Developmental and Anatomical Constraints on Vertebrate Genome Evolution

Pendant ma thèse de doctorat, j'ai utilisé des espèces modèles, comme la souris et le poisson-zèbre, pour étudier les facteurs qui affectent l'évolution des gènes et leur expression. Plus précisément, j'ai montré que l'anatomie et le développement sont des facteurs clés à prendre en compte, car ils influencent la vitesse d'évolution de la séquence des gènes, l'impact sur eux de mutations (i.e. la délétion du gène est-elle létale ?), et leur tendance à se dupliquer. Où et quand il est exprimé impose à un gène certaines contraintes ou au contraire lui donne des opportunités d'évoluer. J'ai pu comparer ces tendances aux modèles classiques d'évolution de la morphologie, que l'on pensait auparavant refléter directement les contraintes s'appliquant sur le génome. Nous avons montré que les contraintes entre ces deux niveaux d'organisation ne peuvent pas être transférées simplement : il n'y a pas de lien direct entre la conservation du génotype et celle de phénotypes comme la morphologie. Ce travail a été possible grâce au développement d'outils bioinformatiques. Notamment, j'ai travaillé sur le développement de la base de données Bgee, qui a pour but de comparer l'expression des gènes entre différentes espèces de manière automatique et à large échelle. Cela implique une formalisation de l'anatomie, du développement et de concepts liés à l'homologie grâce à l'utilisation d'ontologies. Une intégration cohérente de données d'expression hétérogènes (puces à ADN, marqueurs de séquence exprimée, hybridations in situ) a aussi été nécessaire. Cette base de données est mise à jour régulièrement et disponible librement. Elle devrait contribuer à étendre les possibilités de comparaison de l'expression des gènes entre espèces pour des études d'évo-devo (évolution du développement) et de génomique. During my PhD, I used model species of vertebrates, such as mouse and zebrafish, to study factors affecting the evolution of genes and their expression. More precisely I have shown that anatomy and development are key factors to take into account, influencing the rate of gene sequence evolution, the impact of mutations (i.e. is the deletion of a gene lethal?), and the propensity of a gene to duplicate. Where and when genes are expressed imposes constraints, or on the contrary leaves them some opportunity to evolve. We analyzed these patterns in relation to classical models of morphological evolution in vertebrates, which were previously thought to directly reflect constraints on the genomes. We showed that the patterns of evolution at these two levels of organization do not translate smoothly: there is no direct link between the conservation of genotype and phenotypes such as morphology. This work was made possible by the development of bioinformatics tools. Notably, I worked on the development of the database Bgee, which aims at comparing gene expression between different species in an automated and large-scale way. This involves the formalization of anatomy, development, and concepts related to homology, through the use of ontologies. A coherent integration of heterogeneous expression data (microarray, expressed sequence tags, in situ hybridizations) is also required. This database is regularly updated and freely available. It should contribute to extend the possibilities for comparison of gene expression between species in evo-devo and genomics studies.

Space-time within general relativity : a structural realist understanding

ABSTRACT This dissertation investigates the, nature of space-time as described by the theory of general relativity. It mainly argues that space-time can be naturally interpreted as a physical structure in the precise sense of a network of concrete space-time relations among concrete space-time points that do not possess any intrinsic properties and any intrinsic identity. Such an interpretation is fundamentally based on two related key features of general relativity, namely substantive general covariance and background independence, where substantive general covariance is understood as a gauge-theoretic invariance under active diffeomorphisms and background independence is understood in the sense that the metric (or gravitational) field is dynamical and that, strictly speaking, it cannot be uniquely split into a purely gravitational part and a fixed purely inertial part or background. More broadly, a precise notion of (physical) structure is developed within the framework of a moderate version of structural realism understood as a metaphysical claim about what there is in the world. So, the developement of this moderate structural realism pursues two main aims. The first is purely metaphysical, the aim being to develop a coherent metaphysics of structures and of objects (particular attention is paid to the questions of identity and individuality of these latter within this structural realist framework). The second is to argue that moderate structural realism provides a convincing interpretation of the world as described by fundamental physics and in particular of space-time as described by general relativity. This structuralist interpretation of space-time is discussed within the traditional substantivalist-relationalist debate, which is best understood within the broader framework of the question about the relationship between space-time on the one hand and matter on the other. In particular, it is claimed that space-time structuralism does not constitute a 'tertium quid' in the traditional debate. Some new light on the question of the nature of space-time may be shed from the fundamental foundational issue of space-time singularities. Their possible 'non-local' (or global) feature is discussed in some detail and it is argued that a broad structuralist conception of space-time may provide a physically meaningful understanding of space-time singularities, which is not plagued by the conceptual difficulties of the usual atomsitic framework. Indeed, part of these difficulties may come from the standard differential geometric description of space-time, which encodes to some extent this atomistic framework; it raises the question of the importance of the mathematical formalism for the interpretation of space-time.

Climate change impact on biodiversity in Switzerland: a review. Journal for Nature Conservation

A noticeable increase in mean temperature has already been observed in Switzerland and summer temperatures up to 4.8 K warmer are expected by 2090. This article reviews the observed impacts of climate change on biodiversity and consider some perspectives for the future at the national level. The following impacts are already evident for all considered taxonomic groups: elevation shifts of distribution toward mountain summits, spread of thermophilous species, colonisation by new species from warmer areas and phenological shifts. Additionally, in the driest areas, increasing droughts are affecting tree survival and fish species are suffering from warm temperatures in lowland regions. These observations are coherent with model projections, and future changes will probably follow the current trends. These changes will likely cause extinctions for alpine species (competition, loss of habitat) and lowland species (temperature or drought stress). In the very urbanised Swiss landscape, the high fragmentation of the natural ecosystems will hinder the dispersal of many species towards mountains. Moreover, disruptions in species interactions caused by individual migration rates or phenological shifts are likely to have consequences for biodiversity. Conversely, the inertia of the ecosystems (species longevity, restricted dispersal) and the local persistence of populations will probably result in lower extinction rates than expected with some models, at least in 21st century. It is thus very difficult to estimate the impact of climate change in terms of species extinctions. A greater recognition by society of the intrinsic value of biodiversity and of its importance for our existence will be essential to put in place effective mitigation measures and to safeguard a maximum number of native species.

Construcció i explotació d'un magatzem de dades per a l'anàlisi estadístic dels resultats del Campionat de Fórmula 1

En els darrers anys les organitzacions han anat agafant consciència de la importància de la gestió de la seva informació. D'aquesta necessitat d'organitzar les pròpies dades d'una forma coherent i eficient per al seu anàlisi sorgeixen els magatzems de dades. El projecte "Construcció i explotació d'un magatzem de dades per a l'anàlisi estadístic dels resultats del Campionat de Fórmula 1" s'emmarca dins aquest context i te com a objectiu el disseny d'un magatzem de dades per a cobrir les necessitats del Institut Català d'Esports de Motor (ICEM) en la gestió de les seves dades referents a la Fórmula 1. En aquest projecte s'han executat les diferents fases necessàries per a la creació d'un nou magatzem. En primer lloc s'ha fet l'anàlisi de requeriments i de les dades disponibles. A continuació s'ha fet el disseny i la implementació física del magatzem de dades. Seguidament s'ha procedit amb l'extracció, transformació i càrrega de dades originals (ETL) i per finalitzar s'han creat els informes. Com a resultat s'han obtingut una sèrie d'informes per a ser consumits de manera immediata pels usuaris del ICEM. Aquests informes han de permetre l'anàlisi de les dades d'una forma senzilla i àgil. A més s'ha implementat un sistema d'actualització automàtic de les dades que per al manteniment de la informació del magatzem.La implementació del magatzem de dades s'ha fet sobre una base de dades Oracle 10g Express Edition i els informes s'ha dissenyat amb l'eina Oracle Discoverer. Per a l'automatització de les dades s'ha fet servir a més visual basic script i l'eina de càrrega SQL*Loader.

Travailler sur les articulations interprofessionnelles en périnatalité: un objectif obstétrical [Interprofessional collaboration in perinatality: an obstetrical goal]

In the field of perinatality, development of prenatal diagnosis and neonatal management have been impressive. But these were also associated with the emergence of the increasingly important emotional dimension for parents and professionals. Obstetricians dealing with the difficult breaking of bad news, the uncertainties of prenatal diagnosis and the complex somatic, psychological and social follow-up have to work in a multidisciplinary approach. The securing role of a coherent teamwork is recognised by parents as well as health care providers This article discusses interprofessional relationship as an obstetrical goal and give some landmarks in order to improve the management and the collaboration with parents.

Diagnostic value of soluble CD14 subtype (sCD14-ST) presepsin for the postmortem diagnosis of sepsis-related fatalities.

The first aim of this study was to assess the diagnostic performance of presepsin (sCD14-ST) in postmortem serum from femoral blood compared to procalcitonin (PCT) to detect sepsis-related fatalities. The second aim was to compare sCD14-ST levels found in postmortem serum to the values in pericardial fluid to investigate the usefulness of the latter as an alternative biological fluid. Two study groups were formed, a sepsis-related fatalities group and a control group. Radiology (unenhanced CT scans and postmortem angiographies), autopsies, histology, neuropathology, and toxicology as well as other postmortem biochemistry investigations were performed in all cases. Microbiological investigations on right cardiac blood were carried out exclusively in septic cases. The results of this study indicated that postmortem serum PCT and sCD14-ST levels, individually considered, allowed septic cases to be identified. Even though increases in both PCT and sCD14-ST concentrations were observed in the control cases, coherent PCT and sCD14-ST results in cases with suspected sepsis allowed the diagnosis to be confirmed. Conversely, no relevant correlation was identified between postmortem serum and pericardial fluid sCD14-ST levels in either the septic or control groups.

Obesity prevention opinions of school stakeholders: a qualitative study.

BACKGROUND: In general, schools are an important setting to implement current recommendations for obesity prevention in children because the vast majority of children attend school. This study investigated the opinions of different school stakeholders on the feasibility and acceptability of current obesity prevention strategies that could be implemented in Swiss schools. METHODS: Research methods were comprised of a qualitative study which included school directors, physical education teachers, catering staff, school nurses and health educators, parents of young adolescents, and young adolescents interviewed (N = 40) categorized into 6 focus groups. Open-ended questions were used to determine the participants' opinion regarding current obesity prevention recommendations, and healthy eating and physical activity promotion strategies. RESULTS: All participants approved the implementation of nutritional standards for food and drinks sold in schools, but thought that increasing the attractiveness of healthy options was the best strategy to improve eating habits. Enjoying participation in physical activity classes or after-school activities was stressed. Participants suggested offering classes for all students with poor physical condition, independent of weight status. Stakeholders called for governmental support and global coordination of interventions balanced with providing schools with enough autonomy to adapt programs relevant to their individual circumstances. They recommended integrating all school stakeholders in obesity prevention initiatives, with special attention to students and local authorities. CONCLUSIONS: Participants agreed that schools are a crucial setting to implement childhood obesity prevention strategies. They called on school stakeholders to join efforts aiming to encourage healthy behaviors and to support and reinforce parents' efforts by spreading consistent and coherent health messages.

The relationships between technology and open education in the development of a resilient higher education

The place of technology in the development of coherent educational responses to environmental and socio-economic disruption is here placed under scrutiny. One emerging area of interest is the role of technology in addressing more complex learning futures, and more especially in facilitating individual and social resilience, or the ability to manage and overcome disruption. However, the extent to which higher education practitioners can utilise technology to this end is framed by their approaches to the curriculum, and the socio-cultural practices within which they are located. This paper discusses how open education might enable learners to engage with uncertainty through social action within a form of higher education that is more resilient to economic, environmental and energy-related disruption. It asks whether open higher education can be (re)claimed by users and communities within specific contexts and curricula, in order to engage with an uncertain world.

Analysis of teachers training for ICT Higher Education

Aquest document pretén recollir aportacions teòriques i pràctiques sobre les pràctiques pedagògiques que incorporen i promouen l'ús de les TIC per tal d'aclarir, facilitar i fer coherent el disseny de la formació dels professors d'educació superior en les TIC. El seu propòsit és trobar alternatives de formació que compleixin amb les necessitats educatives del professor, així com per superar o atenuar les dificultats i/o la manca de voluntat a les quals s'enfronta en la pràctica educativa en introduir aplicacions de les TIC.

La dinàmica de les práctiques científiques des del punt de vista de l'experiencialisme

La tesi doctoral titulada "La Dinàmica de les Pràctiques Científiques des d'un punt de vista experiencialista" té com a objectiu oferir una alternativa a les tesis de Kuhn defensades a l'"Estructura de les Revolucions Científiques". En aquest sentit, s'utilitzaran diferents experiments i models teòrics actuals en l'àmbit de les ciències cognitives per tal de superar la teoria estructuralista de la cognició, quee Kuhn proposa com la base de la seva filosofia de la ciència. Contràriament a aquesta teoria, l'experiencialisme se situa lluny de les tesis estructuralistes, en la mesura en què assumeix que la cognició humana emergeix des de la dinàmica interactiva dels agents cognitius humans entre ells en un entorn material, en tant que agents corporals. A partir d'aquesta interacció dinàmica, l'ésser humà genera un horitzó de sentit. Ja que la interacció entre els éssers humans en un entorn cultural i material és complex, dinàmic i canviant, la generació de sentit emergent no és com una estructura semàntica, coherent i sistemàtica, sinó que ha de ser considerada com un conjunt asistemàtic de perspectives exploratòries que se succeeixen en el temps, en funció dels diferents contextos i propòsits que un agent corporal porta a terme al llarg de la seva interacció dinàmica i temporal amb l'entorn. Com a resultat de tot això, els èssers humans apliquen diferents criteris interactius que donen lloc a diferents perspectives per categoritzar o estructurar el món material i cultural. Aquest punt de vista és completament diferent del kuhnià, donat que el segon argumenta que cada èsser humà té la seva pròpia Gestalt o estructura semàntica que projecta "a priori" sobre la realitat. Aquesta diferència serà molt important no només des d'un punt de vista teòric, sinó també des d'un punt de vista pràctic. Per exemple, s'argumentarà que en l'àmbit de la didàctica de les ciències empíriques, es poden produir canvis beneficiosos significatius si s'utilitzen tesis extretes del model experiencialista de la cognició humana, i es deixen de banda el cognitivisme i el teoreticisme, que són actualment les bases teòriques de la manera en qué funciona l'educació científica. Finalment, conclourem afirmant que la visió experiencialista de la cognició implica assumir una forta relació entre l'ètica i la ciència, puix que els èssers humans són capaços d'utilitzar diferents criteris interactius per explorar la realitat i, per tant, sempre poden buscar millors estragègies per entendre's els uns amb els altres.

A Bayesian network approach to the database serch problem in criminal proceedings

Background The 'database search problem', that is, the strengthening of a case - in terms of probative value - against an individual who is found as a result of a database search, has been approached during the last two decades with substantial mathematical analyses, accompanied by lively debate and centrally opposing conclusions. This represents a challenging obstacle in teaching but also hinders a balanced and coherent discussion of the topic within the wider scientific and legal community. This paper revisits and tracks the associated mathematical analyses in terms of Bayesian networks. Their derivation and discussion for capturing probabilistic arguments that explain the database search problem are outlined in detail. The resulting Bayesian networks offer a distinct view on the main debated issues, along with further clarity. Methods As a general framework for representing and analyzing formal arguments in probabilistic reasoning about uncertain target propositions (that is, whether or not a given individual is the source of a crime stain), this paper relies on graphical probability models, in particular, Bayesian networks. This graphical probability modeling approach is used to capture, within a single model, a series of key variables, such as the number of individuals in a database, the size of the population of potential crime stain sources, and the rarity of the corresponding analytical characteristics in a relevant population. Results This paper demonstrates the feasibility of deriving Bayesian network structures for analyzing, representing, and tracking the database search problem. The output of the proposed models can be shown to agree with existing but exclusively formulaic approaches. Conclusions The proposed Bayesian networks allow one to capture and analyze the currently most well-supported but reputedly counter-intuitive and difficult solution to the database search problem in a way that goes beyond the traditional, purely formulaic expressions. The method's graphical environment, along with its computational and probabilistic architectures, represents a rich package that offers analysts and discussants with additional modes of interaction, concise representation, and coherent communication.

Reviu la vil·la romana de Tossa

Descripció de les actuacions al jaciment arqueològic de la vil•la romana dels Ametllers de Tossa de Mar, durant l’estiu del 2000. La finalitat d’aquestes actuacions era realitzar un recorregut coherent i atractiu des del punt de vista museístic i turístic, per tal de presentar el jaciment als habitants i als visitants de la vil•la

A new perspective on the zoogeography of the sibling mouse-eared bat species Myotis myotis and Myotis blythii: Morphological, genetical and ecological evidence

The actual geographic distribution of the two sibling mouse-eared bat species Myotis myotis and Myotis blythii, which occur widely sympatrically in the western Palaearctic region, remains largely controversial. This concerns particularly the specific attribution of marginal populations from the Mediterranean islands and from adjacent areas of North Africa and Asia, which are morphologically intermediate between continental M. myotis and M. blythii from Europe. This study attempts to clarify this question by using four different approaches: cranial morphology, external morphology, genetics and trophic ecology. The three latter methods show unambiguously that North Africa, Malta, Sardinia and Corsica are presently inhabited by monospecific populations of M. myotis. In contrast, cranial morphometrics do not yield conclusive results. These results contradict all recent studies, which attribute North African and Maltese mouse-eared bats to M. blythii and consider that Sardinia and Corsica harbour sympatric populations of the two species. As concerns south-eastern populations, doubts are also expressed about the attribution of the subspecific taxon omari which may actually refer to M. myotis instead of M. blythii. Protein electrophoresis is presently the only absolute method available for determining M. myotis and M. blythii throughout their distribution ranges. However, species identification may be approached by relying on less sophisticated morphometrical methods as presented in this study. Species-specific habitat specializations are probably responsible for the differences observed between the geographic distributions of M. myotis and M. blythii, as they provide a logical groundwork for a coherent model of speciation for these two bat species.

Phylogeny and circumscription of Sapindaceae revisited: molecular sequence data, morphology and biogeography support recognition of a new family, Xanthoceraceae

Background and aims Recent studies have adopted a broad definition of Sapindaceae that includes taxa traditionally placed in Aceraceae and Hippocastanaceae, achieving monophyly but yielding a family difficult to characterize and for which no obvious morphological synapomorphy exists. This expanded circumscription was necessitated by the finding that the monotypic, temperate Asian genus Xanthoceras, historically placed in Sapindaceae tribe Harpullieae, is basal within the group. Here we seek to clarify the relationships of Xanthoceras based on phylogenetic analyses using a dataset encompassing nearly 3/4 of sapindaceous genera, comparing the results with information from morphology and biogeography, in particular with respect to the other taxa placed in Harpullieae. We then re-examine the appropriateness of maintaining the current broad, morphologically heterogeneous definition of Sapindaceae and explore the advantages of an alternative family circumscription. Methods Using 243 samples representing 104 of the 142 currently recognized genera of Sapindaceae s. lat. (including all in Harpullieae), sequence data were analyzed for nuclear (ITS) and plastid (matK, rpoB, trnD-trnT, trnK-matK, trnL-trnF and trnS-trnG) markers, adopting the methodology of a recent family-wide study, performing single-gene and total evidence analyses based on maximum likelihood (ML) and maximum parsimony (MP) criteria, and applying heuristic searches developed for large datasets, viz, a new strategy implemented in RAxML (for ML) and the parsimony ratchet (for MP). Bootstrap analyses were performed for each method to test for congruence between markers. Key results Our findings support earlier suggestions that Harpullieae are polyphyletic: Xanthoceras is confirmed as sister to all other sampled taxa of Sapindaceae s. lat.; the remaining members belong to three other clades within Sapindaceae s. lat., two of which correspond respectively to the groups traditionally treated as Aceraceae and Hippocastanaceae, together forming a clade sister to the largely tropical Sapindaceae s. str., which is monophyletic and morphologically coherent provided Xanthoceras is excluded. Conclusion To overcome the difficulties of a broadly circumscribed Sapindaceae, we resurrect the historically recognized temperate families Aceraceae and Hippocastanaceae, and describe a new family, Xanthoceraceae, thus adopting a monophyletic and easily characterized circumscription of Sapindaceae nearly identical to that used for over a century.

Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India

The aim of the present study was to compare polymerase chain reaction (PCR)-based methods - spoligotyping and mycobacterial interspersed repetitive units (MIRU) typing - with the gold-standard IS6110 restriction fragment length polymorphism (RFLP) analysis in 101 isolates of Mycobacterium tuberculosis to determine the genetic diversity of M. tuberculosis clinical isolates from Delhi, North India. Spoligotyping resulted in 49 patterns (14 clusters); the largest cluster was composed of Spoligotype International Types (SITs)26 [Central-Asian (CAS)1-Delhi lineage], followed by SIT11 [East-African-Indian (EAI) 3-Indian lineage]. A large number of isolates (75%) belonged to genotypic lineages, such as CAS, EAI and Manu, with a high specificity for the Indian subcontinent, emphasising the complex diversity of the phylogenetically coherent M. tuberculosis in North India. MIRU typing, using 11 discriminatory loci, was able to distinguish between all but two strains based on individual patterns. IS6110-RFLP analysis (n = 80 strains) resulted in 67 unique isolates and four clusters containing 13 strains. MIRUs discriminated all 13 strains, whereas spoligotyping discriminated 11 strains. Our results validate the use of PCR-based molecular typing of M. tuberculosis using repetitive elements in Indian isolates and demonstrate the usefulness of MIRUs for discriminating low-IS6110-copy isolates, which accounted for more than one-fifth of the strains in the present study.