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In evolution alternative genetic trajectories can potentially lead to similar phenotypic outcomes. However, certain trajectories are preferred over others. These preferences bias the genomes of living organisms and the underlying processes can be observed in ongoing evolution. We have studied a variety of biases that can be found in bacterial chromosomes and determined the selective causes and functional consequences for the cell. We have quantified codon usage bias in highly expressed genes and shown that it is selected to optimise translational speed. We further demonstrated that the resulting differences in decoding speed can be used to regulate gene expression, and that the use of ‘non-optimal’ codons can be detrimental to reading frame maintenance. Biased gene location on the chromosome favours recombination between genes within gene families and leads to co-evolution. We have shown that such recombinational events can protect these gene families from inactivation by mobile genetic elements, and that chromosome organization can be selectively maintained because inversions can lead to the formation of unstable hybrid operons. We have used the development of antibiotic resistance to study how different bacterial lifestyles influence evolutionary trajectories. For this we used two distinct pairs of antibiotics and disease-causing bacteria, namely (i) Mycobacterium tuberculosis that is treated with rifampicin and (ii) Escherichia coli that is treated with ciprofloxacin. We have shown that in the slow-growing Mycobacterium tuberculosis, resistance mutations are selected for high-level resistance. Fitness is initially less important, and over time fitness costs can be ameliorated by compensatory mutations. The need for rapid growth causes the selection of ciprofloxacin resistance in Escherichia coli not only to be selected on the basis of high-level resistance but also on high fitness. Compensatory evolution is therefore not required and is not observed. Taken together, our results show that the evolution of a phenotype is the product of multiple steps and that many factors influence which trajectory is the most likely to occur and be most beneficial. Over time, selection will favour this particular trajectory and lead to biased evolution, affecting genome sequence and organization.

Under det senaste decenniet har barns och ungas tillgång till olika digitala medier ökat. De flesta elever möter det engelska språket varje dag på något sätt och de är inte bara konsumenter av språket utan de producerar också engelska i olika aktiviteter på fritiden. Syftet med studien är att undersöka vilket utrymme elevernas extramurala engelska får inom ramen för skolans engelskundervisning och i vilken utsträckning eleverna har användning av engelskan de lär sig i skolans undervisning i sina fritidsaktiviteter. Extramural engelska är ett begrepp som innefattar all den engelska som eleverna kommer i kontakt med utanför skolan. Studien omfattar tre lärare och nio elever i årskurs 4-6 från tre olika kommuner i Jönköpings län. Studien har en fenomenografiskt inspirerad ansats och materialinsamlingen har gjorts genom semistrukturerade intervjuer. Resultatet visar att lärarna arbetat mer eller mindre med en inkludering av elevernas extramurala engelska i engelskundervisningen. Något som var gemensamt för samtliga intervjuade lärare var att de såg en signifikant skillnad i språkliga förmågor mellan de elever som spelade mycket onlinespel och de elever som inte gjorde det. Flertalet av de intervjuade eleverna ansåg sig på ett eller annat sätt ha användning av den engelska de lär sig i skolan på sin fritid. En slutsats som dras är att det är viktigt att undervisande lärare sätter sig in i var, i vilken form och på vilket sätt eleverna möter engelska i sin fritid för att kunna inkludera det i undervisningen i engelska. / Over the past decade, children and adolescents have had an increased access to digital media. Most students get exposed to the English language in some way every day and they are not just consumers, they are also producers of English when they are engaged in different activities in their spare time. The aim of the study is to look into how extramural English is included in English school curriculum and to what extent students have use for the English they learn at school in their spare time activities. Extramural English includes all the English that students come into contact with outside of school. Three teachers and nine students, all from Jönköping county, are included in this study. The students are in grades 4-6. The study has a fenomenographically inspired approach and semi-structured intervjuews have been used to collect the data. The result reveals that the teachers have been working more or less with including the students’ extramural English in school. All teachers that participated in the interviews mentioned that they saw a significant difference in the students’ linguistic abilities between the ones who played a great number of online games and the students who did not. Most of the interviewed students felt in one way or another that they had use for the English they learn at school in their spare time. A conclusion drawn from the results of this study is that it is important for teachers to determine where, in what form and in what way students come into contact with English in their spare time in order to include it in the English school curriculum.

Phospholipase C enzymes are important cell signalling enzymes that catalyse the cleavage of phosphatidylinositol 4,5-bisphophate PI(4,5)P₂ into two biologically active second messenger molecules. These are the inositol 1,4,5-trisphosphate which initiates Ca²⁺ release from the endoplasmic reticulum and the diacylglycerol that activates protein kinase C. Although this basic function is shared between the different isoforms, the PLC family encompasses a diverse collection of proteins with various domain structures in addition to the PLC-specific domains. The neuron-specific “6th family” of these enzymes, PLCηs have most recently been identified with two members, PLCη1 and PLCη2. The aim of the thesis is to characterise the PLCη2 variant from several aspects. Firstly, it describes that PLCη2 possesses a high sensitivity towards Ca²⁺. Secondly, it investigates how the Ca²⁺-induced enzymatic activity of PLCη2 is controlled by its different domains. Also it provides evidence that the pleckstrin homology domain targets PLCη2 to membranes by recognising PI(3,4,5)P₃. Moreover, the uniquely structured EF-hand is responsible for the Ca²⁺-sensitivity of the enzyme. Finally, it is demonstrated that the C2 domain is important for activity. The initial biochemical characterisation is followed by the description of a physiological role for PLCη2. It is shown using a neuroblast model that PLCη2 is crucial for neuronal differentiation and neurite growth. Further efforts were made to assess how PLCη2 is responsible for this effect. It was revealed that it might be involved in regulating intracellular Ca²⁺ dynamics, transcriptional activity and actin reorganisation in differentiating neurons. As the functions of PLCη2 are just beginning to come to light, more aspects for future research are also suggested in the thesis. Hopefully, this and the data presented within the thesis will stimulate even greater interest in this fascinating new field of research.

<p>Becoming antibiotic resistant is often associated with fitness costs for the resistant bacteria. This is seen as a loss of competitiveness against the antibiotic-sensitive wild-type in an antibiotic-free environment. In this study, the physiological alterations associated with fitness cost of antibiotic resistance <i>in vitro</i> (in the laboratory medium), and <i>in vivo</i> (in a mouse infection model), are identified in the model system of fusidic acid resistant (Fus^R) <i>Salmonella</i> <i>enterica</i> serovar Typhimurium.</p><p>Fus^R mutants have mutations in <i>fusA</i>, the gene that encodes translation elongation factor G (EF-G). Fus^R EF-G has a slow rate of regeneration of active EF-G·GTP off the ribosome, resulting in a slow rate of protein synthesis. The low fitness of Fus^R mutants <i>in vitro</i>, and <i>in vivo</i>, can be explained in part by a slow rate of protein synthesis and resulting slow growth. However, some Fus^R mutants with normal rates of protein synthesis still suffer from reduced fitness <i>in vivo</i>. We observed that Fus^R mutants have perturbed levels of the global regulatory molecule ppGpp. One consequence of this is an inefficient induction of RpoS, a regulator of general stress reponse and an important virulence factor for <i>Salmonella</i>. In addition, we found that Fus^R mutants have reduced amounts of heme, a co-factor of catalases and cytochromes. As a consequence of the heme defect, Fus^R mutants have a reduced ability to withstand oxidative stress and a low rate of aerobic respiration.</p><p>The pleiotropic phenotypes of Fus^R mutants suggest that antibiotic resistance can be associated with broad changes in bacterial physiology. Knowledge of physiological alterations that reduce the fitness of antibiotic-resistant mutants can be useful in identifying novel targets for antimicrobial agents. Drugs that alter the levels of global transcriptional regulators such as ppGpp or RpoS deserve attention as potential antimicrobial agents. Finally, the observation that Fus^R mutants have increased sensitivity to several unrelated classes of antibiotics suggests that the identification of physiological cost of resistance can help in optimizing treatment of resistant bacterial populations.</p>

Becoming antibiotic resistant is often associated with fitness costs for the resistant bacteria. This is seen as a loss of competitiveness against the antibiotic-sensitive wild-type in an antibiotic-free environment. In this study, the physiological alterations associated with fitness cost of antibiotic resistance in vitro (in the laboratory medium), and in vivo (in a mouse infection model), are identified in the model system of fusidic acid resistant (FusR) Salmonella enterica serovar Typhimurium. FusR mutants have mutations in fusA, the gene that encodes translation elongation factor G (EF-G). FusR EF-G has a slow rate of regeneration of active EF-G·GTP off the ribosome, resulting in a slow rate of protein synthesis. The low fitness of FusR mutants in vitro, and in vivo, can be explained in part by a slow rate of protein synthesis and resulting slow growth. However, some FusR mutants with normal rates of protein synthesis still suffer from reduced fitness in vivo. We observed that FusR mutants have perturbed levels of the global regulatory molecule ppGpp. One consequence of this is an inefficient induction of RpoS, a regulator of general stress reponse and an important virulence factor for Salmonella. In addition, we found that FusR mutants have reduced amounts of heme, a co-factor of catalases and cytochromes. As a consequence of the heme defect, FusR mutants have a reduced ability to withstand oxidative stress and a low rate of aerobic respiration. The pleiotropic phenotypes of FusR mutants suggest that antibiotic resistance can be associated with broad changes in bacterial physiology. Knowledge of physiological alterations that reduce the fitness of antibiotic-resistant mutants can be useful in identifying novel targets for antimicrobial agents. Drugs that alter the levels of global transcriptional regulators such as ppGpp or RpoS deserve attention as potential antimicrobial agents. Finally, the observation that FusR mutants have increased sensitivity to several unrelated classes of antibiotics suggests that the identification of physiological cost of resistance can help in optimizing treatment of resistant bacterial populations.

Le traitement la forme d'un produit et la formalisation de l'information impliquée dans le processus de liaison entre les activités de Conception et d'Analyse Mécanique sont essentiels. Dans ce travail, un cadre générique la définition d'un modèle intermédiaire est proposé. Le modèle de forme de référence est polyédrique mais également enrichi avec une description de plus haut niveau. La représentation mixte de forme qui en découle permet de transférer quelques hypothèses et objectifs du problème considéré en termes de contraintes qui doivent satisfaites pendant la génération du modèle intermédiaire, où, plus tard dans le processus, pendant la génération modèle de simulation où effectuer l'analyse mécanique. De plus, la relation qu'il y a entre l'application d'un ( mécanique et la suppression d'un sous-domaine de forme est mise en évidence. En particulier, la formulation critère mécanique a posteriori supportant les transformations de forme est fournie.

Cette thèse porte sur le vieillissement des grands ouvrages en béton armé et précontraint dotés d’une fonction de confinement comme les bâtiments réacteurs des centrales nucléaires. Elle vise en particulier l'analyse probabiliste de l’évolution de leurs états de fissuration et de perméabilité dans le temps sous chargements Thermo-Hydro-Mécaniques (THM) simultanés et variables. L’étanchéité de telles structures est due à la faible perméabilité du béton mais reste conditionnée surtout par la maîtrise de la fissuration. Or, l'évolution de la perméabilité, l'apparition des fissures et leur propagation dépendent fortement de plusieurs aléas (les conditions de mise en œuvre, la variabilité spatio-temporelle des propriétés du béton et des chargements THM subis par la structure, etc.). Ainsi, la prise en compte de ces aléas dans les modèles numériques de vieillissement est une nécessité afin de permettre une meilleure évaluation de la performance de la structure dans son état présent et, surtout, permettre une prévision plus précise et plus fiable de son état futur. Pour y parvenir, cette thèse propose une stratégie globale de modélisation stochastique Thermo-Hydro-Mécanique avec post-traitement de la Fuite (THM-F), à l’échelle de Volumes Structurels Représentatifs, adaptée à la complexité du problème traité, au nombre important de paramètres THM-F intervenant dans les calculs et à son coût numérique. En particulier, les points suivants sont traités :(a) Modélisation du vieillissement tenant compte des effets de jeune âge : La modélisation des phénomènes de vieillissement est basée sur un modèle THM-F chaîné. En particulier, la modélisation proposée de la fissuration repose sur le couplage des lois d’échelle énergétique et des champs aléatoires autocorrélés selon une formulation locale, régularisée et vieillissante de l’endommagement. Cela permet une meilleure évaluation du risque de fissuration tant d’un point de vue qualitatif que quantitatif. Par conséquent, la prévision de l’étanchéité est aussi améliorée.(b) Identification des paramètres THM-F les plus influents : En appliquant une méthode d’analyse de sensibilité de type OFAT (One-Factor-At-a-Time) au modèle THM-F retenu, l’effet de la variabilité des différents paramètres en entrée sur la réponse numérique est quantifié. Cela permet de hiérarchiser les effets et de classifier les paramètres selon leur importance vis-à-vis du vieillissement (particulièrement en termes de fissuration et d’étanchéité).(c) Analyse de la propagation d’incertitudes THM-F : Des méthodes basées sur les surfaces de réponse (plans d’expérience adaptatifs, chaos polynomiaux) sont proposées pour construire des méta-modèles THM-F et analyser la propagation d’incertitudes moyennant un coût et une précision raisonnables. Étant donné la nature explicite des méta-modèles, la méthode de Monte Carlo est directement appliquée pour accéder à des fonctions de répartition, des indicateurs de sensibilité globaux et des analyses de fiabilité.L’applicabilité du modèle stochastique THM-F proposé aux grands ouvrages de confinement en béton armé et précontraint est évaluée en se basant sur la maquette VeRCoRs (enceinte de confinement à l’échelle 1 :3) selon des critères de représentativité physique du comportement et des mesures d’incertitudes simulés et de coût numérique. / Concrete is a heterogeneous, multiphasic and ageing material. Consequently, its properties show intrinsically spatiotemporal variations. For large reinforced and prestressed concrete structures such as Nuclear Containment Buildings (NCB), these variations directly affect the kinetic of their ageing process in terms of cracking, drying, creep and tightness. They also lead, within the structure's volume, to a non-negligible spatial heterogeneity of the concrete's behavior to the applied Thermo-Hydro-Mechanical (THM) loads during the operational lifespan. Consequently, the introduction of such variations in numerical models is a mandatory step to enhance the assessment of these structures’ present behavior and the accuracy of predictive analyses of their future one. With that aim in view, the thesis suggests a global coupling strategy of THM-L models (Thermo-Hydro-Mechanical with Leakage estimation) and non-intrusive stochastic approaches adapted for the strongly non-linear and time consuming simulations of ageing phenomena and the large number of inputs they require. Applied to the VeRCoRs mock-up (1:3 scaled containment building) at the scale of Representative Structural Volumes (RSV), this thesis addresses the following issues:(a) RSV-based modeling of concrete ageing from the early age phase: The modeling of concrete’s ageing is based on a staggered Thermo-Hydro-Mechanical with Leakage evaluation (THM-L) strategy. In particular, concrete cracking is modeled according to a Stochastic Size Effect Law (SSEL) and a regularized, local, ageing and damage-based constitutive model. The spatial heterogeneity of the concrete's properties (mainly the Young's modulus) is described using Random Fields (RF). This leads to a better description of concrete cracking both qualitatively and quantitatively. Accordingly, the modeling of the structural tightness is also improved.(b) Most influential THM-L parameters: Using a 1st order sensitivity analysis strategy (One-Factor-At-a-Time OFAT perturbation method), the relative effect of the THM-F parameters on the computed behavior is quantified. The obtained results show a hierarchized list of the most influential parameters and their associated physical phenomena. A selection is then achieved to keep relevant parameters only for uncertainty propagation step and higher-order sensitivity analyses throughout the THM-L coupling path.(c) Uncertainties propagation through THM-L calculation steps: Surface Response Methods (SRM) are used to define the associated RSV-based THM-L meta-models. For the stochastic modeling of concrete’s cracking an original Adaptive-SRM-based algorithm is suggested. Whereas for continuous THM-L quantities, a Polynomial Chaos based strategy is retained. Finally, as the meta-models are explicit within a defined and bounded domain, crude Monte Carlo Method is applied, at low cost, aiming at the CDFs and the reliability analysis of the considered variables of interest.Eventually, the suggested SFEM shall lead operators to a better quantification of uncertainties related to the behavior of their strategic civil engineering structures. This remains a crucial step towards the enhancement of durability assessment and repair/maintenance operations planning.

Cette recherche porte sur le développement d’un modèle de structure de géométrie complexe équipée de composants à comportement non linéaire viscoélastique dans le but de simuler sa réponse à des excitations définies par des densités spectrales de puissance (DSP). L’application industrielle concerne l’isolation vibratoire d’un module de refroidissement automobile monté sur plot de suspension en élastomère. Une revue du comportement des élastomères en fonction de leurs conditions d’environnement et de sollicitations identifie les paramètres des différents modèles analysés. Des essais préliminaires ont été menés pour définir les intervalles des niveaux de sollicitations et quantifier l’échauffement des plots. La caractérisation expérimentale de la suspension porte sur des plots en élastomère munis de leurs interfaces afin d’agréger dans un seul modèle les non linéarités du comportement viscoélastique, des glissements et des frottements. Les boucles effort-déflexion axiales et radiales mesurées sont traitées avec un système expert développé spécialement pour caler les paramètres du modèle retenu. Il s’agit du modèle de Dahl généralisé qu’il a fallu étendre aux aspects viscoélastiques. Ce processus de calage automatique a été codé avec un logiciel développé sous Octave/Matlab. Des méthodes d’interpolations et extrapolations rendent opérationnel ce modèle sur toute la gamme fonctionnement de l’application définie dans l’espace fréquence-déflexion. Ce processus a été codé dans le module UserSubroutine pour Abaqus. Soumettre le système mécanique non linéaire à des excitations définies par une DSP nécessite de s’appesantir sur le traitement des vibrations aléatoires. En effet il faut, pour calculer les réponses, considérer le passage fréquence-temps et inversement pour les comparer éventuellement aux exigences des normes. De plus, la taille et la complexité du modèle EF de la structure industrielle rendent impossible une résolution temporelle sur l’ensemble de ses degrés de liberté. Il s’agit alors de faire appel à des techniques d’homogénéisation et de condensation dynamique afin de prévoir la réponse aux excitations à large bande fréquentielle dans le but d’analyser les performances de l’isolation vibratoire. / This research work regards the development of a complex structure model with non-linear viscoelastic components. The purpose of this study is to simulate the response of this structure submitted to a random vibration excitation based on a power spectral density definition (PSD). The industrial applicative case is the vibratory insulation of a automotive engine cooling module supported by elastomer mounts. A brief review of elastomers behavior depending on solicitations types enables to identify the parameters of the different investigated models. Preliminary tests have been conducted to define the range of amplitudes of excitations and evaluate the internal warming of rubbers during the full structure validation test. The experimental characterization of the suspension is based on rubbers mounts and their interfaces with the cooling module, in order to take into account in a unique model all nonlinearities due to the viscoelastic behavior, the slidings, and the friction. Measured force-deflection hysteretic cycles in axial and radial direction are post-processed with an expert system developed to obtain the parameters of the retained model: the modified Dahl’s model, generalized to viscoleastic aspect. This process has been developed with Octave/Matlab code. Interpolation and extrapolation methods enable to obtain a good model response on the global operating range. These methods have been coded in an Abaqus UserSubroutine. Imposing random vibration excitation of a non linear mechanical system based on PSD imposes to take into account signal processing aspects. To evaluate response levels versus norms requirements, it’s mandatory to consider the time-frequency transfer. In addition, the size and the complexity of the total finite element model of the industrial structure don’t allow a global resolution in the time domain for all the degrees of freedom. Homogenization and dynamic reduction techniques are used to evaluate the response of the system submitted to large frequency range excitations, and to analyse the behavior of the suspension.

The study of fungal diversity may lead to many fundamental discoveries and conclusions. Molecular genetics, and particularly high throughput sequencing methods using short DNA fragments as barcodes, has recently experienced a boom. The most frequently used marker for fungal research is the partial region of nuclear ribosomal DNA called ITS (Internal Transcribed Spacer). It occurs in the form of tandem repetitions of up to 200 copies. This fact greatly simplifies its amplification from the environment but also introduces some negatives. One of them can be an existence of intragenomic and intraspecific variability which confounds diversity estimates by exaggerating the real number of species. Using alternative low-copy markers can easily prevent these problems. In this study EF-1α and RPB2 protein- coding genes were compared with traditionally used ITS1 and ITS2 markers. An artificial mock community was created by blending genomic DNA of different fungal lineages. The community was sequenced for all markers and the data were processed according to guidelines commonly used in environmental studies. The results show that ITS2 is unequivocally a more suitable marker for environmental studies than other compared markers. The average coefficient of overestimation was deemed to be approximately two for ITS1, ITS2,...