Doctor en Ciencias, Mención Astronomía / Observing the changes in the orbital period of transiting exoplanets produced by gravitational perturbations allows to detect unseen orbital companions in the system. With this technique,known asTransitTimingVariations(TTVs),itispossibletodetectperturbers down to Earth-like masses, overcoming the limits of current Radial Velocity searches. This PhDthesishasled to along termproject: TransitMonitoringin theSouth(TraMoS)project, which consists in a methodical and homogeneous monitoring of transiting exoplanets observable from the Southern Hemisphere with the goal of searching for orbital companions, and potentially finding Earth-mass planets. Aditionally, the cumulative light curves provide improvedvalues of thephysicalparameters of theplanets, such as orbitalinclination and radius, and from those absolute mass and mean planetary density, which are critical to our model understanding of thephysics of exoplanetary interiors and their evolution. Also, establishing thepresence orabsence of otherplanetashelpsdeterminethe architecture of multi-planetary systems, and therefore is key to discriminate between different models of formation and evolution of exoplanets. In thisThesisIpresent the observations and analysis of29 transits of4 exoplanets: OGLETR-111b, WASP-5b, WASP-4b and WASP-7b. Based on the analysis of the light curves of these exoplanets we refined the ephemeris and physical parameters of all these exoplanets. Based on the temporal analysis, we found no evidence of the presence of additional planets with masses larger than ∼10 Min those systems. We place strong limits in the mass of ~10 M⊕possible perturbers especially in the orbital resonances with the transiting planets. These results support the formation theories that predict a paucity of planetary companions to Jupiter-like planets.

O Circovirus suíno tipo 2 (PCV2) é um vírus ubíquo que tem sido associado a um número de síndromes em suínos. Entre elas, a Síndrome Multissistêmica do Definhamento dos Suínos (SMDS) tornou-se uma das principais causas de perdas econômicas na suinocultura nacional. No entanto, existe incerteza se o PCV2 é, de fato, o único agente responsável por esse quadro, essencialmente porque a administração isolada do vírus a animais suscetíveis não tem sido capaz de reproduzir experimentalmente a síndrome. Em vista disso, um número de outros agentes infecciosos (e não infecciosos) tem sido examinados e sua potencial participação no desenvolvimento da SMDS tem sido pesquisada. No presente estudo foram realizados experimentos visando determinar se outro(s) agente(s) com genoma de DNA circular poderia(m) desempenhar algum papel no desenvolvimento da SMDS. Para tanto, a técnica denominada “amplificação por círculo rolante com múltiplos primers” (ACRMP) foi empregada. A ACRMP é baseada na atividade da DNA polimerase do fago phi29, uma enzima capaz de sintetizar novas moléculas de DNA a partir de um molde de DNA circular. Numa segunda etapa, o DNA amplificado é clivado com enzimas de restrição, ocasionando a linearização de grande quantidade de cópias do DNA alvo original. Como a ACRMP é realizada com primers aleatórios, nenhum conhecimento prévio da seqüência de nucleotídeos alvo é necessário. Portanto, pode-se teoricamente amplificar DNA circular de qualquer microorganismo, o que a torna ideal para o propósito do presente estudo. O DNA extraído de soros de 67 suínos com sinais clínicos de SMDS, assim como de 63 suínos saudáveis, foram submetidos à ACRMP. O principal achado deste estudo foi que o genoma de um (ou mais) anelovírus foi(ram) detectado(s) em 88,9% (56/63) dos suínos saudáveis, ao passo que o(s) mesmo(s) agente(s) somente foi(ram) detectado(s) em 16,4% (11/67) dos soros de suínos com sinais clínicos da SMDS. Alguns fragmentos de DNA potencialmente correspondentes a fragmentos de genomas virais foram seqüenciados, revelando que pelo menos um deles corresponde a uma seqüência de anelovírus suíno ainda não descrita. No entanto, outro genoma correspondente a um anelovírus foi encontrado na mesma amostra, sugerindo que mais de um vírus pode estar presente em amostras de soro. Estes resultados demonstraram que os anelovírus, de grande variabilidade genética, são significativamente mais prevalentes em suínos clinicamente saudáveis do que em suínos com SMDS. / Porcine circovirus type 2 (PCV2) is an ubiquitous virus that has been associated to a number of syndromes in swine. Among these, Postweaning Multisystemic Wasting Syndrome (PMWS) has become a major cause of economic losses in swine worldwide. However, there is uncertainty as to whether PCV2 is in fact the sole agent responsible for the disease, essentially because the disease has not been experimentally reproduced when PCV2 is inoculated onto susceptible animals. In view of that, a number of other infectious (and non infectious) agents have been examined and their potential role in PMWS searched for. This study was carried out to determine whether any other agent(s) with circular DNA genome might be playing some role in PMWS. In order to achieve that, a technique called “randomly primed rolling circle amplification” (RPRCA) was employed. RPRCA is based on the activity of bacteriophage phi29 DNA polymerase, an enzyme that synthesizes new DNA molecules starting from a circularized DNA template. In a second phase, the amplified DNA is cleaved with restriction enzymes, so giving rise to large amounts of linearized copies of the original target DNA. As RPRCA is performed with random priming, no previous knowledge of the target nucleotide sequence is necessary. Therefore, it is theoretically possible to amplify circular DNA of any microorganism, thus making it ideal for the purpose of the present study. DNA extracted from sera of 67 pigs with clinical signs of PMWS as well as from 63 healthy pigs was submitted to RPRCA. The major finding of this study was that the genome of one (or more) anelloviruses was detected in 88,9% (56/63) of the healthy pigs, whereas the same agent was only detected in 16,4% (11/67) of pigs with clinical signs of PMWS. Some of the DNA fragments corresponding to the putative virus genomes were sequenced and revealed at least one non-previously described anellovirus sequence. However, other anellovirus could be found on the same sample, suggesting that more than one genome are present in samples of serum. These results demonstrate that anelovírus, of great genetic variability, were significantly more prevalent in healthy pigs than in pigs with PMWS.

O Circovirus suíno tipo 2 (PCV2) é um vírus ubíquo que tem sido associado a um número de síndromes em suínos. Entre elas, a Síndrome Multissistêmica do Definhamento dos Suínos (SMDS) tornou-se uma das principais causas de perdas econômicas na suinocultura nacional. No entanto, existe incerteza se o PCV2 é, de fato, o único agente responsável por esse quadro, essencialmente porque a administração isolada do vírus a animais suscetíveis não tem sido capaz de reproduzir experimentalmente a síndrome. Em vista disso, um número de outros agentes infecciosos (e não infecciosos) tem sido examinados e sua potencial participação no desenvolvimento da SMDS tem sido pesquisada. No presente estudo foram realizados experimentos visando determinar se outro(s) agente(s) com genoma de DNA circular poderia(m) desempenhar algum papel no desenvolvimento da SMDS. Para tanto, a técnica denominada “amplificação por círculo rolante com múltiplos primers” (ACRMP) foi empregada. A ACRMP é baseada na atividade da DNA polimerase do fago phi29, uma enzima capaz de sintetizar novas moléculas de DNA a partir de um molde de DNA circular. Numa segunda etapa, o DNA amplificado é clivado com enzimas de restrição, ocasionando a linearização de grande quantidade de cópias do DNA alvo original. Como a ACRMP é realizada com primers aleatórios, nenhum conhecimento prévio da seqüência de nucleotídeos alvo é necessário. Portanto, pode-se teoricamente amplificar DNA circular de qualquer microorganismo, o que a torna ideal para o propósito do presente estudo. O DNA extraído de soros de 67 suínos com sinais clínicos de SMDS, assim como de 63 suínos saudáveis, foram submetidos à ACRMP. O principal achado deste estudo foi que o genoma de um (ou mais) anelovírus foi(ram) detectado(s) em 88,9% (56/63) dos suínos saudáveis, ao passo que o(s) mesmo(s) agente(s) somente foi(ram) detectado(s) em 16,4% (11/67) dos soros de suínos com sinais clínicos da SMDS. Alguns fragmentos de DNA potencialmente correspondentes a fragmentos de genomas virais foram seqüenciados, revelando que pelo menos um deles corresponde a uma seqüência de anelovírus suíno ainda não descrita. No entanto, outro genoma correspondente a um anelovírus foi encontrado na mesma amostra, sugerindo que mais de um vírus pode estar presente em amostras de soro. Estes resultados demonstraram que os anelovírus, de grande variabilidade genética, são significativamente mais prevalentes em suínos clinicamente saudáveis do que em suínos com SMDS. / Porcine circovirus type 2 (PCV2) is an ubiquitous virus that has been associated to a number of syndromes in swine. Among these, Postweaning Multisystemic Wasting Syndrome (PMWS) has become a major cause of economic losses in swine worldwide. However, there is uncertainty as to whether PCV2 is in fact the sole agent responsible for the disease, essentially because the disease has not been experimentally reproduced when PCV2 is inoculated onto susceptible animals. In view of that, a number of other infectious (and non infectious) agents have been examined and their potential role in PMWS searched for. This study was carried out to determine whether any other agent(s) with circular DNA genome might be playing some role in PMWS. In order to achieve that, a technique called “randomly primed rolling circle amplification” (RPRCA) was employed. RPRCA is based on the activity of bacteriophage phi29 DNA polymerase, an enzyme that synthesizes new DNA molecules starting from a circularized DNA template. In a second phase, the amplified DNA is cleaved with restriction enzymes, so giving rise to large amounts of linearized copies of the original target DNA. As RPRCA is performed with random priming, no previous knowledge of the target nucleotide sequence is necessary. Therefore, it is theoretically possible to amplify circular DNA of any microorganism, thus making it ideal for the purpose of the present study. DNA extracted from sera of 67 pigs with clinical signs of PMWS as well as from 63 healthy pigs was submitted to RPRCA. The major finding of this study was that the genome of one (or more) anelloviruses was detected in 88,9% (56/63) of the healthy pigs, whereas the same agent was only detected in 16,4% (11/67) of pigs with clinical signs of PMWS. Some of the DNA fragments corresponding to the putative virus genomes were sequenced and revealed at least one non-previously described anellovirus sequence. However, other anellovirus could be found on the same sample, suggesting that more than one genome are present in samples of serum. These results demonstrate that anelovírus, of great genetic variability, were significantly more prevalent in healthy pigs than in pigs with PMWS.

O Circovirus suíno tipo 2 (PCV2) é um vírus ubíquo que tem sido associado a um número de síndromes em suínos. Entre elas, a Síndrome Multissistêmica do Definhamento dos Suínos (SMDS) tornou-se uma das principais causas de perdas econômicas na suinocultura nacional. No entanto, existe incerteza se o PCV2 é, de fato, o único agente responsável por esse quadro, essencialmente porque a administração isolada do vírus a animais suscetíveis não tem sido capaz de reproduzir experimentalmente a síndrome. Em vista disso, um número de outros agentes infecciosos (e não infecciosos) tem sido examinados e sua potencial participação no desenvolvimento da SMDS tem sido pesquisada. No presente estudo foram realizados experimentos visando determinar se outro(s) agente(s) com genoma de DNA circular poderia(m) desempenhar algum papel no desenvolvimento da SMDS. Para tanto, a técnica denominada “amplificação por círculo rolante com múltiplos primers” (ACRMP) foi empregada. A ACRMP é baseada na atividade da DNA polimerase do fago phi29, uma enzima capaz de sintetizar novas moléculas de DNA a partir de um molde de DNA circular. Numa segunda etapa, o DNA amplificado é clivado com enzimas de restrição, ocasionando a linearização de grande quantidade de cópias do DNA alvo original. Como a ACRMP é realizada com primers aleatórios, nenhum conhecimento prévio da seqüência de nucleotídeos alvo é necessário. Portanto, pode-se teoricamente amplificar DNA circular de qualquer microorganismo, o que a torna ideal para o propósito do presente estudo. O DNA extraído de soros de 67 suínos com sinais clínicos de SMDS, assim como de 63 suínos saudáveis, foram submetidos à ACRMP. O principal achado deste estudo foi que o genoma de um (ou mais) anelovírus foi(ram) detectado(s) em 88,9% (56/63) dos suínos saudáveis, ao passo que o(s) mesmo(s) agente(s) somente foi(ram) detectado(s) em 16,4% (11/67) dos soros de suínos com sinais clínicos da SMDS. Alguns fragmentos de DNA potencialmente correspondentes a fragmentos de genomas virais foram seqüenciados, revelando que pelo menos um deles corresponde a uma seqüência de anelovírus suíno ainda não descrita. No entanto, outro genoma correspondente a um anelovírus foi encontrado na mesma amostra, sugerindo que mais de um vírus pode estar presente em amostras de soro. Estes resultados demonstraram que os anelovírus, de grande variabilidade genética, são significativamente mais prevalentes em suínos clinicamente saudáveis do que em suínos com SMDS. / Porcine circovirus type 2 (PCV2) is an ubiquitous virus that has been associated to a number of syndromes in swine. Among these, Postweaning Multisystemic Wasting Syndrome (PMWS) has become a major cause of economic losses in swine worldwide. However, there is uncertainty as to whether PCV2 is in fact the sole agent responsible for the disease, essentially because the disease has not been experimentally reproduced when PCV2 is inoculated onto susceptible animals. In view of that, a number of other infectious (and non infectious) agents have been examined and their potential role in PMWS searched for. This study was carried out to determine whether any other agent(s) with circular DNA genome might be playing some role in PMWS. In order to achieve that, a technique called “randomly primed rolling circle amplification” (RPRCA) was employed. RPRCA is based on the activity of bacteriophage phi29 DNA polymerase, an enzyme that synthesizes new DNA molecules starting from a circularized DNA template. In a second phase, the amplified DNA is cleaved with restriction enzymes, so giving rise to large amounts of linearized copies of the original target DNA. As RPRCA is performed with random priming, no previous knowledge of the target nucleotide sequence is necessary. Therefore, it is theoretically possible to amplify circular DNA of any microorganism, thus making it ideal for the purpose of the present study. DNA extracted from sera of 67 pigs with clinical signs of PMWS as well as from 63 healthy pigs was submitted to RPRCA. The major finding of this study was that the genome of one (or more) anelloviruses was detected in 88,9% (56/63) of the healthy pigs, whereas the same agent was only detected in 16,4% (11/67) of pigs with clinical signs of PMWS. Some of the DNA fragments corresponding to the putative virus genomes were sequenced and revealed at least one non-previously described anellovirus sequence. However, other anellovirus could be found on the same sample, suggesting that more than one genome are present in samples of serum. These results demonstrate that anelovírus, of great genetic variability, were significantly more prevalent in healthy pigs than in pigs with PMWS.

Les Myeloid-Derived Suppressor Cells (MDSC) sont une population hétérogène de cellules myéloïdes immatures, regroupées en deux sous-populations : les monocytiques-MDSC (M-MDSC) et les polymorphonucléaires-MDSC (PMN-MDSC). Ces cellules ont des capacités immunosuppressives et peuvent exprimer le ligand PD-L1 induisant l’anergie des lymphocytes T qui expriment le marqueur PD-1. Au cours du sepsis, divers bouleversements immunologiques surviennent, et la fonction majeure des MDSC est probablement de réguler l’hyper-inflammation en participant à l’état d’immunodépression rencontré chez les patients. Ceux-ci ont alors un risque de développer des infections secondaires, et de réactiver des virus jusque-là en latence. Notre étude a pour objectifs de mettre en évidence l’origine des MDSC dans le sepsis, et d’approfondir leurs rôles dans l’état d’immunosuppression, notamment dans la réactivation du Torque Teno Virus (TTV). Nos résultats montrent tant ex vivo qu’in vitro, que dans le sepsis, les MDSC sont produites par la moelle osseuse, sous l’influence du G-CSF et de l’IL-6. Ces cellules exprimant PD-L1, sont augmentées dans le sang très tôt dans le sepsis et persistes au cours de l’hospitalisation. L’augmentation de la charge virale du TTV est observée dans le sang périphérique des patients, mais n’est pas corrélée à la fréquence des MDSC. Ces résultats suggèrent que lors d’un sepsis, l’orage cytokinique stimule la production de MDSC exprimant PD-L1 par la moelle osseuse, qui une fois en périphérie, vont participer à l’immunosuppression générale. / Myeloid-Derived Suppressor Cells (MDSC) are a heterogeneous population of immature myeloid cell, and are regrouped in two subsets: the monocytic-MDSC (M-MDSC) and the polymorphonuclear-MDSC (PMN-MDSC). These cells have immunosuppressive capacities and mainly act on T cells. MDSC can express the ligand PD-L1 and induce PD-1 expressing-T cells exhaustion. During sepsis, several immunological changes occur, and MDSC probably downregulate the hyper-inflammatory state, contributing to the immunosuppression phase encountered in patients after a sepsis. Immunocompromised patients can develop secondary infections, and reactivate latent virus. The aims of our study were to highlight the origin of MDSC in sepsis, and to explore their roles in the immunosuppression state, especially in the Torque Teno Virus (TTV) reactivation. Our results show, both ex vivo and in vitro, that in sepsis, MDSC originate from bone marrow are induced by G-CSF and IL-6. These PD-L1 expressing-cells are increased in peripheral blood very early in sepsis, and persist during hospitalization. These MDSC are able to inhibit T cells in vitro. The increase of TTV viral load is observed in peripheral blood of patients but is not correlated with MDSC frequencies. These results suggest that during sepsis, the cytokine storm boosts PD-L1 expressing MDSC’s production by bone marrow, which contribute in peripheral blood to the immunosuppression

To protect public health, drinking water systems are monitored for indicator organisms that correlate with fecal contamination and suggest the presence of human pathogens. Total coliforms, fecal coliforms, and E. coli are the most commonly used indicator organisms. These bacteria generally colocate with fecal pollution, but some limitations exist. In particular, the ability of indicator bacteria to predict the presence of enteric viruses is questionable because of distinct transport and survival characteristics of bacteria and viruses. Although viral indicators of enteric viruses have been proposed, none have been implemented into the current regulatory framework. In this thesis, the correlation of bacteria and viruses in drinking water sources and treatment systems is reviewed, and the potential of Torque Teno virus (TTV) to qualify as an indicator virus is discussed. TTV is unique among enteric viruses as it infects approximately 80% of healthy individuals worldwide, is transmitted by the fecal-oral route, causes no observable illness, and lacks seasonal fluctuations.

Some viral metagenomic serum samples contain a huge amount of Anellovirus, which is a genetically diverse family with a few conserved regions making it hard to efficiently characterize. Multiple sequence alignment of the Anelloviruses found in the sample must be constructed to get a clear picture of Anellovirus diversity and to identify stable regions. Using available multiple sequence alignment software directly on these fragments results in an MSA of a very poor quality due to their diversity, misaligned regions and low-quality regions present in the sequence. An efficient MSA must be constructed in order to characterize these Anellovirus present in the samples. Pairwise alignment is used to align one fragment to the database sequences at a time. The fragments are then aligned to the database sequences using the start and end position from the pairwise alignment results. The algorithm will also exclude non-aligned portions of the fragments, as these are very hard to handle properly and are often products of misassembly or chimeric sequenced fragments. Other tools to aid further analysis were developed, such as finding a non-overlapping window that contains the most fragments, find consensus of the alignment and extract any regions from the MSA for further analysis. An MSA was constructed with a high percent of correctly aligned bases compared to an MSA constructed using MSA softwares. The minimal number of genomes found in the sampled sequence was found as well as a distribution of the fragments along the database sequence. Moreover, highly conserved region and the window containing most fragments were extracted from the MSA and phylogenetic trees were constructed for these regions.

L'objectif de ce travail de thèse concerne l'étude et la mise en œuvre de deux modèles de cavitation dans le solveur NSMB (Navier-Stokes-Multi-Blocks): les modèles HEM (Homogeneous Equilibrium Model) et une équation pour le taux de vide: le modèle à transport de taux de vide (TTV). Le phénomène de cavitation est modélisé par différentes équations d'état de mélange liquide-vapeur (EOS). Des simulations numériques sont réalisées sur des écoulements diphasiques compressibles unidimensionnels et bidimensionnels avec des conditions d'interface et comparées à des solutions de référence. De plus, la méthode TTV basée sur le taux de vide incluant les termes source pour la vaporisation et la condensation dans le logiciel libre open source OpenFOAM est également présentée sur la géométrie Venturi pour capturer le phénomène du jet réentrant. La modélisation de la turbulence joue un rôle majeur dans la capture des comportements instationnaires et un limiteur est introduit pour réduire la viscosité turbulente afin de mieux prédire la structure à deux phases. Une comparaison de divers modèles de cavitation couplés avec des modèles de turbulence est étudiée. Les résultats computationnels sont comparés aux données expérimentales existantes. / The objective of this thesis work concerns the study and implement of two cavitation models in the NSMB (Navier-Stokes-Multi-Blocks) flow solver: the Homogeneous Equilibrium Models (HEM) and a void ratio Transport-based Equation Model (TEM). The cavitation phenomenon is modeled by different liquid-vapor mixture equation of state (EOS). Numerical simulation are performed on some one- and two-dimensional compressible two-phase flows with interface conditions and compared with reference solutions. Moreover, The TEM based method for the void ratio including the source terms for vaporization and condensation in the free, open source software OpenFOAM is also presented on the Venturi geometry to capture the re-entrant jet phenomenon. The turbulence modeling plays a major role in the capture of unsteady behaviors and a limiter is introduced to reduce the eddy-viscosity to better predict the two-phase structure. A comparison of various cavitation models coupled with turbulence models are investigated. Computational results are compared with existing experimental data.

This is a study of vocabulary size that examines the numbers of French words that students on different university levels know. It also compares how the vocabulary size differs depending on the students’ levels of acquisition. The method we use is the Vocabulary Size Test “TTV”, (Test de la Taille du Vocabulaire) that measures the number of French words on different levels of frequency, where the maximum number of words to obtain is 10 000. We have created two groups on different levels of acquisition at the University of Stockholm: group 1 consists of first semester students, and group 2 of a mixture of students from third and fourth semester of French. In the results, we can see that group 2 has obtained a significantly higher number of words on the test than group 1, namely 8 224 verses 6 831. Further we have found that not all students follow the predicted pattern when it comes to word frequency, which predicts that the largest amount of words is to be found in the highest frequency word span. We discuss advantages and inconveniences of different vocabulary size tests, and explain the importance of word frequency in this type of study.

The non-pathogenic porcine circovirus type 1 (PCV1) was originally isolated as a persistent contaminant of the porcine kidney cell line PK-15. Whereas, porcine circovirus type 2 (PCV2) causes postweaning multisystemic wasting syndrome (PMWS) in pigs, which is devastating to the swine industry. My objectives were to determine the effect of maternally derived antibodies on PCV2 infection, assess the role of 2 amino acid substitutions in the PCV2 capsid protein in PCV2 attenuation, evaluate the effect of Rep gene exchange between PCV1 and PCV2 on growth characteristics of a chimeric PCV2, and evaluate the role of open reading frame (ORF) 3 of PCV2 in virus replication and pathogenesis in pigs. Under field conditions, PCV2 infection is widespread and most breeding pigs are seropositive. Assessment of the role of PCV2 maternal antibodies in preventing PCV2 infection in piglets provided evidence that higher levels of maternal antibody provide more protection to piglets. Two amino acid substitutions in the PCV2 capsid protein that enhanced virus replication in vitro and attenuated the virus in vivo were evaluated for their pathogenicity in pigs. The results indicated that P110A and R191S are collectively responsible for virus attenuation. PCV1 replicates better in PK-15 cells and grows at least 1-log titer higher than PCV2. A chimeric PCV with the rep gene of PCV1 replacing that of PCV2 in the genomic backbone of PCV2 replicated more rapidly than PCV1 and PCV2, and more efficiently than PCV2, although to a titer similar to PCV1. The ORF3 of PCV2 is believed to encode a protein involved in apoptosis. The ORF3 start codon was mutated from ATG to GTG and the resulting mutant muPCV2 was infectious in vitro and in pigs; therefore ORF3 is dispensable for virus replication. The pathogenicity of muPCV2 was compared with PCV2 in vivo. Delayed viremia and seroconversion, decreased viral loads, lower level of IgG antibodies, and lower amounts of PCV2 antigen in mesenteric lymph nodes suggested attenuation of muPCV2. However, there was no significant difference in histological or gross lesions in tissues between PCV2- and muPCV2-inoculated groups. The role of ORF3 in attenuation needs to be further elucidated. / Ph. D.