Genomics of wine yeast: functional analysis of new and variable genes

Projecte de recerca elaborat a partir d’una estada a l’Institut National de la Recherche Agronomique, França, entre 2007 i 2009. Saccharomyces cerevisiae ha estat el llevat utilitzat durant mil.lenis en l'elaboració de vins. Tot i així, es té poc coneixement sobre les pressions de selecció que han actuat en la modelització del genoma dels llevats vínics. S’ha seqüenciat el genoma d'una soca vínica comercial, EC1118, obtenint 31 supercontigs que cobreixen el 97% del genoma de la soca de referència, S288c. S’ha trobat que el genoma de la soca vínica es diferencia bàsicament en la possessió de 3 regions úniques que contenen 34 gens implicats en funcions claus per al procés fermentatiu. A banda, s’han dut a terme estudis de filogènia i synteny (ordre dels gens) que mostren que una d'aquestes tres regions és pròxima a una espècie relacionada amb el gènere Saccharomyces, mentre que les altres dos regions tenen un origen no-Saccharomyces. S’ha identificat mitjançant PCR i seqüenciació a Zygosaccharomyces bailii, una espècie contaminant de les fermentacions víniques, com a espècie donadora d'una de les dues regions. Les hibridacions naturals entre soques de diferents espècies dins del grup Saccharomyces sensu stricto ja han estat descrites. El treball és el primer que presenta hibridacions entre espècies Saccharomyces i no-Saccharomyces (Z. bailii, en aquest cas). També s’assenyala que les noves regions es troben freqüent i diferencialment presents entre els clades de S. cerevisiae, trobant-se de manera gairebé exclusiva en el grup de les soques víniques, suggerint que es tracta d'una adquisició recent de transferència gènica. En general, les dades demostren que el genoma de les soques víniques pateix una constant remodelació mitjançant l'adquisició de gens exògens. Els resultats suggereixen que aquests processos estan afavorits per la proximitat ecològica i estan implicats en l'adaptació molecular de les soques víniques a les condicions d'elevada concentració en sucres, poc nitrogen i elevades concentracions en etanol.

Changes in the vascular reactivity of the isolated tail arteries of spontaneous and renovascular hypertensive rats to endogenous and exogenous noradrenaline.

We have investigated the changes in the responses to noradrenaline of isolated tail arteries of spontaneously hypertensive (SHR) and renovascular hypertensive rats (Wistar-Kyoto: two-kidney, one-clip model, WKY:2K1C) compared with normotensive (Wistar-Kyoto, WKY) rats. Renovascular hypertension was induced by 4 weeks' unilateral renal artery clipping. Arteries were vasoconstricted with exogenous noradrenaline, electrical field stimulation or high potassium. The effects of the latter two stimuli were abolished by reserpine and so were presumably dependent on the presence of endogenous noradrenaline. In the SHR the maximal vasoconstriction produced by all three stimuli was greater than in WKY. Dose-response curves were steeper and there was no change in threshold. Vascular mass was greater. We interpret these results as showing an increase in vascular reactivity in the SHR caused by structural adaptation. The WKY:2K1C responses to noradrenaline could also be explained in terms of structural adaptation but there was no increase in vascular mass. Sensitivity to potassium and electrical stimulation was decreased, suggesting a defect in vascular neurotransmission. This was supported by the observations of a decreased arterial noradrenaline content and of decreased sensitivity to cocaine.

L'intégration de l'adaptation au changement climatique dans la conduite des politiques publiques: déficit de mise en oeuvre ou déficit de légitimité?

L'échec des tentatives de juguler les émissions globales de gaz à effet de serre a mené au renforcement d'un discours sur la nécessité de l'adaptation au changement climatique. Il est de plus souvent considéré qu'une transformation de l'action publique serait nécessaire afin de réduire les impacts de grande magnitude qui découlent du changement climatique. Depuis les années 2000, on constate ainsi un développement des activités étatiques dans le domaine de l'adaptation. Cette évolution suscite une question centrale: quels sont les effets réels que provoque l'intégration de l'adaptation au changement climatique dans la conduite des politiques publiques et comment expliquer les éventuelles limites à ces processus? La littérature spécialisée sur l'adaptation fait preuve d'un certain réductionnisme à l'égard de la complexité de l'action publique en considérant que lorsque la capacité d'agir contre le problème de la vulnérabilité au changement climatique existe, toute forme d'inaction publique serait un déficit de mise en oeuvre provoqué par des barrières à l'action qu'il faudrait lever. A contrario, cette thèse considère l'adaptation comme une norme de politique publique dont l'intégration est susceptible de provoquer des changements institutionnels dans la forme et le contenu des politiques publiques, et des effets concrets sur les acteurs vulnérables au changement climatique. Afin de mesurer les effets de l'intégration politique de l'adaptation, un concept est formulé sur la base d'un idéal-type du régime institutionnel adaptatif, soit une construction théorique des régulations qu'impliquerait une gestion cohérente du système socioécologique complexe dans lequel s'insère le système climatique. L'auteur propose un cadre d'analyse empirique des processus publics d'adaptation qu'il applique ensuite à deux États: l'Inde (politique agricole) et la Suisse (politique du tourisme hivernal), avec pour objectif de repérer des mécanismes explicatifs communs aux effets de l'intégration dans ces deux contextes extrêmement dissemblables. L'étude débouche sur six résultats qui constituent une contribution appréciable à la littérature. L'auteur montre: premièrement, que l'intégration politique de l'adaptation conduit à une production d'actes symboliques, qui s'explique notamment par le manque de pression publique à agir sur le problème de la vulnérabilité au changement climatique; deuxièmement, que le processus d'intégration agit sur la réalité sociale par le biais d'un mécanisme d'attribution de ressources publiques à certains acteurs du champ politique; troisièmement, que les groupes sociaux qui bénéficient de ces ressources publiques ne sont pas nécessairement les plus vulnérables, mais ceux détenant les ressources d'action nécessaires à l'activation de l'intervention publique; quatrièmement, que l'absence de clefs de répartition des coûts de l'adaptation, de procédures de monitoring et d'instruments d'action contraignants limitent les effets des programmes publics d'adaptation; cinquièmement, que la faible articulation institutionnelle entre objectif d'adaptation et objectifs de protection de l'environnement accentue le risque de processus d'adaptation produisant des externalités environnementales; sixièmement, que les transformations dont la littérature souligne la nécessité ne sont pas nécessairement faisables ni désirables. Sur la base de cette analyse, cette thèse s'écarte de la littérature dominante en concluant que les processus publics d'adaptation ne souffrent pas d'un déficit de mise en oeuvre, mais d'un déficit de légitimité lié à leurs effets pernicieux. L'auteur formule alors trois recommandations pour améliorer la légitimité de ces politiques et trois questions ouvertes sur le futur politique de l'adaptation.

Stomach content analyses of Simulium perflavum Roubaud 1906 (Diptera: Simuliidae) larvae from streams in Central Amazônia, Brazil

Stomach contents of Simulium perflavum Roubaud larvae were analyzed and compared with plankton and periphyton collected in five streams, in Central Amazonia (Manaus and Presidente Figueiredo counties), in Sep./Oct.1996 (dry season) and Feb./Mar. 1997 (rainy season). A total of 1,400 last-instar larvae were dissected; the stomach contents were analyzed using different methods: fresh and after oxidation. A total of 87 taxa (algae, diatoms and rotifers) were found in the stomach contents. In each stream, qualitative samples of plankton and periphyton were collected; these were mounted between slides and cover slips. A total of 94 taxa of plankton and 54 taxa of periphyton were collected. One species of Rotifera was present in the stomach contents, plankton and periphyton. Cluster analysis based on species composition of the organisms present in the stomach contents grouped the streams into two major groups, each belonging to a different drainage area. Correlations based on presence/absence of species of microalgae in the stomach contents, plankton and periphyton indicated significant associations (p<0.05) between stomach contents and plankton and between plankton and periphyton (z test); the Sorensen coefficient and cluster analysis corroborate the same associations.

Recent studies on Schistosoma intercalatum: taxonomic status, puzzling distribution and transmission foci revisited

Schistosoma intercalatum, which causes human rectal schistosomiasis in Africa, still presents a great interest for its imprecise taxonomic status and its puzzling distribution in Africa. Two geographically isolated strains of S. intercalatum are recognized, the Lower Guinea strain and the Congo strain, which differ from each other in a number of morphological, biological and biochemical characteristics. Recent molecular data using RAPD markers indicate high divergence between the two strains, with values of Nei and Li's similarity indice allowing recognition of two genetically distinct taxa: experiments on pre- and post-isolating mechanisms are in progress in order to re-evaluate the taxonomic status of this polytypic species. With regard to its geographical distribution, S. intercalatum is characterized by the existence of two stable endemic areas (localized in Lower Guinea and North East of Democratic Republic of Congo) which correspond to the historical areas of species discovery, and the emergence during the last 15 years of new foci of the Lower Guinea strain outside previously known endemic areas. The absence of local adaptation of the Lower Guinea strain to its intermediate host, supported by experimental studies, may help to facilitate the spread of this strain. Nevertheless, the present restricted distribution of this species remains puzzling, because its potential snail hosts (bulinids) are widely distributed throughout much of Africa. Recent experimental and epidemiological studies suggest that interspecific sexual interactions between human schistosomes could have a role in limiting the distribution of S. intercalatum: the competitive sexual processes acting among human schistosomes show that S. haematobium and S. mansoni are always competitively dominant over S. intercalatum. These epidemiological observations lead the authors to distinguish three kinds of transmission foci for S. intercalatum.

Maps as risk mitigation tools. Adaptation of the Swiss hazard assessment and mapping methodology to a Moroccan site: Beni Mellal

Dans le contexte climatique actuel, les régions méditerranéennes connaissent une intensification des phénomènes hydrométéorologiques extrêmes. Au Maroc, le risque lié aux inondations est devenu problématique, les communautés étant vulnérables aux événements extrêmes. En effet, le développement économique et urbain rapide et mal maîtrisé augmente l'exposition aux phénomènes extrêmes. La Direction du Développement et de la Coopération suisse (DDC) s'implique activement dans la réduction des risques naturels au Maroc. La cartographie des dangers et son intégration dans l'aménagement du territoire représentent une méthode efficace afin de réduire la vulnérabilité spatiale. Ainsi, la DDC a mandaté ce projet d'adaptation de la méthode suisse de cartographie des dangers à un cas d'étude marocain (la ville de Beni Mellal, région de Tadla-Azilal, Maroc). La méthode suisse a été adaptée aux contraintes spécifiques du terrain (environnement semi-aride, morphologie de piémont) et au contexte de transfert de connaissances (caractéristiques socio-économiques et pratiques). Une carte des phénomènes d'inondations a été produite. Elle contient les témoins morphologiques et les éléments anthropiques pertinents pour le développement et l'aggravation des inondations. La modélisation de la relation pluie-débit pour des événements de référence, et le routage des hydrogrammes de crue ainsi obtenus ont permis d'estimer quantitativement l'aléa inondation. Des données obtenues sur le terrain (estimations de débit, extension de crues connues) ont permis de vérifier les résultats des modèles. Des cartes d'intensité et de probabilité ont été obtenues. Enfin, une carte indicative du danger d'inondation a été produite sur la base de la matrice suisse du danger qui croise l'intensité et la probabilité d'occurrence d'un événement pour obtenir des degrés de danger assignables au territoire étudié. En vue de l'implémentation des cartes de danger dans les documents de l'aménagement du territoire, nous nous intéressons au fonctionnement actuel de la gestion institutionnelle du risque à Beni Mellal, en étudiant le degré d'intégration de la gestion et la manière dont les connaissances sur les risques influencent le processus de gestion. L'analyse montre que la gestion est marquée par une logique de gestion hiérarchique et la priorité des mesures de protection par rapport aux mesures passives d'aménagement du territoire. Les connaissances sur le risque restent sectorielles, souvent déconnectées. L'innovation dans le domaine de la gestion du risque résulte de collaborations horizontales entre les acteurs ou avec des sources de connaissances externes (par exemple les universités). Des recommandations méthodologiques et institutionnelles issues de cette étude ont été adressées aux gestionnaires en vue de l'implémentation des cartes de danger. Plus que des outils de réduction du risque, les cartes de danger aident à transmettre des connaissances vers le public et contribuent ainsi à établir une culture du risque. - Severe rainfall events are thought to be occurring more frequently in semi-arid areas. In Morocco, flood hazard has become an important topic, notably as rapid economic development and high urbanization rates have increased the exposure of people and assets in hazard-prone areas. The Swiss Agency for Development and Cooperation (SADC) is active in natural hazard mitigation in Morocco. As hazard mapping for urban planning is thought to be a sound tool for vulnerability reduction, the SADC has financed a project aimed at adapting the Swiss approach for hazard assessment and mapping to the case of Morocco. In a knowledge transfer context, the Swiss method was adapted to the semi-arid environment, the specific piedmont morphology and to socio-economic constraints particular to the study site. Following the Swiss guidelines, a hydro-geomorphological map was established, containing all geomorphic elements related to known past floods. Next, rainfall / runoff modeling for reference events and hydraulic routing of the obtained hydrographs were carried out in order to assess hazard quantitatively. Field-collected discharge estimations and flood extent for known floods were used to verify the model results. Flood hazard intensity and probability maps were obtained. Finally, an indicative danger map as defined within the Swiss hazard assessment terminology was calculated using the Swiss hazard matrix that convolves flood intensity with its recurrence probability in order to assign flood danger degrees to the concerned territory. Danger maps become effective, as risk mitigation tools, when implemented in urban planning. We focus on how local authorities are involved in the risk management process and how knowledge about risk impacts the management. An institutional vulnerability "map" was established based on individual interviews held with the main institutional actors in flood management. Results show that flood hazard management is defined by uneven actions and relationships, it is based on top-down decision-making patterns, and focus is maintained on active mitigation measures. The institutional actors embody sectorial, often disconnected risk knowledge pools, whose relationships are dictated by the institutional hierarchy. Results show that innovation in the risk management process emerges when actors collaborate despite the established hierarchy or when they open to outer knowledge pools (e.g. the academia). Several methodological and institutional recommendations were addressed to risk management stakeholders in view of potential map implementation to planning. Hazard assessment and mapping is essential to an integrated risk management approach: more than a mitigation tool, danger maps represent tools that allow communicating on hazards and establishing a risk culture.

Design of Novel Frequency Generation Circuit with Application to Ultra-Wideband Distributed Oscillators

Given the urgence of a new paradigm in wireless digital trasmission which should allow for higher bit rate, lower latency and tigher delay constaints, it has been proposed to investigate the fundamental building blocks that at the circuital/device level, will boost the change towards a more efficient network architecture, with high capacity, higher bandwidth and a more satisfactory end user experience. At the core of each transciever, there are inherently analog devices capable of providing the carrier signal, the oscillators. It is strongly believed that many limitations in today's communication protocols, could be relieved by permitting high carrier frequency radio transmission, and having some degree of reconfigurability. This led us to studying distributed oscillator architectures which work in the microwave range and possess wideband tuning capability. As microvave oscillators are essentially nonlinear devices, a full nonlinear analyis, synthesis, and optimization had to be considered for their implementation. Consequently, all the most used nonlinear numerical techniques in commercial EDA software had been reviewed. An application of all the aforementioned techniques has been shown, considering a systems of three coupled oscillator ("triple push" oscillator) in which the stability of the various oscillating modes has been studied. Provided that a certain phase distribution is maintained among the oscillating elements, this topology permits a rise in the output power of the third harmonic; nevertheless due to circuit simmetry, "unwanted" oscillating modes coexist with the intenteded one. Starting with the necessary background on distributed amplification and distributed oscillator theory, the design of a four stage reverse mode distributed voltage controlled oscillator (DVCO) using lumped elments has been presented. All the design steps have been reported and for the first time a method for an optimized design with reduced variations in the output power has been presented. Ongoing work is devoted to model a wideband DVCO and to implement a frequency divider.

Experimental evidence and ecological perspectives for the adaptation of Schistosoma mansoni Sambon, 1907 (Digenea: Schistosomatidae) to a wild host, the water-rat, Nectomys squamipes Brants, 1827 (Rodentia: Sigmodontinae)

Due to the semi aquatic habits and the overlap of the geographical distribution of the water-rat, Nectomys spp., with schistosomiasis endemic areas, these wild rodents are very likely to acquire Schistosoma mansoni infection in their daily activities. The role of the water-rat in the S. mansoni cycle would be substantiated if one could prove that these rodents acquire the parasite during their own activity time, a completely independent time schedule of human activities. To pursue this goal, we performed two field experiments in the municipality of Sumidouro, State of Rio de Janeiro, Brazil, a schistosomiasis endemic area where N. squamipes is found naturally infected. One experiment was devised as a series of observations of activity time of the water-rat. The other experiment was a test of the occurrence of late transmission of S. mansoni to the water-rat. The daily activity pattern showed that the water-rat is active chiefly just after sunset. At both diurnal and late exposition essays the water-rat sentinels got infected by S. mansoni. These findings clarify ecological and behavioral components necessary to the adaptation of S. mansoni to the water-rat as a non human definitive host and the existence of a transmission cycle involving this animals as a reservoir.

Mesurer la stigmatisaion perçue chez les personnes souffrant de troubles psychiques : traduction française, validation et adaptation de la Stigma Scale

L'objectif de l'étude présentée est d'adapter et de valider une version française de la Stigma Scale (King, 2007) auprès d'une population de personnes souffrant de troubles psychiques. Dans une première phase, la stabilité temporelle (fidélité test-retest), la cohérence interne et la validité convergente de l'instrument original à 28 items traduit en français ont été évaluées auprès d'un échantillon de 183 patients. Les résultats d'analyses factorielles confirmatoires ne nous ont pas permis de confirmer la structure originale de l'instrument. Nous avons donc proposé, sur la base des résultats d'une analyse factorielle exploratoire, une version courte de l'échelle de stigmatisation (9 items) qui conserve la structure en trois facteurs du modèle original. Dans une deuxième phase, nous avons examiné les qualités psychométriques et validé cette version abrégée de l'échelle de stigmatisation auprès d'un second échantillon de 234 patients. Les indices d'ajustements de notre analyse factorielle confirmatoire confirme la structure en trois facteurs de la version abrégée de la Stigma Scale. Les résultats suggèrent que la version française abrégée de l'échelle de stigmatisation constitue un instrument utile, fiable et valide dans l'autoévaluation de la stigmatisation perçue par des personnes souffrant de troubles psychiques. - Aim People suffering from mental illness are exposed to stigma. However, only few tools are available to assess stigmatization as perceived from the patient's perspective. The aim of this study is to adapt and validate a French version of the Stigma Scale (King, 2007). This self-report questionnaire has a three-factor structure: discrimination, disclosure and positive aspects of mental illness. Discrimination subscale refers to perceived negative reactions by others. Disclosure subscale refers mainly to managing disclosure to avoid discrimination and finally positive aspects subscale taps into how patients are becoming more accepting, more understanding toward their illness. Method In the first step, internal consistency, convergent validity and test-retest reliability of the French adaptation of the 28-item scale have been assessed on a sample of 183 patients. Results of confirmatory factor analyses (CFA) did not confirm the hypothesized structure. In light of the failed attempts to validate the original version, an alternative 9-item short-form version of the Stigma Scale, maintaining the integrity of the original model, was developed based on results of exploratory factor analyses in the first sample and cross- validated in a new sample of 234 patients. Results Results of CFA did not confirm that the data fitted well to the three-factor model of the 28-item Stigma Scale (χ2/άί=2.02, GFI=0.77, AGFI=0.73, RMSEA=0.07, CFI=0.77 et NNFI=0.75). Cronbach's α are excellent for discrimination (0.84) and disclosure (0.83) subscales but poor for potential positive aspects (0.46). External validity is satisfactory. Overall Stigma Scale total score is negatively correlated with score on Rosenberg's Self-Esteem Scale (r = -0.49), and each sub-scale is significantly correlated with a visual analogue scale that refers to the specific aspect of stigma (0.43 < |r| < 0.60). Intraclass correlation coefficients between 0.68 and 0.89 indicate good test- retest reliability. Results of CFA demonstrate that the items chosen for the short version of the Stigma Scale have the expected fit properties fa2/df=1.02, GFI=0.98, AGFI=0.98, RMSEA=0.01, CFI=1.0 et NNFI=1.0). Considering the small number (3 items) of items in each subscales of the short version of the Stigma Scale, a coefficients for the discrimination (0.57), disclosure (0.80) and potential positive aspects subscales (0.62) are considered as good. Conclusion Our results suggest that the 9-item French short-version of the Stigma Scale is a useful, reliable and valid self-report questionnaire to assess perceived stigmatization in people suffering from mental illness. The time of completion is really short and questions are well understood and accepted by the patients.

Managing Climate Insecurity by Ensuring Continuous Capital Accumulation : 'Climate Refugees' and 'Climate Migrants'

Numerous recent reports by non-governmental organisations (NGOs), academics and international organisations have focused on so-called 'climate refugees'. This article examines the turn from a discourse of 'climate refugees', in which organisations perceive migration as a failure of both mitigation and adaptation to climate change, to one of 'climate migration', in which organisations promote migration as a strategy of adaptation. Its focus is the promotion of climate migration management, and it explores the trend of these discourses through two sections. First, it provides an empirical account of the two discourses, emphasising the differentiation between them. It then focuses on the discourse of climate migration, its origins, extent and content, and the associated practices of 'migration management'. The second part argues that the turn to the promotion of 'climate migration' should be understood as a way to manage the insecurity created by climate change. However, international organisations enacts this management within the forms of neoliberal capitalism, including the framework of governance. Therefore, the promotion of 'climate migration' as a strategy of adaptation to climate change is located within the tendencies of neoliberalism and the reconfiguration of southern states' sovereignty through governance.

Prismatic adaptation changes visuospatial representation in the inferior parietal lobule.

Prismatic adaptation has been shown to induce a realignment of visuoproprioceptive representations and to involve parietocerebellar networks. We have investigated in humans how far other types of functions known to involve the parietal cortex are influenced by a brief exposure to prismatic adaptation. Normal subjects underwent an fMRI evaluation before and after a brief session of prismatic adaptation using rightward deviating prisms for one group or after an equivalent session using plain glasses for the other group. Activation patterns to three tasks were analyzed: (1) visual detection; (2) visuospatial short-term memory; and (3) verbal short-term memory. The prismatic adaptation-related changes were found bilaterally in the inferior parietal lobule when prisms, but not plain glasses, were used. This effect was driven by selective changes during the visual detection task: an increase in neural activity was induced on the left and a decrease on the right parietal side after prismatic adaptation. Comparison of activation patterns after prismatic adaptation on the visual detection task demonstrated a significant increase of the ipsilateral field representation in the left inferior parietal lobule and a significant decrease in the right inferior parietal lobule. In conclusion, a brief exposure to prismatic adaptation modulates differently left and right parietal activation during visual detection but not during short-term memory. Furthermore, the visuospatial representation within the inferior parietal lobule changes, with a decrease of the ipsilateral hemifield representation on the right and increase on the left side, suggesting thus a left hemispheric dominance.