Étude des mécanismes moléculaires influençant la variation de phase des adhésines P, F1651 et CS31A présentes chez des souches d'Escherichia coli pathogènes.

F1651, les pili Pap et l’antigène CS31A associé aux antigènes de surface K88 sont tout trois des membres de la famille de type P des facteurs d’adhérence jouant un rôle prépondérant lors de l’établissement d’une maladie causée par des souches Escherichia coli pathogènes, en particulier des souches d’E. coli pathogènes extra-intestinales (ExPEC, Extra-intestinal pathogenic E. coli). Leur expression est sous le contrôle d’un mécanisme de régulation transcriptionnel dépendant de l’état de méthylation de l’ADN, résultant dans l’existence de deux populations définies, l’une exprimant l’adhésine (population ON) et l’autre ne l’exprimant pas (population OFF). Malgré de fortes identités de séquences, ces trois systèmes diffèrent l’un de l’autre, principalement par le pourcentage de cellules ON rencontrées. Ainsi, quand CS31A est systématiquement orienté vers un état considéré comme OFF, F1651 présente une phase ON particulièrement élevée et Pap montre deux états OFF et ON bien distincts, selon le phénotype de départ. La protéine régulatrice sensible à la leucine (Lrp, Leucine-responsive regulatory protein) joue un rôle essentiel dans la réversibilité de ce phénomène épigénétique et il est supposé que les différences de séquences au niveau de la région régulatrice modifient la localisation à ces sites de fixation de Lrp; ce qui résulte, en final, aux différences de phase existant entre CS31A, F1651 et Pap.À l’aide de divers techniques parmi lesquelles l’utilisation de gènes rapporteurs, mutagénèses dirigées et d’analyse des interactions ADN-protéines in vitro, nous montrons dans ce présent projet que la phase OFF prédominante chez CS31A est principalement due à une faible interaction de Lrp avec la région distale de l’opéron clp, et que la présence d’un homologue du régulateur local PapI joue un rôle également clef dans la production de CS31A. Dans le cas de F1651, nous montrons dans cette étude que le taux élevé de cellules en phase ON est dû à une altération dans le maintien de Lrp sur les sites répresseurs 1-3. Ceci est dû à la présence de deux nucléotides spécifiques, situé de part et d’autre du site répresseur 1, qui défavorisent la fixation de Lrp sur ce site précis. Tout comme dans le cas de CS31A, la formation d’un complexe, activateur ou répresseur de la phase ON, dépend également de l’action de du régulatuer local FooI, qui favorise alors le déplacement de Lrp des sites répresseurs 1-3 vers les sites activateurs 4-6.

The evolution of inter-genomic variation in arbuscular mycorrhizal fungi

Contexte: Les champignons mycorhiziens à arbuscules (AMF) établissent des relations symbiotiques avec la plupart des plantes grâce à leurs réseaux d’hyphes qui s’associent avec les racines de leurs hôtes. De précédentes études ont révélé des niveaux de variation génétique extrêmes pour des loci spécifiques permettant de supposer que les AMF peuvent contenir des milliers de noyaux génétiquement divergents dans un même cytoplasme. Si aucun processus de reproduction sexuée n’a jusqu’ici été observé chez ces mycorhizes, on constate cependant que des niveaux élevés de variation génétique peuvent être maintenus à la fois par l’échange de noyaux entre hyphes et par des processus fréquents de recombinaison entre noyaux. Les AMF se propagent par l’intermédiaire de spores qui contiennent chacune un échantillon d’une population initiale de noyaux hétérogènes, directement hérités du mycélium parent. À notre connaissance les AMF sont les seuls organismes qui ne passent jamais par un stade mononucléaire, ce qui permet aux noyaux de diverger génétiquement dans un même cytoplasme. Ces aspects singuliers de la biologie des AMF rendent l’estimation de leur diversité génétique problématique. Ceci constitue un défi majeur pour les écologistes sur le terrain mais également pour les biologistes moléculaires dans leur laboratoire. Au-delà même des problématiques de diversité spécifique, l’amplitude du polymorphisme entre noyaux mycorhiziens est mal connue. Le travail proposé dans ce manuscrit de thèse explore donc les différents aspects de l’architecture génomique singulière des AMF. Résultats L’ampleur du polymorphisme intra-isolat a été déjà observée pour la grande sous-unité d’ARN ribosomal de l’isolat Glomus irregulare DAOM-197198 (précédemment identifié comme G. intraradices) et pour le gène de la polymerase1-like (PLS) de Glomus etunicatum isolat NPI. Dans un premier temps, nous avons pu confirmer ces résultats et nous avons également pu constater que ces variations étaient transcrites. Nous avons ensuite pu mettre en évidence la présence d’un goulot d’étranglement génétique au moment de la sporulation pour le locus PLS chez l’espèce G. etunicatum illustrant les importants effets d’échantillonnage qui se produisaient entre chaque génération de spore. Enfin, nous avons estimé la différentiation génétique des AMF en utilisant à la fois les réseaux de gènes appliqués aux données de séquençage haut-débit ainsi que cinq nouveaux marqueurs génomiques en copie unique. Ces analyses révèlent que la différenciation génomique est présente de manière systématique dans deux espèces (G. irregulare et G. diaphanum). Conclusions Les résultats de cette thèse fournissent des preuves supplémentaires en faveur du scénario d’une différenciation génomique entre noyaux au sein du même isolat mycorhizien. Ainsi, au moins trois membres du genre Glomus, G. irregulare, G. diaphanum and G. etunicatum, apparaissent comme des organismes dont l’organisation des génomes ne peut pas être décrit d’après un modèle Mendélien strict, ce qui corrobore l’hypothèse que les noyaux mycorhiziens génétiquement différenciés forment un pangenome.

Contributions of local, lateral and contextual habitat variables to explaining variation in fisheries productivity metrics in the littoral zone of a reservoir

Puisque l’altération des habitats d’eau douce augmente, il devient critique d’identifier les composantes de l’habitat qui influencent les métriques de la productivité des pêcheries. Nous avons comparé la contribution relative de trois types de variables d’habitat à l’explication de la variance de métriques d’abondance, de biomasse et de richesse à l’aide de modèles d’habitat de poissons, et avons identifié les variables d’habitat les plus efficaces à expliquer ces variations. Au cours des étés 2012 et 2013, les communautés de poissons de 43 sites littoraux ont été échantillonnées dans le Lac du Bonnet, un réservoir dans le Sud-est du Manitoba (Canada). Sept scénarios d’échantillonnage, différant par l’engin de pêche, l’année et le moment de la journée, ont été utilisés pour estimer l’abondance, la biomasse et la richesse à chaque site, toutes espèces confondues. Trois types de variables d’habitat ont été évalués: des variables locales (à l’intérieur du site), des variables latérales (caractérisation de la berge) et des variables contextuelles (position relative à des attributs du paysage). Les variables d’habitat locales et contextuelles expliquaient en moyenne un total de 44 % (R2 ajusté) de la variation des métriques de la productivité des pêcheries, alors que les variables d’habitat latérales expliquaient seulement 2 % de la variation. Les variables les plus souvent significatives sont la couverture de macrophytes, la distance aux tributaires d’une largeur ≥ 50 m et la distance aux marais d’une superficie ≥ 100 000 m2, ce qui suggère que ces variables sont les plus efficaces à expliquer la variation des métriques de la productivité des pêcheries dans la zone littorale des réservoirs.

Inference for nonparametric high-frequency estimators with an application to time variation in betas

We consider the problem of conducting inference on nonparametric high-frequency estimators without knowing their asymptotic variances. We prove that a multivariate subsampling method achieves this goal under general conditions that were not previously available in the literature. We suggest a procedure for a data-driven choice of the bandwidth parameters. Our simulation study indicates that the subsampling method is much more robust than the plug-in method based on the asymptotic expression for the variance. Importantly, the subsampling method reliably estimates the variability of the Two Scale estimator even when its parameters are chosen to minimize the finite sample Mean Squared Error; in contrast, the plugin estimator substantially underestimates the sampling uncertainty. By construction, the subsampling method delivers estimates of the variance-covariance matrices that are always positive semi-definite. We use the subsampling method to study the dynamics of financial betas of six stocks on the NYSE. We document significant variation in betas within year 2006, and find that tick data captures more variation in betas than the data sampled at moderate frequencies such as every five or twenty minutes. To capture this variation we estimate a simple dynamic model for betas. The variance estimation is also important for the correction of the errors-in-variables bias in such models. We find that the bias corrections are substantial, and that betas are more persistent than the naive estimators would lead one to believe.

Ecology And Seasonal Variation Of Microalgal Community In An Oil Refinery Effluent Holding Pond: Monitoring And Assessment

The microalgal community as primary producers has to play a significant role in the biotic and abitoic interactions of any aquatic ecosystem. Whenever a community is exposed to a pollutant, responses can occur because individuals acclimate to pollutant caused changes and selection can occur favouring resistant genotypes within a population and selection among species can result in changes in community structure. The microalgal community of industrial effluent treatment systems are continuously exposed to pollutants and there is little data available on the structure and seasonal variation of microalgal community of industrial effluent holding ponds, especially of a complex effluent like that of refinery. The aim of the present study was to investigate the annual variation in the ecology, biomass, productivity and community structure of the algal community of a refinery effluent holding pond. The results of the study showed the pond to be a eutrophic system with a resistant microalgal community with distinct seasonal variation in species composition

Polimorfismos del gen Butirilcolinesterasa responsables de reacciones adversas en pacientes consumidores de “cocaína”

La butirilcolinesterasa humana (BChE; EC 3.1.1.8) es una enzima polimórfica sintetizada en el hígado y en el tejido adiposo, ampliamente distribuida en el organismo y encargada de hidrolizar algunos ésteres de colina como la procaína, ésteres alifáticos como el ácido acetilsalicílico, fármacos como la metilprednisolona, el mivacurium y la succinilcolina y drogas de uso y/o abuso como la heroína y la cocaína. Es codificada por el gen BCHE (OMIM 177400), habiéndose identificado más de 100 variantes, algunas no estudiadas plenamente, además de la forma más frecuente, llamada usual o silvestre. Diferentes polimorfismos del gen BCHE se han relacionado con la síntesis de enzimas con niveles variados de actividad catalítica. Las bases moleculares de algunas de esas variantes genéticas han sido reportadas, entre las que se encuentra las variantes Atípica (A), fluoruro-resistente del tipo 1 y 2 (F-1 y F-2), silente (S), Kalow (K), James (J) y Hammersmith (H). En este estudio, en un grupo de pacientes se aplicó el instrumento validado Lifetime Severity Index for Cocaine Use Disorder (LSI-C) para evaluar la gravedad del consumo de “cocaína” a lo largo de la vida. Además, se determinaron Polimorfismos de Nucleótido Simple (SNPs) en el gen BCHE conocidos como responsables de reacciones adversas en pacientes consumidores de “cocaína” mediante secuenciación del gen y se predijo el efecto delos SNPs sobre la función y la estructura de la proteína, mediante el uso de herramientas bio-informáticas. El instrumento LSI-C ofreció resultados en cuatro dimensiones: consumo a lo largo de la vida, consumo reciente, dependencia psicológica e intento de abandono del consumo. Los estudios de análisis molecular permitieron observar dos SNPs codificantes (cSNPs) no sinónimos en el 27.3% de la muestra, c.293A>G (p.Asp98Gly) y c.1699G>A (p.Ala567Thr), localizados en los exones 2 y 4, que corresponden, desde el punto de vista funcional, a la variante Atípica (A) [dbSNP: rs1799807] y a la variante Kalow (K) [dbSNP: rs1803274] de la enzima BChE, respectivamente. Los estudios de predicción In silico establecieron para el SNP p.Asp98Gly un carácter patogénico, mientras que para el SNP p.Ala567Thr, mostraron un comportamiento neutro. El análisis de los resultados permite proponer la existencia de una relación entre polimorfismos o variantes genéticas responsables de una baja actividad catalítica y/o baja concentración plasmática de la enzima BChE y algunas de las reacciones adversas ocurridas en pacientes consumidores de cocaína.

Small-area variation in health care affecting the choice of cesarean delivery: the case of a Colombian health insurer

In the midst of health care reform, Colombia has succeeded in increasing health insurance coverage and the quality of health care. In spite of this, efficiency continues to be a matter of concern, and small-area variations in health care are one of the plausible causes of such inefficiencies. In order to understand this issue, we use individual data of all births from a Contributory-Regimen insurer in Colombia. We perform two different specifications of a multilevel logistic regression model. Our results reveal that hospitals account for 20% of variation on the probability of performing cesarean sections. Geographic area only explains 1/3 of the variance attributable to the hospital. Furthermore, some variables from both demand and supply sides are found to be also relevant on the probability of undergoing cesarean sections. This paper contributes to previous research by using a hierarchical model and by defining hospitals as cluster. Moreover, we also include clinical and supply induced demand variables.

Predation in Ground-Nesting Birds: an Experimental Study Using Natural Egg-Color Variation

We tested the hypothesis that cryptically colored eggs would suffer less predation than conspicuous eggs in the ground-nesting red-legged partridge, Alectoris rufa. We used A. rufa as a model species because it has a wide range of natural egg colors, the eggs are widely available from breeding farms, and nests are easily mimicked because they are scrapes containing no vegetation. The study was conducted in the spring of 2001 in forest and fallow fields of central Spain in Castilla La Mancha, Ciudad Real. We used 384 clutches of natural eggs that were white, white spotted, brown, or brown spotted. Within clutches, eggs were consistent in color and size; among clutches, color differences were distributed across habitats. Clutches were checked once after 2 wk of exposure. Cryptic coloration had a survival advantage that was dependent on the local suite of predators. Rodent predation was nonselective with respect to clutch color; however, avian predation was significantly higher for conspicuous clutches. In addition, there was an interaction of landscape and egg color for avian predation. In forest landscapes, the clutches with highest survival were brown spotted, whereas in fallow landscapes, brown and brown spotted clutches had higher survival than white and white potted clutches. Thus, both the predator suite and the landscape had significant effects on the value of cryptic egg coloration. Our study is relevant for conservationists and managers in charge of restocking programs in hunting areas. The release of other partridge species or their hybrids could result in hybridization with wild partridges, potentially leading to nonoptimal clutch pigmentation and reduced survival of the native species. We therefore recommend that local authorities, managers, and conservationists be cautious with the use of alien species and hybrids and release only autochthonous species of partridges within their natural ranges.

Stand and within-stand factors influencing Golden-winged Warbler use of regenerating stands in the central Appalachian Mountains

The Golden-winged Warbler (Vermivora chrysoptera) is currently being considered for protected status under the U.S. Endangered Species Act. The creation of breeding habitat in the Appalachian Mountains is considered a conservation priority for this songbird, which is dependent on extensively forested landscapes with adequate availability of young forest. We modeled abundance of Golden-winged Warbler males in regenerating harvested forest stands that were 0-17 years postharvest at both mid-Appalachian and northeast Pennsylvania regional scales using stand and within-stand characteristics of 222 regenerating stands, 2010-2011. Variables that were most influential at the mid-Appalachian scale were different than those in the northeast region. Across the mid-Appalachian ecoregion, the proportion of young forest cover, i.e., shrub/scrub cover, within 1 km of regenerating stands best explained abundance of Golden-winged Warblers. Golden-winged Warbler response was best explained by a concave quadratic relationship in which abundance was highest with 5-15% land in young forest cover. We also found evidence that the amount of herbaceous cover, i.e., the amount of grasses and forbs, within a regenerating stand positively influenced abundance of Golden-winged Warblers. In northeastern Pennsylvania, where young forest cover is found in high proportions, the distance to the nearest regenerating stand best explained variation in abundance of Golden-winged Warblers. Abundance of Golden-winged Warblers was <1 male per survey when another regenerating stand was >1500 m away. When modeling within-stand features in the northeast region, many of the models were closely ranked, indicating that multiple variables likely explained Golden-winged Warbler response to within-stand conditions. Based on our findings, we have proposed several management guidelines for land managers interested in creating breeding habitat for Golden-winged Warblers using commercial timber operations. For example, we recommend when managing for Golden-winged Warblers in the central Appalachian Mountains that managers should strive for 15% young forest in a heavily forested landscape (>70% forest cover) and cluster stands within 1-2 km of other young forest habitats.

The variation in transparency of amniotic membrane used in ocular surface regeneration

Background/aims: Scant consideration has been given to the variation in structure of the human amniotic membrane (AM) at source or to the significance such differences might have on its clinical transparency. Therefore, we applied our experience of quantifying corneal transparency to AM. Methods: Following elective caesarean, AM from areas of the fetal sac distal and proximal (ie, adjacent) to the placenta was compared with freeze-dried AM. The transmission of light through the AM samples was quantified spectrophotometrically; also, tissue thickness was measured by light microscopy and refractive index by refractometry. Results: Freeze-dried and freeze-thawed AM samples distal and proximal to the placenta differed significantly in thickness, percentage transmission of visible light and refractive index. The thinnest tissue (freeze-dried AM) had the highest transmission spectra. The thickest tissue (freeze-thawed AM proximal to the placenta) had the highest refractive index. Using the direct summation of fields method to predict transparency from an equivalent thickness of corneal tissue, AM was found to be up to 85% as transparent as human cornea. Conclusion: When preparing AM for ocular surface reconstruction within the visual field, consideration should be given to its original location from within the fetal sac and its method of preservation, as either can influence corneal transparency.

Tracking larval insect movement within soil using high resolution X-ray microtomography

1. In contrast to above-ground insects, comparatively little is known about the behaviour of subterranean insects, due largely to the difficulty of studying them in situ. 2. The movement of newly hatched (neonate) clover root weevil (Sitona lepidus L. Coleoptera: Curculinidae) larvae was studied non-invasively using recently developed high resolution X-ray microtomography. 3. The movement and final position of S. lepidus larvae in the soil was reliably established using X-ray microtomography, when compared with larval positions that were determined by destructively sectioning the soil column. 4. Newly hatched S. lepidus larvae were seen to attack the root rhizobial nodules of their host plant, white clover (Trifolium repens L.). Sitona lepidus larvae travelled between 9 and 27 mm in 9 h at a mean speed of 1.8 mm h(-1). 5. Sitona lepidus larvae did not move through the soil in a linear manner, but changed trajectory in both the lateral and vertical planes.

Exploring the spatial variation of take-all (Gaeumannomyces graminis var. tritici) for site-specific management

The fungus Gaeumannomyces graminis var. tritici (Ggt), commonly known as the take-all fungus, causes damage to roots of wheat and barley that limits crop growth and causes loss of yield. There was little knowledge on the within-field spatial variation of take-all and relations with features in the growing crop, selected soil properties and spectral information from remotely sensed imagery. Geostatistical analyses showed that take-all, chlorosis and leaf area index had similar patchy distributions. Many of the spectral bands from a hyperspectral image also had similar spatial patterns to take-all and chlorosis. Relations between take-all and mineral nitrogen, elevation and pH were generally weaker.

Individual Differences in Amygdala and Ventromedial Prefrontal Cortex Activity are Associated with Evaluation Speed and Psychological Well-being

Using functional magnetic resonance imaging, we examined whether individual differences in amygdala activation in response to negative relative to neutral information are related to differences in the speed with which such information is evaluated, the extent to which such differences are associated with medial prefrontal cortex function, and their relationship with measures of trait anxiety and psychological well-being (PWB). Results indicated that faster judgments of negative relative to neutral information were associated with increased left and right amygdala activation. In the prefrontal cortex, faster judgment time was associated with relative decreased activation in a cluster in the ventral anterior cingulate cortex (ACC, BA 24). Furthermore, people who were slower to evaluate negative versus neutral information reported higher PWB. Importantly, higher PWB was strongly associated with increased activation in the ventral ACC for negative relative to neutral information. Individual differences in trait anxiety did not predict variation in judgment time or in amygdala or ventral ACC activity. These findings suggest that people high in PWB effectively recruit the ventral ACC when confronted with potentially aversive stimuli, manifest reduced activity in subcortical regions such as the amygdala, and appraise such information as less salient as reflected in slower evaluative speed.

The formation of large-scale current sheets within magnetic clouds

Magnetic clouds are a class of interplanetary coronal mass ejections (CME) predominantly characterised by a smooth rotation in the magnetic field direction, indicative of a magnetic flux rope structure. Many magnetic clouds, however, also contain sharp discontinuities within the smoothly varying magnetic field, suggestive of narrow current sheets. In this study we present observations and modelling of magnetic clouds with strong current sheet signatures close to the centre of the apparent flux rope structure. Using an analytical magnetic flux rope model, we demonstrate how such current sheets can form as a result of a cloud’s kinematic propagation from the Sun to the Earth, without any external forces or influences. This model is shown to match observations of four particular magnetic clouds remarkably well. The model predicts that current sheet intensity increases for increasing CME angular extent and decreasing CME radial expansion speed. Assuming such current sheets facilitate magnetic reconnection, the process of current sheet formation could ultimately lead a single flux rope becoming fragmented into multiple flux ropes. This change in topology has consequences for magnetic clouds as barriers to energetic particle propagation.

Characteristic magnetic field and speed properties of interplanetary coronal mass ejections and their sheath regions

Prediction of the solar wind conditions in near-Earth space, arising from both quasi-steady and transient structures, is essential for space weather forecasting. To achieve forecast lead times of a day or more, such predictions must be made on the basis of remote solar observations. A number of empirical prediction schemes have been proposed to forecast the transit time and speed of coronal mass ejections (CMEs) at 1 AU. However, the current lack of magnetic field measurements in the corona severely limits our ability to forecast the 1 AU magnetic field strengths resulting from interplanetary CMEs (ICMEs). In this study we investigate the relation between the characteristic magnetic field strengths and speeds of both magnetic cloud and noncloud ICMEs at 1 AU. Correlation between field and speed is found to be significant only in the sheath region ahead of magnetic clouds, not within the clouds themselves. The lack of such a relation in the sheaths ahead of noncloud ICMEs is consistent with such ICMEs being skimming encounters of magnetic clouds, though other explanations are also put forward. Linear fits to the radial speed profiles of ejecta reveal that faster-traveling ICMEs are also expanding more at 1 AU. We combine these empirical relations to form a prediction scheme for the magnetic field strength in the sheaths ahead of magnetic clouds and also suggest a method for predicting the radial speed profile through an ICME on the basis of upstream measurements.