concern for negative impacts, and value for positive impacts on services) between alien species richness (total and per plant life strategy) and the potential provision of selected services. Potential conflicts were identified for all combinations of plant strategy and ecosystem service, with an emphasis for those concerning conflicts with carbon sequestration, water regulation and wood production. Lower levels of conflict were obtained between invasive plant strategies and the habitat for biodiversity supporting service. The added value of the proposed framework in the context of landscape management and planning is discussed in perspective of anticipation of conflicts, mitigation of negative impacts, and potentiation of positive effects of plant invasions on ecosystems and their services.

Promise for plant pest control: root-associated pseudomonads with insecticidal activities.

Insects are an important and probably the most challenging pest to control in agriculture, in particular when they feed on belowground parts of plants. The application of synthetic pesticides is problematic owing to side effects on the environment, concerns for public health and the rapid development of resistance. Entomopathogenic bacteria, notably Bacillus thuringiensis and Photorhabdus/Xenorhabdus species, are promising alternatives to chemical insecticides, for they are able to efficiently kill insects and are considered to be environmentally sound and harmless to mammals. However, they have the handicap of showing limited environmental persistence or of depending on a nematode vector for insect infection. Intriguingly, certain strains of plant root-colonizing Pseudomonas bacteria display insect pathogenicity and thus could be formulated to extend the present range of bioinsecticides for protection of plants against root-feeding insects. These entomopathogenic pseudomonads belong to a group of plant-beneficial rhizobacteria that have the remarkable ability to suppress soil-borne plant pathogens, promote plant growth, and induce systemic plant defenses. Here we review for the first time the current knowledge about the occurrence and the molecular basis of insecticidal activity in pseudomonads with an emphasis on plant-beneficial and prominent pathogenic species. We discuss how this fascinating Pseudomonas trait may be exploited for novel root-based approaches to insect control in an integrated pest management framework.

Peroxisome proliferator-activated receptor structures: ligand specificity, molecular switch and interactions with regulators.

Peroxisome proliferator-activated receptors (PPARs) compose a family of nuclear receptors that mediate the effects of lipidic ligands at the transcriptional level. In this review, we highlight advances in the understanding of the PPAR ligand binding domain (LBD) structure at the atomic level. The overall structure of PPARs LBD is described, and important protein ligand interactions are presented. Structure-activity relationships between isotypes structures and ligand specificity are addressed. It is shown that the numerous experimental three-dimensional structures available, together with in silico simulations, help understanding the role played by the activating function-2 (AF-2) in PPARs activation and its underlying molecular mechanism. The relation between the PPARs constitutive activity and the intrinsic stability of the active conformation is discussed. Finally, the interactions of PPARs LBD with co-activators or co-repressors, as well as with the retinoid X receptor (RXR) are described and considered in relation to PPARs activation.

Cell-matrix interactions in Schistosomal portal fibrosis: a dynamic event

In recent years, one of the most significant progress in the understanding of liver diseases was the demonstration that liver fibrosis is a dynamic process resulting from a balance between synthesis and degradation of several matrix components, collagen in particular. Thus, fibrosis has been found to be a very early event during liver diseases, be it of toxic, viral or parasitic origin, and to be spontaneously reversible, either partially or totally. In liver fibrosis cell matrix interactions are dependent on the existence of the many factors (sometimes acting in combination) which produce the same events at the cellular and molecular levels. These events are: (i) the recruitment of fiber-producing cells, (ii) their proliferation, (iii) the secretion of matrix constituents of the extracellular matrix, and (iv) the remodeling and degradation of the newly formed matrix. All these events represent, at least in principle, a target for a therapeutic intervention aimed at influencing the experimentally induced hepatic fibrosis. In this context, hepatosplenic schistosomiasis is of particular interest, being an immune cell-mediated granulomatous disease and a model of liver fibrosis allowing extensive studies in human and animals as well as providing original in vitro models.

Immunoregulation in human Schistosomiasis by idiotypic interactions and lymphokine-mediated mechanisms

Anti-idiotypic (anti-Id) T cells from schistosomiasis patients or former patients proliferate upon exposure to polyclonal or monoclonal anti-soluble egg antigen (SEA) antibodies. Chloroquine does not inhibit, the response, which is induced by F(ab')2 (but not soluble Fab) fragments of these antibodies. Purified T cells from former patients require macrophages or exogenous IL-1 to respond to anti-SEA Ids and can respond to matrix-bound Fab fragments in the presence of IL-1. These anti-Id T cells recognize the Ids directly. Chronic schistosomiasis patients immunoregulate the production of a non-IL-2 lymphokine that stimulates IL-2 receptor expression on resting T cells. This regulation is reversed upon chemotherapeutic cure.

The role of behavior in the survival of Biomphalaria glabrata in biossays with the plant molluscicide Phytolacca dodecandra

This work examines the role of behavior in the survival of Biomphalaria glabrata exposed to 25, 50 75 and 100 mgl-1 of Phytolacca dodecandra. Time-lapse cinematography was used to quantify accurately the following parameters: (a) frequency of exits from the solution, (b) time spent out of the solution and (c) time elapsed until the first exit from the solution. These behavior patterns were statistically compared between surviving snails and those which later died. The proportion of surviving snails leaving the liquid medium was significantly higher than that of dying snails. In addition, the surviving group spent significantly more time out of the solution than the group which died, except for the 100 mgl-1 concentration. However, no significant difference was detected in the time elapsed until the first exit from the solution. It can be concluded that both the tendency to leave the P. dodecandra solutions, and the time spent out of them, contributed significantly to snail survival. Molluscicide bioassays should take into account the possibility that some behavior patterns of planorbids might contribute to the protection of the snails.

Biodiversity of amoebae and amoebae-resisting bacteria in a drinking water treatment plant

The complex ecology of free-living amoebae (FLA) and their role in spreading pathogenic microorganisms through water systems have recently raised considerable interest. In this study, we investigated the presence of FLA and amoebae-resisting bacteria (ARB) at various stages of a drinking water plant fed with river water. We isolated various amoebal species from the river and from several points within the plant, mostly at early steps of water treatment. Echinamoeba- and Hartmannella-related amoebae were mainly recovered in the drinking water plant whereas Acanthamoeba- and Naegleria-related amoebae were recovered from the river water and the sand filtration units. Some FLA isolates were recovered immediately after the ozonation step, thus suggesting resistance of these microorganisms to this disinfection procedure. A bacterial isolate related to Mycobacterium mucogenicum was recovered from an Echinamoeba-related amoeba isolated from ozone-treated water. Various other ARB were recovered using co-culture with axenic Acanthamoeba castellanii, including mycobacteria, legionella, Chlamydia-like organisms and various proteobacteria. Noteworthy, a new Parachlamydia acanthamoebae strain was recovered from river water and from granular activated carbon (GAC) biofilm. As amoebae mainly multiply in sand and GAC filters, optimization of filter backwash procedures probably offers a possibility to better control these protists and the risk associated with their intracellular hosts

Prenatal Representations of Family in Parents and Coparental Interactions as Predictors of Triadic Interactions During Infancy

In this study, we explored the predictive role of family interactions and family representations in mothers and fathers during pregnancy for postnatal motherfatherinfant interactions during the first 2 years after birth. Families (N = 42) were seen at the fifth month of pregnancy and at 3 and 18 months after birth. During pregnancy, parents were asked to play with their baby at the first meeting by using a doll in accordance with the procedure of the prenatal Lausanne Trilogue Play (LTP; A. Corboz-Warnery & E. Fivaz-Depeursinge, 2001; E. Fivaz-Depeursinge, F. Frascarolo-Moutinot, & A. Corboz-Warnery, 2010). Family representations were assessed by administering the Family System Test (T. Gehring, 1998). Marital satisfaction and the history of the couple were assessed through self-reported questionnaires. At 3 and 18 months, family interactions were assessed in the postnatal LTP. Infant temperament was assessed through parent reports. Results show that (a) prenatal interactions and child temperament are the most important predictors of family interactions and (b) paternal representations are predictive of family interactions at 3 months. These results show that observational assessment of nascent family interactions is possible during pregnancy, which would allow early screening of family maladjustment. The findings also highlight the necessity of taking into account paternal representations as a significant variable in the development of family interactions.