Chemical and isotopic equilibrium between CO2 and CH4 in fumarolic gas discharges: Generation of CH4 in arc magmatic-hydrothermal systems

The chemical and isotopic composition of fumarolic gases emitted from Nisyros Volcano, Greece, and of a single gas sample from Vesuvio, Italy, was investigated in order to determine the origin of methane (CH,) within two subduction-related magmatic-hydrothermal environments. Apparent temperatures derived from carbon isotope partitioning between CH4 and CO2 of around 340degreesC for Nisyros and 470degreesC for Vesuvio correlate well with aquifer temperatures as measured directly and/or inferred from compositional data using the H2O-H-2-CO2-CO-CH4 geothermometer. Thermodynamic modeling reveals chemical equilibrium between CH4, CO2 and H2O implying that carbon isotope partitioning between CO2 and CH, in both systems is controlled by aquifer temperature. N-2/(3) He and CH4/(3) He ratios of Nisyros fumarolic gases are unusually low for subduction zone gases and correspond to those of midoceanic ridge environments. Accordingly, CH4 may have been primarily generated through the reduction of CO, by H, in the absence of any organic matter following a Fischer-Tropsch-type reaction. However, primary occurrence of minor amounts of thermogenic CH4 and subsequent re-equilibration with co-existing CO2 cannot be ruled out entirely- CO2/He-3 ratios and delta(13)C(CO2) values imply that the evolved CO2 either derives from a metasomatized mantle or is a mixture between two components, one outgassing from an unaltered mantle and the other released by thermal breakdown of marine carbonates. The latter may contain traces of organic matter possibly decomposing to CH4 during thermometamorphism. Copyright (C) 2004 Elsevier Ltd.

Inferring the mode of origin of polyploid species from next-generation sequence data.

Many eukaryote organisms are polyploid. However, despite their importance, evolutionary inference of polyploid origins and modes of inheritance has been limited by a need for analyses of allele segregation at multiple loci using crosses. The increasing availability of sequence data for nonmodel species now allows the application of established approaches for the analysis of genomic data in polyploids. Here, we ask whether approximate Bayesian computation (ABC), applied to realistic traditional and next-generation sequence data, allows correct inference of the evolutionary and demographic history of polyploids. Using simulations, we evaluate the robustness of evolutionary inference by ABC for tetraploid species as a function of the number of individuals and loci sampled, and the presence or absence of an outgroup. We find that ABC adequately retrieves the recent evolutionary history of polyploid species on the basis of both old and new sequencing technologies. The application of ABC to sequence data from diploid and polyploid species of the plant genus Capsella confirms its utility. Our analysis strongly supports an allopolyploid origin of C. bursa-pastoris about 80 000 years ago. This conclusion runs contrary to previous findings based on the same data set but using an alternative approach and is in agreement with recent findings based on whole-genome sequencing. Our results indicate that ABC is a promising and powerful method for revealing the evolution of polyploid species, without the need to attribute alleles to a homeologous chromosome pair. The approach can readily be extended to more complex scenarios involving higher ploidy levels.

Sediment budget monitoring of a debris-flow torrent (French Prealps)

The Manival near Grenoble (French Prealps) is a very active debris-flow torrent equipped with a large sediment trap (25 000 m3) protecting an urbanized alluvial fan from debris-flows. We began monitoring the sediment budget of the catchment controlled by the trap in Spring 2009. Terrestrial laser scanner is used for monitoring topographic changes in a small gully, the main channel, and the sediment trap. In the main channel, 39 cross-sections are surveyed after every event. Three periods of intense geomorphic activity are documented here. The first was induced by a convective storm in August 2009 which triggered a debris-flow that deposited ~1,800 m3 of sediment in the trap. The debris-flow originated in the upper reach of the main channel and our observations showed that sediment outputs were entirely supplied by channel scouring. Hillslope debris-flows were initiated on talus slopes, as revealed by terrestrial LiDAR resurveys; however they were disconnected to the main channel. The second and third periods of geomorphic activity were induced by long duration and low intensity rainfall events in September and October 2009 which generate small flow events with intense bedload transport. These events contribute to recharge the debris-flow channel with sediments by depositing important gravel dunes propagating from headwaters. The total recharge in the torrent subsequent to bedload transport events was estimated at 34% of the sediment erosion induced by the August debris-flow.

De novo T cell generation and cell cycle analysis of CD4 and CD8 T cells during HIV-disease

RESUME POUR UN LARGE PUBLIC Parmi les globules blancs, les lymphocytes T 004 jouent un rôle primordial dans la coordination de la réponse immunitaire contre les pathogènes et les lymphocytes T CD8 dans leur élimination. Lors d'une infection par le virus de l'immunodéficience humaine (VIH-1), non seulement les cellules T CD4 sont les principales cibles d'infections, mais aussi elles disparaissent progressivement tout au long de la maladie. Ce phénomène, appelé aussi épuisement des lymphocytes T CD4, est la principale cause provoquant le Syndrome d'Immunodéficience Acquise (SIDA). Malgré de grands efforts de recherche, nous ne sommes toujours pas en mesure de dire si ce phénomène est dû à un défaut dans la production de nouvelles cellules ou à une destruction massive de cellules en circulation. Dans cette étude, nous nous proposions, dans un premier temps, de comparer la production de nouvelles cellules T CD4 et CD8 chez des individus VIH-négatifs et positifs. Les cellules nouvellement produites portent un marqueur commun que l'on appelle TREC et qui est facilement mesurable. En considérant des paramètres cliniques, nous étions en mesure de déterminer le niveau de TRECs de cellules T CD4 et CD8 dans différentes phases de la maladie. De là, nous avons pu déterminer que le niveau de TREC est toujours plus bas dans les cellules T CD8 de patients VIH-positifs comparativement à notre groupe contrôle. Nous avons pu déterminer par une analyse ultérieure que cette différence est due à une forte prolifération de ces cellules chez les patients VIH-positifs, ce qui a pour effet de diluer ce marqueur. En revanche, la production de nouvelles cellules T CD4 chez des patients VIH-positifs est accentuée lors de la phase précoce de la maladie et largement réprimée lors de la phase tardive. Dans un second temps, nous avons effectué une analyse à grande échelle de l'expression de gènes associés à la division cellulaire sur des lymphocytes T CD4 et CD8 d'individus VIH-¬positifs et négatifs, avec comme contrôle des cellules proliférant in vitro. De cette étude, nous avons pu conclure que les cellules T CD8 de patients VIH-positifs étaient en état de prolifération, alors que les lymphocytes T CD4 présentaient des défauts majeurs conduisant à un arrêt de la division cellulaire. Nos résultats montrent que la capacité à produire de nouvelles cellules chez des patients VIH¬positifs reste active longtemps pendant la maladie, mais que l'incapacité des cellules T CD4 à proliférer peut enrayer la reconstitution immunitaire chez ces individus. ABSTRACT The hallmark of HIV-1 infection is the depletion of CD4 T cells. Despite extensive investigation, the mechanisms responsible for the loss of CD4 T cells have been elucidated only partially. In particular, it remains controversial whether CD4 T cell depletion results from a defect in T cell production or from a massive peripheral destruction. In this study, de novo T cell generation has been investigated by measuring T cell receptor rearrangement excision circles (TRECs) on large cohorts of HIV-negative (N=120) and HIV-1 infected (N=298) individuals. Analysis of TREC levels was performed in HIV-infected subjects stratified by the stage of HIV disease based on CD4 T cell counts (early: >500 CD4 T cells/µl; intermediate: <500>200; late: <200) and by age (20 to 60 years, n = 259). Our data show that TREC levels in CD8 T cells were significantly lower in HIV-infected subjects at any stage of disease compared to the control group. In contrast, TREC levels in CD4 T cells were significantly higher in HIV-infected subjects at early stages disease while no significant differences were observed at intermediate stages of the disease and were severely reduced only at late stages of disease. To investigate further the status of cell cycle in peripheral CD4 and CD8 T cells in HIV-1 infections, we determined the pattern of gene expression with the microarray technology. In particular, CD4 and CD8 T cells of HIV-1 infected and HIV-negative subjects were analysed by Cell Cycle cDNA expression array. The patterns of gene expression were compared to in vitro stimulated CD4 and CD8 T cells and this analysis showed that CD8 T cells of HIV-1 infected subjects had a pattern of gene expression very similar to that of in vitro stimulated CD8 T cells thus indicating ongoing cell cycling. In contrast, CD4 T cells of HIV-1 infected subjects displayed a complex pattern of gene expression. In fact, CD4 T cells expressed high levels of genes typically associated with cell activation, but low levels of cell cycle genes. Therefore, these results indicated that activated CD4 T cells of HIV-1 infected subjects were in cell cycle arrest. Taking together these results indicate that thymus function is preserved for long time during HIV- 1 infection and the increase observed in early stage disease may represent a compensatory mechanism to the depletion of CD4 T cells. However, we provide evidence for a cell cycle arrest of peripheral CD4 T cells that may prevent potentially the replenishment of CD4 T cells. RESUME Les mécanismes responsables de la perte des lymphocytes T CD4 lors de l'infection pas VIH n'ont été élucidés que partiellement. Nous ne savons toujours pas si l'épuisement des lymphocytes T CD4 résulte d'un défaut dans la production de cellules ou d'une destruction périphérique massive. Dans cette étude, la production de cellules T a été étudiée en mesurant les cercles d'excision générés lors du réarrangement du récepteur au cellules T (TRECs) chez des individus VIH-négatifs (N=120) et VIH-1 positifs (N=298). L'analyse des niveaux de TREC a été faite chez sujets HIV-infectés en considérant les phases de la maladie sur la base des comptes CD4 (phase précoce: > 500 cellules CD4/µl; intermédiaire: < 500>200; tardive: < 200) et par âge. Nos données démontrent que les niveaux de TRECs des cellules T CD8 étaient significativement plus bas chez les sujets VIH-1 infectés, à tous les stades de la maladie comparativement au groupe contrôle. En revanche, les niveaux de TRECs des cellules T CD4 étaient significativement plus élevés chez les sujets VIH-1 infectés durant la phase précoce de la maladie, tandis qu'aucune différence significative n'était observée durant la phase intermédiaire et étaient très réduits dans la phase tardive. Dans une deuxième partie, nous avons utilisé la technique des biopuces à d'ADN complémentaire pour analyser la régulation du cycle cellulaire chez les lymphocytes T CD4 et CD8 périphériques lors d'une infection au VIH-1. Des profils d'expression ont été déterminés et comparés à ceux de cellules T CD4 et CD8 stimulées in vitro, démontrant que les cellules T CD8 des sujets VIH-positifs avaient un profil d'expression très semblable à celui des cellules stimulées in vitro en prolifération. En revanche, les lymphocytes T CD4 des sujets VIH-1 positifs avaient un profil d'expression de gène plus complexe. En fait, leur profil montrait une sur- expression de gènes associés à une activation cellulaire, mais une sous-expression de ceux induisant une division. Ainsi, ces résultats indiquent que les lymphocytes T CD4 d'individus VIH-positifs présentent des dérégulations qui conduisent à un arrêt du cycle cellulaire. Ces résultats montrent que la fonction thymique est préservée longtemps pendant l'infection au VIH-1 et que l'augmentation de la quantité de TRECs dans la phase précoce de la maladie peut représenter un mécanisme compensatoire à l'épuisement des cellules T CD4. Cependant, nous démontrons aussi un clair dysfonctionnement du cycle cellulaire chez les cellules T CD4 d'individus infectés par VIH-1 ce qui peut enrayer la reconstitution du système immunitaire.

Sediment budget monitoring of debris-flow and bedload transport in the Manival Torrent, SE France

Steep mountain catchments typically experience large sediment pulses from hillslopes which are stored in headwater channels and remobilized by debris-flows or bedload transport. Event-based sediment budget monitoring in the active Manival debris-flow torrent in the French Alps during a two-year period gave insights into the catchment-scale sediment routing during moderate rainfall intensities which occur several times each year. The monitoring was based on intensive topographic resurveys of low- and high-order channels using different techniques (cross-section surveys with total station and high-resolution channel surveys with terrestrial and airborne laser scanning). Data on sediment output volumes from the main channel were obtained by a sediment trap. Two debris-flows were observed, as well as several bedload transport flow events. Sediment budget analysis of the two debris-flows revealed that most of the debris-flow volumes were supplied by channel scouring (more than 92%). Bedload transport during autumn contributed to the sediment recharge of high-order channels by the deposition of large gravel wedges. This process is recognized as being fundamental for debris-flow occurrence during the subsequent spring and summer. A time shift of scour-and-fill sequences was observed between low- and high-order channels, revealing the discontinuous sediment transfer in the catchment during common flow events. A conceptual model of sediment routing for different event magnitude is proposed.

Thymus-independent generation of NK1+ T cells in vitro from fetal liver precursors.

NK1.1+TCR alpha beta+ (NK1+) T cells are an unusual subset of mouse TCR alpha beta+ cells found primarily in adult thymus and liver. In contrast to conventional TCR alpha beta+ cells, NK1+ T cells have a TCR repertoire that is highly skewed to V alpha14 and to Vbeta8, -7, and -2. The developmental origin and ligand specificity of NK1+ T cells are controversial. We show here that NK1+ T cells with a typically biased V alpha and V beta repertoire develop in cytokine-supplemented suspension cultures of fetal liver established from either normal or athymic mice. Furthermore, NK1+ T cell development in fetal liver cultures is abrogated in beta2m-deficient mice (which lack MHC class I and other related molecules) and can be partially inhibited by the presence of anti-CD1 mAbs. Moreover, mixing experiments indicate that recombination-deficient SCID fetal liver cells can reconstitute NK1+ T cell development in beta2m-deficient fetal liver cultures. Collectively, our data demonstrate that NK1+ T cells can develop extrathymically from fetal liver precursors and that a beta2m-associated ligand (putatively CD1) present on nonlymphoid cells is essential for their positive selection and/or expansion.

Impacts of upland open drains upon runoff generation: a numerical assessment of catchment-scale impacts

Shallow upland drains, grips, have been hypothesized as responsible for increased downstream flow magnitudes. Observations provide counterfactual evidence, often relating to the difficulty of inferring conclusions from statistical correlation and paired catchment comparisons, and the complexity of designing field experiments to test grip impacts at the catchment scale. Drainage should provide drier antecedent moisture conditions, providing more storage at the start of an event; however, grips have higher flow velocities than overland flow, thus potentially delivering flow more rapidly to the drainage network. We develop and apply a model for assessing the impacts of grips on flow hydrographs. The model was calibrated on the gripped case, and then the gripped case was compared with the intact case by removing all grips. This comparison showed that even given parameter uncertainty, the intact case had significantly higher flood peaks and lower baseflows, mirroring field observations of the hydrological response of intact peat. The simulations suggest that this is because delivery effects may not translate into catchment-scale impacts for three reasons. First, in our case, the proportions of flow path lengths that were hillslope were not changed significantly by gripping. Second, the structure of the grip network as compared with the structure of the drainage basin mitigated against grip-related increases in the concentration of runoff in the drainage network, although it did marginally reduce the mean timing of that concentration at the catchment outlet. Third, the effect of the latter upon downstream flow magnitudes can only be assessed by reference to the peak timing of other tributary basins, emphasizing that drain effects are both relative and scale dependent. However, given the importance of hillslope flow paths, we show that if upland drainage causes significant changes in surface roughness on hillslopes, then critical and important feedbacks may impact upon the speed of hydrological response. Copyright (c) 2012 John Wiley & Sons, Ltd.

Quadrant/octant sequencing and the role of coherent structures in bed load sediment entrainment

To permit the tracking of turbulent flow structures in an Eulerian frame from single-point measurements, we make use of a generalization of conventional two-dimensional quadrant analysis to three-dimensional octants. We characterize flow structures using the sequences of these octants and show how significance may be attached to particular sequences using statistical mull models. We analyze an example experiment and show how a particular dominant flow structure can be identified from the conditional probability of octant sequences. The frequency of this structure corresponds to the dominant peak in the velocity spectra and exerts a high proportion of the total shear stress. We link this structure explicitly to the propensity for sediment entrainment and show that greater insight into sediment entrainment can be obtained by disaggregating those octants that occur within the identified macroturbulence structure from those that do not. Hence, this work goes beyond critiques of Reynolds stress approaches to bed load entrainment that highlight the importance of outward interactions, to identifying and prioritizing the quadrants/octants that define particular flow structures. Key Points <list list-type=''bulleted'' id=''jgrf20196-list-0001''> <list-item id=''jgrf20196-li-0001''>A new method for analysing single point velocity data is presented <list-item id=''jgrf20196-li-0002''>Flow structures are identified by a sequence of flow states (termed octants) <list-item id=''jgrf20196-li-0003''>The identified structure exerts high stresses and causes bed-load entrainment

The anticancer drug metabolites endoxifen and 4-hydroxy-tamoxifen induce toxic effects on Daphnia pulex in a two-generation study.

Although pharmaceutical metabolites are found in the aquatic environment, their toxicity on living organisms is poorly studied in general. Endoxifen and 4-hydroxy-tamoxifen (4OHTam) are two metabolites of the widely used anticancer drug tamoxifen for the prevention and treatment of breast cancers. Both metabolites have a high pharmacological potency in vertebrates, attributing prodrug characteristics to tamoxifen. Tamoxifen and its metabolites are body-excreted by patients, and the parent compound is found in sewage treatment plan effluents and natural waters. The toxicity of these potent metabolites on non-target aquatic species is unknown, which forces environmental risk assessors to predict their toxicity on aquatic species using knowledge on the parent compounds. Therefore, the aim of this study was to assess the sensitivity of two generations of the freshwater microcrustacean Daphnia pulex towards 4OHTam and endoxifen. Two chronic tests of 4OHTam and endoxifen were run in parallel and several endpoints were assessed. The results show that the metabolites 4OHTam and endoxifen induced reproductive and survival effects. For both metabolites, the sensitivity of D. pulex increased in the second generation. The intrinsic rate of natural increase (r) decreased with increasing 4OHTam and endoxifen concentrations. The No-Observed Effect Concentrations (NOECs) calculated for the reproduction of the second generation exposed to 4OHTam and endoxifen were <1.8 and 4.3μg/L, respectively, whereas the NOECs that were calculated for the intrinsic rate of natural increase were <1.8 and 0.4μg/L, respectively. Our study raises questions about prodrug and active metabolites in environmental toxicology assessments of pharmaceuticals. Our findings also emphasize the importance of performing long-term experiments and considering multi-endpoints instead of the standard reproduction outcome.

Generation and interconnection capacity expansion in cross-border electricity markets : the need for policy coordination

Electricity is a strategic service in modern societies. Thus, it is extremely important for governments to be able to guarantee an affordable and reliable supply, which depends to a great extent on an adequate expansion of the generation and transmission capacities. Cross- border integration of electricity markets creates new challenges for the regulators, since the evolution of the market is now influenced by the characteristics and policies of neighbouring countries. There is still no agreement on why and how regions should integrate their electricity markets. The aim of this thesis is to improve the understanding of integrated electricity markets and how their behaviour depends on the prevailing characteristics of the national markets and the policies implemented in each country. We developed a simulation model to analyse under what circumstances integration is desirable. This model is used to study three cases of interconnection between two countries. Several policies regarding interconnection expansion and operation, combined with different generation capacity adequacy mechanisms, are evaluated. The thesis is composed of three papers. The first paper presents a detailed description of the model and an analysis of the case of Colombia and Ecuador. It shows that market coupling can bring important benefits, but the relative size of the countries can lead to import dependency issues in the smaller country. The second paper compares the case of Colombia and Ecuador with the case of Great Britain and France. These countries are significantly different in terms of electricity sources, hydro- storage capacity, complementarity and demand growth. We show that complementarity is essential in order to obtain benefits from integration, while higher demand growth and hydro- storage capacity can lead to counterintuitive outcomes, thus complicating policy design. In the third paper, an extended version of the model presented in the first paper is used to analyse the case of Finland and its interconnection with Russia. Different trading arrangements are considered. We conclude that unless interconnection capacity is expanded, the current trading arrangement, where a single trader owns the transmission rights and limits the flow during peak hours, is beneficial for Finland. In case of interconnection expansion, market coupling would be preferable. We also show that the costs of maintaining a strategic reserve in Finland are justified in order to limit import dependency, while still reaping the benefits of interconnection. In general, we conclude that electricity market integration can bring benefits if the right policies are implemented. However, a large interconnection capacity is only desirable if the countries exhibit significant complementarity and trust each other. The outcomes of policies aimed at guaranteeing security of supply at a national level can be quite counterintuitive due to the interactions between neighbouring countries and their effects on interconnection and generation investments. Thus, it is important for regulators to understand these interactions and coordinate their decisions in order to take advantage of the interconnection without putting security of supply at risk. But it must be taken into account that even when integration brings benefits to the region, some market participants lose and might try to hinder the integration process. -- Dans les sociétés modernes, l'électricité est un service stratégique. Il est donc extrêmement important pour les gouvernements de pouvoir garantir la sécurité d'approvisionnement à des prix abordables. Ceci dépend en grande mesure d'une expansion adéquate des capacités de génération et de transmission. L'intégration des marchés électriques pose des nouveaux défis pour les régulateurs, puisque l'évolution du marché est maintenant influencée par les caractéristiques et les politiques des pays voisins. Il n'est pas encore claire pourquoi ni comment les marches électriques devraient s'intégrer. L'objectif de cette thèse est d'améliorer la compréhension des marchés intégrés d'électricité et de leur comportement en fonction des caractéristiques et politiques de chaque pays. Un modèle de simulation est proposé pour étudier les conditions dans lesquelles l'intégration est désirable. Ce modèle est utilisé pour étudier trois cas d'interconnexion entre deux pays. Plusieurs politiques concernant l'expansion et l'opération de l'interconnexion, combinées avec différents mécanismes de rémunération de la capacité, sont évalués. Cette thèse est compose de trois articles. Le premier présente une description détaillée du modèle et une analyse du cas de la Colombie et de l'Equateur. Il montre que le couplage de marchés peut amener des bénéfices importants ; cependant, la différence de taille entre pays peut créer des soucis de dépendance aux importations pour le pays le plus petit. Le second papier compare le cas de la Colombie et l'Equateur avec le cas de la Grande Bretagne et de la France. Ces pays sont très différents en termes de ressources, taille des réservoirs d'accumulation pour l'hydro, complémentarité et croissance de la demande. Nos résultats montrent que la complémentarité joue un rôle essentiel dans l'obtention des bénéfices potentiels de l'intégration, alors qu'un taux élevé de croissance de la demande, ainsi qu'une grande capacité de stockage, mènent à des résultats contre-intuitifs, ce qui complique les décisions des régulateurs. Dans le troisième article, une extension du modèle présenté dans le premier article est utilisée pour analyser le cas de la Finlande et de la Russie. Différentes règles pour les échanges internationaux d'électricité sont considérées. Nos résultats indiquent qu'à un faible niveau d'interconnexion, la situation actuelle, où un marchand unique possède les droits de transmission et limite le flux pendant les heures de pointe, est bénéfique pour la Finlande. Cependant, en cas d'expansion de la capacité d'interconnexion, «market coupling» est préférable. préférable. Dans tous les cas, la Finlande a intérêt à garder une réserve stratégique, car même si cette politique entraine des coûts, elle lui permet de profiter des avantages de l'intégration tout en limitant ca dépendance envers les importations. En général, nous concluons que si les politiques adéquates sont implémentées, l'intégration des marchés électriques peut amener des bénéfices. Cependant, une grande capacité d'interconnexion n'est désirable que si les pays ont une complémentarité importante et il existe une confiance mutuelle. Les résultats des politiques qui cherchent à préserver la sécurité d'approvisionnement au niveau national peuvent être très contre-intuitifs, étant données les interactions entre les pays voisins et leurs effets sur les investissements en génération et en interconnexion. Il est donc très important pour les régulateurs de comprendre ces interactions et de coordonner décisions à fin de pouvoir profiter de l'interconnexion sans mettre en danger la sécurité d'approvisionnement. Mais il faut être conscients que même quand l'intégration amène de bénéfices pour la région, certains participants au marché sont perdants et pourraient essayer de bloquer le processus d'intégration.