Genomics and the origin of species.

Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.

Routine therapeutic drug monitoring in patients treated with 10-360 mg/day citalopram

From data collected during routine TDM, plasma concentrations of citalopram (CIT) and its metabolites demethylcitalopram (DCIT) and didemethylcitalopram (DDCIT) were measured in 345 plasma samples collected in steady-state conditions. They were from 258 patients treated with usual doses (20-60 mg/d) and from patients medicated with 80-360 mg/d CIT. Most patients had one or several comedications, including other antidepressants, antipsychotics, lithium, anticonvulsants, psychostimulants and somatic medications. Dose-corrected CIT plasma concentrations (C/D ratio) were 2.51 +/- 2.25 ng mL-1 mg-1 (n = 258; mean +/- SD). Patients >65 years had significantly higher dose-corrected CIT plasma concentrations (n = 56; 3.08 +/- 1.35 ng mL-1 mg-1) than younger patients (n = 195; 2.35 +/- 2.46 ng mL-1 mg-1) (P = 0.03). CIT plasma concentrations in the generally recommended dose range were [mean +/- SD, (median)]: 57 +/- 64 (45) ng/mL (10-20 mg/d; n = 64), 117 +/- 95 (91) ng/mL (21-60 mg/d; n = 96). At higher than usual doses, the following concentrations of CIT were measured: 61-120 mg/d CIT, 211 +/- 103 (190) ng/mL (n = 93); 121-200 mg/d: 339 +/- 143 (322) ng/mL (n = 70); 201-280 mg/d: 700 +/- 408 (565) ng/mL (n = 18); 281-360 mg/d: 888 +/- 620 (616) ng/mL (n = 4). When only one sample per patient (at the highest daily dose if repeated dosages) is considered, there is a linear and significant correlation (n = 48, r = 0.730; P < 0.001) between daily dose (10-200 mg/d) and CIT plasma concentrations. In experiments with dogs, DDCIT was reported to affect the QT interval when present at concentrations >300 ng/mL. In this study, DDCIT concentration reached 100 ng/mL in a patient treated with 280 mg/d CIT. Twelve other patients treated with 140-320 mg/d CIT had plasma concentrations of DDCIT within the range 52-73 ng/mL. In a subgroup comprised of patients treated with > or =160 mg/d CIT and with CIT plasma concentrations < or =300 ng/mL, and patients treated with < or =200 mg/d CIT and CIT plasma concentrations > or = 600 ng/mL, the enantiomers of CIT and DCIT were also analyzed. The highest S-CIT concentration measured in this subgroup was 327 ng/mL in a patient treated with 140 mg/d CIT, but the highest S-CIT concentration (632 ng/mL) was measured in patient treated with 360 mg/d CIT. In conclusion, there is a highly linear correlation between CIT plasma concentrations and CIT doses, well above the usual dose range.

A Picture of Performance Goals in the Social Plenum: The Interpersonal Antecedents and Consequences of Performance Goals

Bien que les activités où la compétence est un enjeu (p. ex. : problème académique) prennent souvent place dans des contextes interpersonnels (p. ex. : classe), hiérarchiques (p. ex. : enseignant-e/élèves), et spécifiques en termes de normes et de valeurs (p. ex. : culture), l'étude des buts de performance-le désir de se montrer compétent-e relativement à autrui-a le plus souvent été conduite au seul niveau intrapersonnel. S'appuyant sur le modèle transactionnel du stress et du coping, le modèle circumplexe des comportements interpersonnels, ainsi que sur la théorie de l'élaboration du conflit, la première partie de cette thèse révèle les conséquences interpersonnelles des buts de performance sur la régulation d'un comportement spécifique, à savoir le conflit sociocognitif (c.-à-d., une situation de confrontation avec un intéractant en désaccord) : les buts de performance-approche-le désir d'être meilleur-e qu'autrui-prédisent une régulation du conflit fortement agentique (dominante), soit la validation de son point de vue au détriment de celui de l'intéractant (que nous désignons régulation compétitive) ; alors que les buts de performance-évitement-le désir de ne pas être moins bon-ne qu'autrui-prédisent une régulation du conflit faiblement agentique (soumise), soit l'invalidation de son point de vue au bénéfice de celui de l'intéractant (que nous désignons régulation protective). De plus, les effets susmentionnés augmentent à mesure que l'intéractant est présenté comme supérieurement (vs. similairement) compétent. S'appuyant sur la littérature sur les structures de buts de groupe, et celle sur la socialisation des valeurs, la seconde partie de cette thèse révèle les antécédents interpersonnels des buts de performance, et plus spécifiquement le rôle du superviseur dans la socialisation des buts de performance : les buts de performance-approche d'un superviseur sont positivement associés avec l'émergence au cours du temps des buts de performance-approche de ses subordonnés (particulièrement lorsqu'ils se perçoivent comme compétents) et celle de leurs buts de performance-évitement (particulièrement lorsqu'ils se perçoivent comme incompétents). En outre, ce phénomène consistant en un processus de socialisation, les effets susmentionnés augmentent lorsque l'identification à l'endogroupe des subordonnées augmente, et lorsque l'adhésion aux valeurs culturelles occidentales dominantes (c.-à-d., rehaussement de soi) du superviseur augmente. Dans leur ensemble, ces résultats soulignent la nécessité d'étudier les buts dans leur plenum social, autrement dit, en adoptant une perspective interpersonnelle (c.-à-d., étudier les effets des buts entre les individus), positionnelle (c.-à-d., entre des individus de différentes positions sociales), et idéologique (c.- à-d., entre des individus se conformant à des normes spécifiques et adhérant à des valeurs spécifiques). -- Although competence-relevant activities (e.g., solving an academic problem) are often embedded in interpersonal (e.g., classroom), hierarchical (e.g., teacher/pupils), and norm-/value-specific (e.g., culture) settings, the study of performance goals-the desire to demonstrate competence relative to others-has mostly been conducted at the intrapersonal level alone. Drawing on the transactional model of stress and coping, the circumplex model of interpersonal behaviors, as well as on the conflict elaboration theory, the first part of this thesis reveals the interpersonal consequences of performance goals on the regulation of a specific behavior, namely socio-cognitive conflict (i.e., a situation of confrontation with a disagreeing interactant): Performance-approach goals-the desire to outperform others- predicted a highly agentic (dominant) conflict regulation, that is, the validation of one's point of view at the expense of that of the interactant (which we labeled competitive regulation); whereas performance-avoidance goals-the desire not to be outperformed by others- predicted a poorly agentic (submissive) conflict regulation, that is, the invalidation of one's point of view to the benefit of that of the interactant (which we labeled protective regulation). Furthermore, both the aforementioned effects were found to increase when the interactant was presented as being superiorly (vs. equally) in competence. Drawing on the literature on group goal structure, as well as on research on socialization of supervisors-based values, the second part of this thesis reveals the interpersonal antecedents of performance-based goals endorsement, focusing-more specifically-on the role of group-supervisors in performance goals socialization: Supervisor's performance-approach goals were positively associated with the emergence over time of subordinates' performance-approach (especially when perceiving themselves as competent) and -avoidance goals (especially when perceiving themselves as incompetent). Furthermore, providing evidence that this phenomenon essentially reflects a socialization process, both the aforementioned effects were found to increase as subordinates' in-group identification increased, and as supervisors' adherence to dominant Western values (i.e., self-enhancement values) increased. Taken together, these results advocate the need to study performance goals in their social plenum, that is, adopting an interpersonal (i.e., studying the effects of goals between individuals), positional (i.e., between individuals from different social positions), and ideological (i.e., between individuals following specific norms and endorsing specific values) perspective.

MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.

A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcription start site profiles, the mapping of transcription factor binding sites based on ChIP-chip data and the identification of quantitative trait loci (QTL) from whole genome SNP profiles. Input to such an analysis is a set of genome coordinates associated with counts or intensities. The output consists of a discrete number of peaks with respective volumes, extensions and center positions. We have developed for this purpose a flexible one-dimensional clustering tool, called MADAP, which we make available as a web server and as standalone program. A set of parameters enables the user to customize the procedure to a specific problem. The web server, which returns results in textual and graphical form, is useful for small to medium-scale applications, as well as for evaluation and parameter tuning in view of large-scale applications, requiring a local installation. The program written in C++ can be freely downloaded from ftp://ftp.epd.unil.ch/pub/software/unix/madap. The MADAP web server can be accessed at http://www.isrec.isb-sib.ch/madap/.

Promoter recognition and activation by the global response regulator CbrB in Pseudomonas aeruginosa.

In Pseudomonas aeruginosa, the CbrA/CbrB two-component system is instrumental in the maintenance of the carbon-nitrogen balance and for growth on carbon sources that are energetically less favorable than the preferred dicarboxylate substrates. The CbrA/CbrB system drives the expression of the small RNA CrcZ, which antagonizes the repressing effects of the catabolite repression control protein Crc, an RNA-binding protein. Dicarboxylates appear to cause carbon catabolite repression by inhibiting the activity of the CbrA/CbrB system, resulting in reduced crcZ expression. Here we have identified a conserved palindromic nucleotide sequence that is present in upstream activating sequences (UASs) of promoters under positive control by CbrB and σ(54) RNA polymerase, especially in the UAS of the crcZ promoter. Evidence for recognition of this palindromic sequence by CbrB was obtained in vivo from mutational analysis of the crcZ promoter and in vitro from electrophoretic mobility shift assays using crcZ promoter fragments and purified CbrB protein truncated at the N terminus. Integration host factor (IHF) was required for crcZ expression. CbrB also activated the lipA (lipase) promoter, albeit less effectively, apparently by interacting with a similar but less conserved palindromic sequence in the UAS of lipA. As expected, succinate caused CbrB-dependent catabolite repression of the lipA promoter. Based on these results and previously published data, a consensus CbrB recognition sequence is proposed. This sequence has similarity to the consensus NtrC recognition sequence, which is relevant for nitrogen control.

Similarities and differences in altitudinal versus latitudinal variation for morphological traits in Drosophila melanogaster.

Understanding how natural environments shape phenotypic variation is a major aim in evolutionary biology. Here, we have examined clinal, likely genetically based variation in morphology among 19 populations of the fruit fly (Drosophila melanogaster) from Africa and Europe, spanning a range from sea level to 3000 m altitude and including locations approximating the southern and northern range limit. We were interested in testing whether latitude and altitude have similar phenotypic effects, as has often been postulated. Both latitude and altitude were positively correlated with wing area, ovariole number, and cell number. In contrast, latitude and altitude had opposite effects on the ratio between ovariole number and body size, which was negatively correlated with egg production rate per ovariole. We also used transgenic manipulation to examine how increased cell number affects morphology and found that larger transgenic flies, due to a higher number of cells, had more ovarioles, larger wings, and, unlike flies from natural populations, increased wing loading. Clinal patterns in morphology are thus not a simple function of changes in body size; instead, each trait might be subject to different selection pressures. Together, our results provide compelling evidence for profound similarities as well as differences between phenotypic effects of latitude and altitude.

Modelling tree population dynamics at the alpine and boreal tree-line ecotones in response to climate and land-use change

Summary Ecotones are sensitive to change because they contain high numbers of species living at the margin of their environmental tolerance. This is equally true of tree-lines, which are determined by attitudinal or latitudinal temperature gradients. In the current context of climate change, they are expected to undergo modifications in position, tree biomass and possibly species composition. Attitudinal and latitudinal tree-lines differ mainly in the steepness of the underlying temperature gradient: distances are larger at latitudinal tree-lines, which could have an impact on the ability of tree species to migrate in response to climate change. Aside from temperature, tree-lines are also affected on a more local level by pressure from human activities. These are also changing as a consequence of modifications in our societies and may interact with the effects of climate change. Forest dynamics models are often used for climate change simulations because of their mechanistic processes. The spatially-explicit model TreeMig was used as a base to develop a model specifically tuned for the northern European and Alpine tree-line ecotones. For the latter, a module for land-use change processes was also added. The temperature response parameters for the species in the model were first calibrated by means of tree-ring data from various species and sites at both tree-lines. This improved the growth response function in the model, but also lead to the conclusion that regeneration is probably more important than growth for controlling tree-line position and species' distributions. The second step was to implement the module for abandonment of agricultural land in the Alps, based on an existing spatial statistical model. The sensitivity of its most important variables was tested and the model's performance compared to other modelling approaches. The probability that agricultural land would be abandoned was strongly influenced by the distance from the nearest forest and the slope, bath of which are proxies for cultivation costs. When applied to a case study area, the resulting model, named TreeMig-LAb, gave the most realistic results. These were consistent with observed consequences of land-abandonment such as the expansion of the existing forest and closing up of gaps. This new model was then applied in two case study areas, one in the Swiss Alps and one in Finnish Lapland, under a variety of climate change scenarios. These were based on forecasts of temperature change over the next century by the IPCC and the HadCM3 climate model (ΔT: +1.3, +3.5 and +5.6 °C) and included a post-change stabilisation period of 300 years. The results showed radical disruptions at both tree-lines. With the most conservative climate change scenario, species' distributions simply shifted, but it took several centuries reach a new equilibrium. With the more extreme scenarios, some species disappeared from our study areas (e.g. Pinus cembra in the Alps) or dwindled to very low numbers, as they ran out of land into which they could migrate. The most striking result was the lag in the response of most species, independently from the climate change scenario or tree-line type considered. Finally, a statistical model of the effect of reindeer (Rangifer tarandus) browsing on the growth of Pinus sylvestris was developed, as a first step towards implementing human impacts at the boreal tree-line. The expected effect was an indirect one, as reindeer deplete the ground lichen cover, thought to protect the trees against adverse climate conditions. The model showed a small but significant effect of browsing, but as the link with the underlying climate variables was unclear and the model was not spatial, it was not usable as such. Developing the TreeMig-LAb model allowed to: a) establish a method for deriving species' parameters for the growth equation from tree-rings, b) highlight the importance of regeneration in determining tree-line position and species' distributions and c) improve the integration of social sciences into landscape modelling. Applying the model at the Alpine and northern European tree-lines under different climate change scenarios showed that with most forecasted levels of temperature increase, tree-lines would suffer major disruptions, with shifts in distributions and potential extinction of some tree-line species. However, these responses showed strong lags, so these effects would not become apparent before decades and could take centuries to stabilise. Résumé Les écotones son sensibles au changement en raison du nombre élevé d'espèces qui y vivent à la limite de leur tolérance environnementale. Ceci s'applique également aux limites des arbres définies par les gradients de température altitudinaux et latitudinaux. Dans le contexte actuel de changement climatique, on s'attend à ce qu'elles subissent des modifications de leur position, de la biomasse des arbres et éventuellement des essences qui les composent. Les limites altitudinales et latitudinales diffèrent essentiellement au niveau de la pente des gradients de température qui les sous-tendent les distance sont plus grandes pour les limites latitudinales, ce qui pourrait avoir un impact sur la capacité des espèces à migrer en réponse au changement climatique. En sus de la température, la limite des arbres est aussi influencée à un niveau plus local par les pressions dues aux activités humaines. Celles-ci sont aussi en mutation suite aux changements dans nos sociétés et peuvent interagir avec les effets du changement climatique. Les modèles de dynamique forestière sont souvent utilisés pour simuler les effets du changement climatique, car ils sont basés sur la modélisation de processus. Le modèle spatialement explicite TreeMig a été utilisé comme base pour développer un modèle spécialement adapté pour la limite des arbres en Europe du Nord et dans les Alpes. Pour cette dernière, un module servant à simuler des changements d'utilisation du sol a également été ajouté. Tout d'abord, les paramètres de la courbe de réponse à la température pour les espèces inclues dans le modèle ont été calibrées au moyen de données dendrochronologiques pour diverses espèces et divers sites des deux écotones. Ceci a permis d'améliorer la courbe de croissance du modèle, mais a également permis de conclure que la régénération est probablement plus déterminante que la croissance en ce qui concerne la position de la limite des arbres et la distribution des espèces. La seconde étape consistait à implémenter le module d'abandon du terrain agricole dans les Alpes, basé sur un modèle statistique spatial existant. La sensibilité des variables les plus importantes du modèle a été testée et la performance de ce dernier comparée à d'autres approches de modélisation. La probabilité qu'un terrain soit abandonné était fortement influencée par la distance à la forêt la plus proche et par la pente, qui sont tous deux des substituts pour les coûts liés à la mise en culture. Lors de l'application en situation réelle, le nouveau modèle, baptisé TreeMig-LAb, a donné les résultats les plus réalistes. Ceux-ci étaient comparables aux conséquences déjà observées de l'abandon de terrains agricoles, telles que l'expansion des forêts existantes et la fermeture des clairières. Ce nouveau modèle a ensuite été mis en application dans deux zones d'étude, l'une dans les Alpes suisses et l'autre en Laponie finlandaise, avec divers scénarios de changement climatique. Ces derniers étaient basés sur les prévisions de changement de température pour le siècle prochain établies par l'IPCC et le modèle climatique HadCM3 (ΔT: +1.3, +3.5 et +5.6 °C) et comprenaient une période de stabilisation post-changement climatique de 300 ans. Les résultats ont montré des perturbations majeures dans les deux types de limites de arbres. Avec le scénario de changement climatique le moins extrême, les distributions respectives des espèces ont subi un simple glissement, mais il a fallu plusieurs siècles pour qu'elles atteignent un nouvel équilibre. Avec les autres scénarios, certaines espèces ont disparu de la zone d'étude (p. ex. Pinus cembra dans les Alpes) ou ont vu leur population diminuer parce qu'il n'y avait plus assez de terrains disponibles dans lesquels elles puissent migrer. Le résultat le plus frappant a été le temps de latence dans la réponse de la plupart des espèces, indépendamment du scénario de changement climatique utilisé ou du type de limite des arbres. Finalement, un modèle statistique de l'effet de l'abroutissement par les rennes (Rangifer tarandus) sur la croissance de Pinus sylvestris a été développé, comme première étape en vue de l'implémentation des impacts humains sur la limite boréale des arbres. L'effet attendu était indirect, puisque les rennes réduisent la couverture de lichen sur le sol, dont on attend un effet protecteur contre les rigueurs climatiques. Le modèle a mis en évidence un effet modeste mais significatif, mais étant donné que le lien avec les variables climatiques sous jacentes était peu clair et que le modèle n'était pas appliqué dans l'espace, il n'était pas utilisable tel quel. Le développement du modèle TreeMig-LAb a permis : a) d'établir une méthode pour déduire les paramètres spécifiques de l'équation de croissance ä partir de données dendrochronologiques, b) de mettre en évidence l'importance de la régénération dans la position de la limite des arbres et la distribution des espèces et c) d'améliorer l'intégration des sciences sociales dans les modèles de paysage. L'application du modèle aux limites alpines et nord-européennes des arbres sous différents scénarios de changement climatique a montré qu'avec la plupart des niveaux d'augmentation de température prévus, la limite des arbres subirait des perturbations majeures, avec des glissements d'aires de répartition et l'extinction potentielle de certaines espèces. Cependant, ces réponses ont montré des temps de latence importants, si bien que ces effets ne seraient pas visibles avant des décennies et pourraient mettre plusieurs siècles à se stabiliser.

Ecotoxicological approaches to assess the long-term effects of four anticancer drugs and metabolites on Daphnia pulex

The aquatic environment is exposed continuously and increasingly to chemical substances such as pharmaceuticals. These medical compounds are released into the environment after having being consumed and body-excreted by patients. Pharmaceutical residues are synthetic molecules that are not always removed by traditional sewage treatment processes and thus escape degradation. Among pharmaceuticals that escape sewage treatment plants (STPs), the anticancer drugs were measured in STP effluents and natural waters. In the aquatic environment, their long-term effects at low concentrations are sparsely known on non-target species. Tamoxifen is an anticancer drug that is widely prescribed worldwide for the prevention and treatment of hormone receptor-positive breast cancers. Two of its metabolites, i.e., endoxifen and 4-hydroxy- tamoxifen (4OHTam), have high pharmacological potency in vivo and such as tamoxifen, they are excreted via faeces by patients. Tamoxifen was measured in STP effluents and natural waters but, to the best of our knowledge, its metabolites concentrations in waters have never been reported. Imatinib is another and recent anticancer compound that targets specific tumour cells. This pharmaceutical is also body excreted and because of its increasing use in cancer treatment, imatinib may reach the natural water. The effects of tamoxifen and imatinib are unknown upon more than one generation of aquatic species. And the effects of 4OHTam, endoxifen have never been studied in ecotoxicology so far. The aims of this thesis were threefold. First, the sensitivity of D. pulex exposed to tamoxifen, 4OHTam, endoxifen or imatinib was assessed using ecotoxicological experiments. Ecotoxicology is the science that considers the toxic effects of natural or synthetic substances, such as pharmaceuticals, on organisms, populations, community and ecosystem. Acute and multigenerational (2-4 generations) tests were performed on daphnids considering several studied endpoints, such as immobilisation, size, reproduction, viability and intrinsic rate of natural increase. Additional prospective assays were designed to evaluate whether 1) low concentrations of tamoxifen and 4OHTam were able to induce toxic effects when used in combination, and 2) daphnids were able to recover when offspring were withdrawn from solutions carrying the pharmaceutical. Second, the stability of tamoxifen, 4OHTam and endoxifen in incubation medium was evaluated in solution exempted from daphnids. Because the nominal concentrations of tamoxifen, 4OHTam and endoxifen did not correspond to the measured, we provide a predictive method to estimate the concentrations of these chemicals during long-term ecotoxicological tests. Finally, changes in protein expressions were analysed in D. pulex exposed 2 or 7 seven days to tamoxifen using ecotoxicoproteomic experiments with a shot-gun approach inducing a peptide fractionation step. Our results show that tamoxifen, 4OHTam and endoxifen induced adverse effects in D. pulex at environmentally relevant concentrations. At very low concentrations, these molecules displayed unusual and teratogenic effects because morphological abnormalities were observed in offspring, such as thick and short antennas, curved spines, premature neonates and aborted eggs. Tamoxifen was the most toxic compound among the test chemicals, followed by 4OHTam, endoxifen and imatinib. Tamoxifen no-observed effect concentrations (NOECs) that were calculated for size, reproduction and intrinsic rate were below or in the range of the concentrations measured in natural waters, i.e., between 0.12 µg/L and 0.67 µg/L. For instance, the tamoxifen NOECs that were calculated for reproduction were between 0.67 and 0.72 µg/L, whereas the NOEC was < 0.15 µg/L when based on morphological abnormalities. The NOECs of 4OHTam were higher but still in the same order of magnitude as tamoxifen environmental concentrations, with a value of 1.48 µg/L. Endoxifen NOEC for the intrinsic rate of natural increase (r) and the reproduction were 0.4 and 4.3 µg/L, respectively. Daphnids that were withdrawn from tamoxifen and 4OHTam were not able to recover. Also, the reproduction of D. pulex was reduced when the treated animals were exposed to the combination of tamoxifen and 4OHTam while no effects were observed when these chemicals were tested individually at the same concentration. Among the anticancer drugs that were tested during this thesis, imatinib was the less toxic molecule towards D. pulex. No effects on size and reproduction were observed within two generations, except for the first whose reproduction decreased at the highest test concentration, i.e., 626 µg/L. Our results also underline the need to use measured or predicted concentrations instead of the nominal during aquatic experiments, particularly when lipophilic molecules are tested. Indeed, notable differences between nominal (i.e., theoretical) and measured concentrations were found with tamoxifen, 4OHTam and endoxifen at all test concentrations. A cost and time sustainable method was proposed to predict the test exposure levels of these chemicals during long-term experiments. This predictive method was efficient particularly for low concentrations, which corresponded to the test concentrations in multigenerational tests. In the ecotoxicoproteomic experiments a total of 3940 proteins were identified and quantified in D. pulex exposed to tamoxifen. These results are currently the largest dataset from D. pulex that is published and the results of proteomic analyses are available for the scientific community. Among these 3940 proteins, 189 were significantly different from controls. After protein annotation, we assumed that treated daphnids with tamoxifen had shifted cost-energy functions, such as reproduction, to maintain their basic metabolism necessary to survive. This metabolic cost hypothesis was supported by the presence of proteins involved in oxidative stress. Biomarkers for early detection of tamoxifen harmful effects on D. pulex were not discovered but the proteins of the vitellogenin-2 family (E9H8K5) and the ryanodine receptor (E9FTU9) are promising potential biomarkers because their expression was already modified after 2 days of treatment. In this thesis, the effects of tamoxifen, 4OHTam and endoxifen on daphnids raise questions about the potential impact of tamoxifen and 4OHTam in other aquatic ecosystems, and therefore, about metabolites in ecotoxicology. Because the NOECs were environmentally relevant, these results suggest that tamoxifen and 4OHTam may be interesting pharmaceuticals to consider in risk assessment. Our findings also emphasize the importance of performing long-term experiments and of considering multi-endpoints instead of the standard reproductive endpoint. Finally, we open the discussion about the importance to measure test exposures or not, during ecotoxicological studies. -- Les milieux aquatiques sont exposés continuellement à un nombre croissant de substances chimiques, notamment les médicaments issus de la médecine vétérinaire et humaine. Chez les patients, les substances administrées sont utilisées par le corps avant d'être éliminées par l'intermédiaire des excrétas dans le système d'eaux usées de la ville. Ces eaux rejoignent ensuite une station de traitement afin d'y éliminer les déchets. Dans le cas des molécules chimiques, il arrive que les processus de traitement d'eaux usées ne soient pas suffisamment efficaces et que ces molécules ne soient pas dégradées. Elles sont alors libérées dans le milieu aquatique avec les effluents de la station d'épuration. Une fois dans l'environnement, ces résidus de médicaments sont susceptibles d'induire des effets sur la faune et la flore aquatique, dont les conséquences à long terme et à faibles concentrations sont peu connues. Les anticancéreux sont une famille de médicaments qui peuvent échapper aux traitements des stations d'épuration et qui sont retrouvées dans le milieu aquatique naturel. Parmi ces substances, le tamoxifen est une molécule utilisée dans le monde entier pour prévenir et traiter les cancers hormonaux dépendant du sein, notamment. Une fois ingéré, le tamoxifen est transformé par le foie en métabolites dont deux d'entre eux, le 4-hydroxy-tamoxifen (4OHTam) et l'endoxifen, possèdent un affinité pour les récepteurs aux estrogènes et une efficacité sur les cellules tumorales supérieure au tamoxifen lui- même. Tout comme la molécule mère, ces métabolites sont principalement éliminés par l'intermédiaire des fèces. Le tamoxifen a déjà été mesuré dans les effluents de stations d'épuration et dans les eaux naturelles, mais aucune valeur n'a été reportée pour ses métabolites jusqu'à présent. Un autre anticancéreux, également éliminé par voie biliaire et susceptible d'atteindre l'environnement, est l'imatinib. Cette récente molécule a révolutionné le traitement et la survie des patients souffrant de leucémie myéloïde chronique et de tumeur stromales gastrointestinales. Les effets du tamoxifen et de l'imatinib sur plusieurs générations d'organismes aquatiques, tels que les microcrustacés Daphnia, sont inconnus et le 4OHTam et l'endoxifen n'ont même jamais été testés en écotoxicologie. Cette thèse s'est articulée autour de trois objectifs principaux. Premièrement, la sensibilité des D. pulex exposés au tamoxifen, 4OHTam, endoxifen et imatinib a été évaluée par l'intermédiaire de tests aigus et de tests sur deux à quatre générations. La mobilité, la taille, la reproduction, la viabilité et la croissance potentielle de la population ont été relevées au cours de ces expériences. Des tests supplémentaires, à but prospectifs, ont également été réalisés afin d'évaluer 1) la capacité de récupération des daphnies, lorsque leurs descendants ont été placés dans un milieu exempté de tamoxifen ou de 4OHTam, 2) les effets chez les daphnies exposées à une solution contenant de faibles concentration de tamoxifen et de 4OHTam mélangés. Le deuxième objectif a été d'évaluer la stabilité du tamoxifen, 4OHTam et endoxifen dilué dans le milieu des daphnies. Après analyses, les concentrations mesurées ne correspondaient pas aux concentrations nominales (c.-à-d., théoriques) et il a été nécessaire de développer une méthode efficace de prédiction des niveaux d'exposition lors de tests de longue durée réalisés avec ces trois molécules. Finalement, des changements dans l'expression des protéines chez des daphnies exposées au tamoxifen ont été investigués par l'intermédiaire d'expériences écotoxicoprotéomiques avec une approche dite de shot-gun avec une étape de fractionnement des protéines. Les résultats obtenus dans cette thèse montrent que le tamoxifen, le 4OHTam et l'endoxifen induisent des effets indésirables chez les daphnies à des niveaux d'exposition proches ou identiques aux concentrations du tamoxifen mesurées dans l'environnement, c'est-à-dire 0.12 et 0.67 µg/L de tamoxifen. Ces molécules ont induit des effets inhabituels tels que la production de : nouveau-nés anormaux, avec des antennes et des queues déformées, des prématurés et des oeufs avortés. Le tamoxifen fut la molécule la plus toxique pour les D. pulex suivie du 4OHTam, de l'endoxifen et enfin de l'imatinib. Lors des expériences sur plusieurs générations, les concentrations n'ayant statistiquement pas d'effet (c.à.d. NOEC en anglais) sur la taille, la reproduction et la croissance intrinsèque de la population étaient du même ordre de grandeur que les concentrations environnementales du tamoxifen. Par exemple, les NOECs du tamoxifen calculées pour la reproduction étaient de 0.67 et 0.72 µg/L, tandis que celle calculée sur la base des anomalies chez les nouveau-nés était < 0.15 µg/L. Les NOECs du 4OHTam se situaient entre 0.16 et 1.48 µg/L et celles de l'endoxifen pour la croissance intrinsèque de la population, ainsi que pour la reproduction, étaient de 0.4 et 4.3 µg/L, respectivement. Dans l'expérience basée sur la récupération des daphnies, la taille et la reproduction ont diminué bien que la descendance fût placée dans un milieu sans substances chimiques. Les daphnies exposées au mélange de tamoxifen et de 4OHTam ont produit moins de nouveau-nés que les contrôles, alors que ces concentrations n'ont pas induit d'effets lorsque testées individuellement. Finalement, l'imatinib n'a pas montré d'effets sur les deux générations testées. Seule la première génération exposée à la plus haute concentration (626 µg/L) a montré une diminution de la reproduction. Les résultats obtenus lors de l'évaluation de la stabilité du tamoxifen, 4OHTam et endoxifen dans le milieu des daphnies ont souligné l'importance d'utiliser des concentrations mesurées ou prédites en écotoxicologie. En effet, des différences notables entre concentrations nominales et mesurées ont été observées à toutes les concentrations et l'hypothèse d'un phénomène d'adsorption sur le verre des récipients a été posée. De ce fait, il a été nécessaire d'élaborer une méthode prédictive efficace et acceptable, en terme de temps et de coûts. Une régression polynomiale basée sur des concentrations mesurées et nominales a permis de prédire avec efficacité les faibles niveaux d'exposition utilisés lors d'expériences écotoxicologiques à long terme, sur plusieurs générations. Suite aux expériences d'écotoxicoprotéomiques, un total de 3940 protéines ont été identifiées et quantifiées chez des daphnies exposées au tamoxifen. Ce nombre est actuellement la plus large série de données publiées et mises à disposition pour la communauté scientifique. Parmi ces protéines, 189 sont significatives et possiblement reliées à des processus de reproduction et de stress. Sur cette base, nous avons émis l'hypothèse que les individus subissant un stress, lié à l'exposition au tamoxifen, ont utilisé leur énergie de base pour favoriser leur survie plutôt que la reproduction. Enfin, la détermination de bio-marqueurs exprimant des dommages précoces des daphnies exposées au tamoxifen n'a pas abouti en tant que telle, mais des protéines prometteuses, telle que la famille de viellogenin-2 (E9H8K5) et le récepteur à la ryanodine (E9FTU9), ont été exprimées après deux jours d'exposition déjà. Ces protéines pourraient faire l'objet d'investigations écotoxicoprotéomiques futures. Les résultats de cette thèse posent certaines questions quant au risque du tamoxifen, du 4OHTam et de l'endoxifen sur la faune et la flore aquatique et plus particulièrement sur les anticancéreux présents dans l'environnement. Les effets toxiques de ces molécules ont été observés à des concentrations environnementales et sur plusieurs générations. La question de considérer les métabolites, et ainsi les pro-médicaments, en écotoxicologie est soulevée, notamment parce que ces molécules peuvent être plus actives et efficaces que la molécule mère. Les expériences chroniques, sur plusieurs générations sont également à favoriser car elles offrent un meilleur reflet de la réalité environnementale que des essais aigus ou d'une génération. L'utilisation de la protéomique permet d'agrandir les connaissances sur les effets des médicaments à un niveau inférieur de l'organisation biologique et ainsi, de mieux comprendre de potentiels mécanismes d'action ou de déterminer de potentiels biomarqueurs. Finalement, il semble important de discuter de l'opportunité de mesurer les concentrations qui sont testées en écotoxicologie afin de ne pas sous-estimer le risque pour la faune et la flore aquatique.

Energy and nutrient intake of Swiss women aged 75-87 years.

OBJECTIVE: Reliable data about the nutrient intake of elderly noninstitutionalized women in Switzerland is lacking. The aim of this study was to assess the energy and nutrient intake in this specific population. SUBJECTS: The 401 subjects were randomly selected women of mean age of 80.4 years (range 75-87) recruited from the Swiss SEMOF (Swiss Evaluation of the Methods of Measurement of Osteoporotic Fracture Risk) cohort study. A validated food frequency questionnaire (FFQ) was submitted to the 401 subjects to assess dietary intake. RESULTS: The FFQ showed a mean daily energy intake of 1544 kcal (+/-447.7). Protein intake was 65.2 g (+/-19.9), that is 1.03 g kg(-1) body weight per day. The mean daily intake for energy, fat, carbohydrate, calcium, magnesium, vitamin C, D and E were below the RNI. However, protein, phosphorus, potassium, iron and vitamin B6 were above the RNI. CONCLUSION: The mean nutrient intake of these free living Swiss elderly women was low compared with standards. Energy dense foods rich in carbohydrate, magnesium, calcium, vitamin D and E as well as regular sunshine exposure is recommended in order to optimise dietary intake.

Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.

Nonalcoholic fatty liver disease (NAFLD) clusters in families, but the only known common genetic variants influencing risk are near PNPLA3. We sought to identify additional genetic variants influencing NAFLD using genome-wide association (GWA) analysis of computed tomography (CT) measured hepatic steatosis, a non-invasive measure of NAFLD, in large population based samples. Using variance components methods, we show that CT hepatic steatosis is heritable (∼26%-27%) in family-based Amish, Family Heart, and Framingham Heart Studies (n = 880 to 3,070). By carrying out a fixed-effects meta-analysis of genome-wide association (GWA) results between CT hepatic steatosis and ∼2.4 million imputed or genotyped SNPs in 7,176 individuals from the Old Order Amish, Age, Gene/Environment Susceptibility-Reykjavik study (AGES), Family Heart, and Framingham Heart Studies, we identify variants associated at genome-wide significant levels (p<5×10(-8)) in or near PNPLA3, NCAN, and PPP1R3B. We genotype these and 42 other top CT hepatic steatosis-associated SNPs in 592 subjects with biopsy-proven NAFLD from the NASH Clinical Research Network (NASH CRN). In comparisons with 1,405 healthy controls from the Myocardial Genetics Consortium (MIGen), we observe significant associations with histologic NAFLD at variants in or near NCAN, GCKR, LYPLAL1, and PNPLA3, but not PPP1R3B. Variants at these five loci exhibit distinct patterns of association with serum lipids, as well as glycemic and anthropometric traits. We identify common genetic variants influencing CT-assessed steatosis and risk of NAFLD. Hepatic steatosis associated variants are not uniformly associated with NASH/fibrosis or result in abnormalities in serum lipids or glycemic and anthropometric traits, suggesting genetic heterogeneity in the pathways influencing these traits.

Screening of illegal intracorporeal containers ("body packing"): is abdominal radiography sufficiently accurate? A comparative study with low-dose CT.

PURPOSE: To evaluate the diagnostic performance of abdominal radiography in the detection of illegal intracorporeal containers (hereafter, packets), with low-dose computed tomography (CT) as the reference standard. MATERIALS AND METHODS: This study was approved by the institutional ethical review board, with written informed consent. From July 2007 to July 2010, 330 people (296 men, 34 women; mean age, 32 years [range, 18-55 years]) suspected of having ingested drug packets underwent supine abdominal radiography and low-dose CT. The presence or absence of packets at abdominal radiography was reported, with low-dose CT as the reference standard. The density and number of packets (≤ 12 or >12) at low-dose CT were recorded and analyzed to determine whether those variables influence interpretation of results at abdominal radiography. RESULTS: Packets were detected at low-dose CT in 53 (16%) suspects. Sensitivity of abdominal radiography for depiction of packets was 0.77 (41 of 53), and specificity was 0.96 (267 of 277). The packets appeared isoattenuated to the bowel contents at low-dose CT in 16 (30%) of the 53 suspects with positive results. Nineteen (36%) of the 53 suspects with positive low-dose CT results had fewer than 12 packets. Packets that were isoattenuated at low-dose CT and a low number of packets (≤12) were both significantly associated with false-negative results at abdominal radiography (P = .004 and P = .016, respectively). CONCLUSION: Abdominal radiography is mainly limited by low sensitivity when compared with low-dose CT in the screening of people suspected of carrying drug packets. Low-dose CT is an effective imaging alternative to abdominal radiography.

Association of genetic variation with systolic and diastolic blood pressure among African Americans: the Candidate Gene Association Resource study.

The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10(-8)) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10(-8)). The top IBC association for SBP was rs2012318 (P= 6.4 × 10(-6)) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10(-6)) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexity.

Use of palm-oil by-products in chicken and rabbit feeds: effect on the fatty acid and tocol composition of meat, liver and plasma

This study was undertaken in the framework of a larger European project dealing with the characterization of fat co- and by-products from the food chain, available for feed uses. In this study, we compare the effects, on the fatty acid (FA) and tocol composition of chicken and rabbit tissues, of the addition to feeds of a palm fatty acid distillate, very low in trans fatty acids (TFA), and two levels of the corresponding hydrogenated by-product, containing intermediate and high levels of TFA. Thus, the experimental design included three treatments, formulated for each species, containing the three levels of TFA defined above. Obviously, due to the use of hydrogenated fats, the levels of saturated fatty acids (SFA) show clear differences between the three dietary treatments. The results show that diets high in TFA (76 g/kg fat) compared with those low in TFA (4.4 g/kg fat) led to a lower content of tocopherols and tocotrienols in tissues, although these differences were not always statistically significant, and show a different pattern for rabbit and chicken. The TFA content in meat, liver and plasma increased from low-to-high TFA feeds in both chicken and rabbit. However, the transfer ratios from feed were not proportional to the TFA levels in feeds, reflecting certain differences according to the animal species. Moreover, feeds containing fats higher in TFA induced significant changes in tissue SFA, monounsaturated fatty acids and polyunsaturated fatty acids composition, but different patterns can be described for chicken and rabbit and for each type of tissue.

Use of recovered frying oils in chicken and rabbit feeds: effect on the fatty acid and tocol composition and on the oxidation levels of meat, liver and plasma

The addition of some fat co- and by-products to feeds is usual nowadays; however, the regulations of their use are not always clear and vary between countries. For instance, the use of recycled cooking oils is not allowed in the European Union, but they are used in other countries. However, oils recovered from industrial frying processes could show satisfactory quality for this purpose. Here we studied the effects of including oils recovered from the frying industry in rabbit and chicken feeds (at 30 and 60 g/kg, respectively) on the fatty acid (FA) and tocol (tocopherol + tocotrienol) compositon of meat, liver and plasma, and on their oxidative stability. Three dietary treatments (replicated eight times) were compared: fresh non-used oil (LOX); oil discarded from the frying industry, having a high content of secondary oxidation compounds (HOX); and an intermediate level (MOX) obtained by mixing 50 : 50 of LOX and HOX. The FA composition of oil diets and tissues was assessed by GC, their tocol content by HPLC, the thiobarbituric acid value was used to assess tissue oxidation status, and the ferrous oxidation-xylenol orange method was used to assess the susceptibility of tissues to oxidation. Our results indicate that FA composition of rabbit and chicken meat, liver and plasma was scarcely altered by the addition of recovered frying oils to feed. Differences were encountered in the FA composition between species, which might be attributed mainly to differences in the FA digestion, absorption and metabolism between species, and to some physiological dietary factors (i.e. coprophagy in rabbits that involves fermentation with FA structure modification). The α-tocopherol (αT) content of tissues was reduced in response to the lower αT content in the recovered frying oil. Differences in the content of other tocols were encountered between chickens and rabbits, which might be attributable to the different tocol composition of their feeds, as well as to species differences in the digestion and metabolism of tocols. Tissue oxidation and susceptibility to oxidation were in general low and were not greatly affected by the degree of oxidation of the oil added to the feeds. The relative content of polyunsaturated fatty acids/αT in these types of samples would explain the differences observed between species in the susceptibility of each tissue to oxidation. According to our results, oils recovered from the frying industry could be useful for feed uses.

Predictors of endocarditis in isolates from cultures of blood following dental extractions in rats with periodontal disease.

Rats with periodontitis and catheter-induced aortic valve vegetations underwent dental extractions. Cultures of blood obtained 1 min later showed polymicrobial bacteremia in 19 of 19 rats, mostly due to viridans streptococci (18 of 19), Morganella (15 of 19), group G streptococci (13 of 19), and Staphylococcus aureus (10 of 19). Viridans streptococci circulated in higher numbers than did group G streptococci and S. aureus (P less than .01). Three days after dental extractions, 18 of 20 rats had endocarditis. Fifteen (83%) of 18 infections were due to group G streptococci, 9 (50%) of 18 were due to S. aureus, and 2 (11%) of 18 were due to viridans streptococci (P less than .05). In vitro, adherence to platelet-fibrin matrices of endocarditis strain 8 of group G streptococcus was two times greater than that of endocarditis strain S. aureus 23 and three to four times greater than that of Streptococcus sanguis 44 and Morganella morganii 93 (P less than 10(-5)). The inoculum size that produced endocarditis in 90% of rats after iv challenge was 10(5) cfu for group G streptococcus strain 8 and 10(7) for S. sanguis 44.