No description available.

No description available.

The intracellular pathogen Legionella pneumophila thrives in both natural and man-made water habitats where it replicates inside freshwater amoebae. L. pneumophila follows a developmental cycle as it grows in amoebae. The actively-multiplying intracellular replicative forms (RFs) differentiate into highly virulent mature infectious forms (MIFs) late in the amoeba infection, and are then released extracellularly. L. pneumophila accidentally infects susceptible humans causing the non-communicable Legionnaires’ disease (LD). MIFs play a central role in the life cycle of L. pneumophila and are thought to be responsible for the transmission of LD. Early reports demonstrated that MIFs were poorly produced inside human macrophages, suggesting that the L. pneumophila progeny from human macrophages has fitness and infectivity disadvantages. Direct comparisons of the L. pneumophila progenies from amoebae and human macrophages have demonstrated that the progeny from amoebae is more morphologically differentiated, resistant to antibiotic challenges, and able to adhere to and initiate infections in host cells than the progeny from macrophages. Analysis of the transcriptomic and proteomic profiles of L. pneumophila inside different hosts has revealed a specific set of genes that are upregulated during differentiation of L. pneumophila into MIFs inside freshwater protozoa but not inside human macrophages, suggesting that these genes may be required for the full differentiation of L. pneumophila and, therefore, for the transmission of LD to susceptible humans. Since the expression of the gene lpg1669, which encodes a putative α-amylase, was upregulated in amoebae (highest level of upregulation among the tested genes) and inside Tetrahymena ciliates, but not inside human macrophages, the role of lpg1669 in the differentiation of L. pneumophila into MIFs was investigated. An isogenic lpg1669 deletion mutant did not display defects in morphological differentiation, in vitro (BYE broth) or in vivo (A. castellanii or U937 human macrophages) growth when compared to its parent strain, suggesting that the gene lpg1669 is not essential for the intracellular differentiation of L. pneumophila. Collectively, these findings demonstrate that L. pneumophila can reach different developmental end points in different hosts and could also provide a clue for the lack of transmission of LD among humans.

No description available.

This study develops techniques for the preparation and counting of testate amoebae for Holocene sea-level reconstructions. In addition, this study provides a ~3000 year relative sea-level reconstruction for south Hinnøya in the Vesterålen islands off mainland Norway, adding new data to a poorly defined period of the Holocene sea-level history of north-western Norway. This is important to quantify rates of glacial-isostatic adjustment (GIA), to refine GIA models, and to establish baseline (pre-industrial) rates of relative sea-level change. Surface sediments from two salt marshes (Storosen and Svinøyosen) in south Hinnøya are used to assess the effects of using different preparation procedures and count totals when analysing for testate amoebae. Analytical efficiency can be improved upon by using a mild alkali, chemical disaggregant (5 % KOH) to break up fibrous salt-marsh sediment and concentrate tests prior to counting. A count total of 100 individuals, rather than 150, can be used to make time gains with little or no effects on assemblages. Training sets of salt-marsh surface testate amoebae, foraminifera and elevational data are established for the two field sites. For testate amoebae, species – elevation relationships are constructed using regression modelling and applied to downcore fossil samples using a transfer function to derive estimates of sea level for the past ~100 years. The greater water depths reconstructed between ~3000 and ~100 years ago are not covered by modern foraminiferal training sets and are therefore estimated qualitatively from the fossil foraminiferal assemblages supplemented by information derived from fossil molluscs. Chronology is based on a combination of AMS14C, 210Pb, 137Cs and a suite of geochemical markers. At south Hinnøya, sea level has been falling at a rate of ~0.5 mm yr-1 over the last 3000 years.

Naegleria fowleri, a free-living ameba, is the causative agent of Primary Amebic Meningoencephalitis. Highly-pathogenic mouse-passaged amebae (Mp) and weakly-pathogenic axenically-grown (Ax) N. fowleri were examined for peptidase activity. Zymography and azocasein peptidase activity assays demonstrated that Mp and Ax N. fowleri exhibited a similar peptidase pattern. Prominent for whole cell lysates, membranes and conditioned medium from Mp and Ax amebae were the presence of an activity band of approximately 58kDa and 100 kDa bands susceptible to the action of cysteine and metallopeptidase inhibitors, respectively. Further roles of the peptidases during the invasion process were examined by in vitro invasion assays in the presence of inhibitors and Cysteine and metallopeptidase inhibitors were found to greatly reduce invasion through the ECM. This study establishes a functional linkage of the expressed peptidases to the invasion process, and these peptidases may serve as a candidate target for therapeutic management of N. fowleri infection.

Les virophages sont des petits virus à ADN possédant une capside icosaédrique de 50-60 nm et un génome de 17 à 26 Kb codant potentiellement pour une vingtaine de gènes. Ils ont été découverts associés à des grands virus à ADN appartenant à l’ordre des Megavirales, pour lesquels leur présence serait délétère.Le premier projet du travail de thèse a été de faire le bilan des propriétés connues des virophages au travers d’une revue. La deuxième partie correspond à un bilan des avancées en matière d’isolement de virus géants dans les amibes – hôtes naturels des Mimiviridae –, pouvant être associés aux virophages. La troisième section se focalise sur la réplication des virophages Sputnik avec différents virus parmi les Mimiviridae, ainsi que sur l’isolement d’une nouvelle souche de Sputnik sans son hôte natif par l’utilisation d’un Mimiviridae en tant que virus rapporteur. La dernière partie est enfin basée sur l’identification d’un nouveau virophage – Zamilon – isolé en association avec un Mimiviridae du groupe C, et présentant une spécificité d'hôtes restreinte. Celle-ci est d'ailleurs étudiée.Les résultats présentés dans cette thèse démontrent une certaine complexité des interactions entre les virophages et leurs hôtes. Au sein d’une même famille d’hôtes, certains virophages possèdent un large spectre de spécificité, alors que d’autres ne peuvent se multiplier qu’avec certains d’entre eux, comme cela a déjà été observé chez les bactériophages. Compte-tenu de leur impact potentiel sur les virus géants, ces résultats soutiennent l’hypothèse d’une régulation des populations virales environnementales par les virophages. / Virophages are small DNA viruses with a 50-60 nm width icosahedral capsid encompassing a 17 to 26 Kb genome, putatively coding approximately 20 genes. They have been discovered in association with large DNA virus belonging to the order of the Megavirales, for which they are noxious.The first project of this thesis work was to recapitulate in a review the known features of the virophages. The second part corresponds to a summary of the advances in the field of giant viruses isolation in amoebas – the common hosts of Mimiviridae –. The third section is focused on the replication of the Sputnik virophages with viruses belonging to the Mimiviridae, and on the isolation of a new Sputnik strain with a Mimiviridae reporter instead of with its natural viral host. Finally, the last part is based on the identification of a new virophage – Zamilon – isolated in combination with a group C Mimiviridae, and exhibiting a restricted spectrum of specificity. The latter is herein studied.The results described herein show the complexity of the interactions between virophages and their giant hosts viruses. Within the same host family, some virophages have a broad-range host spectrum whereas others are limited to some viruses, a feature already described for bacteriophages. Regarding the potential impact of the virophages over their host viruses, these results support the hypothesis of a virophages’ major role in a regulation of viral populations in environment.

The motivating question behind this body of research is Smale’s 17th problem: Can a zero of n complex polynomial equations in n unknowns be found approximately, on the average, in polynomial time with a uniform algorithm? While certain aspects and viewpoints of this problem have been solved, the analog over the real numbers largely remains open. This is an important question with applications in celestial mechanics, kinematics, polynomial optimization, and many others. Let A = {α_1, . . . , α_n+k } ⊂ Zn. The A-discriminant variety is, among other things, a tool that can be used to categorize polynomials based on the topology of their real solution set. This fact has made it useful in solving aspects and special cases of Smale’s 17th problem. In this thesis, we take a closer look at the structure of the A-discriminant with an eye toward furthering progress on analogs of Smale’s 17th problem. We examine a mostly ignored form called the Horn uniformization. This represents the discriminant in a compact form. We study properties of the Horn uniformization to find structural properties that can be used to better understand the A-discriminant variety. In particular, we use a little known theorem of Kapranov limiting the normals of the A-discriminant amoeba. We give new O(n^2) bounds on the number of components in the complement of the real A-discriminant when k = 3, where previous bounds had been O(n^6) or even exponential before that. We introduce new tools that can be used in discovering various types of extremal A-discriminants as well as examples found with these tools: a family of A-discriminant varieties with the maximal number of cusps and a family that appears to asymptotically admit the maximal number of chambers. Finally we give sage code that efficiently plots the A-discriminant amoeba for k = 3. Then we switch to a non-Archimedean point of view. Here we also give O(n^2) bounds for the number of connected components in the complement of the non- Archimedean A-discriminant amoeba when k = 3, but we also get a bound of O(n^(2(k−1)(k−2)) )when k > 3. As in the real case, we also give a family exhibiting O(n^2) connected components asymptotically. Finally we give code that efficiently plots the p-adic A-discriminant amoeba for all k ≥ 3. These results help us understand the structure of the A-discriminant to a degree, as yet, unknown. This can ultimately help in solving Smale’s 17th problem as it gives a better understanding of how complicated the solution set can be.

Mimivirus est le 1er virus géant découvert. Quelques années plus tard une nouvelle entité́ biologique a été décrite, les virophages. Si leurs principales caractéristiques sont maintenant bien définies et acceptées, leur position dans le monde viral ainsi que les interactions qu’ils pourraient avoir avec leur virus-hôte sont encore discutées. La famille des virophages s’élargit. Dans cette optique, le premier objectif de thèse a été de faire un bilan des propriétés connues des virophages au travers d’une revue de la littérature scientifique. La deuxième section repose sur l’analyse des bases de données métagénomiques à la recherche de séquences de virophages et de Megavirales. En criblant le métagénome Bioreactor, nous avons détecté des séquences étroitement liées au virophage Zamilon. Le génome de ce dernier a été décrit et partiellement assemblé. La troisième partie du travail est basée sur l’étude des interactions entre les Mimiviridae et les virophages. Nous avons observé́ qu’un groupe de mimivirus a développé́ une résistance contre l’infection par le virophage Zamilon. C’est en essayant de comprendre ce mécanisme de résistance jusque-là inconnu dans le monde viral que nous avons décrit pour la première fois un système de défense appelé MIMIVIRE. Enfin, la dernière partie est centrée sur l’étude d’une protéine impliquée dans la traduction chez les mimivirus. Les résultats de ce travail suggèrent que cette protéine régule l'expression d’autres protéines virales. Les éléments inédits présentés dans cette thèse contribuent à soutenir l’idée de l’existence d’une quatrième branche du vivant, distincte des 3 domaines connus. / Mimivirus is the first largest virus described. Some years later, virophage, a new biological entity has been discovered. Virophage is a small virus able to infect other giant viruses for which the presence can be deleterious. If their main features have been widely accepted, their position in the viral world and their interactions with host’s viruses are still discussed. The family of virophages is expanding. The first objective of this thesis work was to summarize the known proprieties and features of virophages through a review paper. The second part refers to the analysis of metagenomic databases in search of virophage and Megavirales sequences. By screening the Bioreactor metagenome, we detected sequences closely related to Zamilon virophage.The genome has been described and partially assembled. The third part was based on the study of the interactions between giant viruses and virophages. We observed that some mimiviruses have developed a resistance against the infection by Zamilon virophage. To understand this mechanism of resistance, we described for the first time a viral defense system called MIMIVIRE. Finally, the last part was focused on the study of a protein involved in the translation apparatus of mimivirus. The results of this study suggest for the first time that a translational protein in mimivirus regulates the expression of their proteins.The results described herein show the potential impact of virophages on their viral hosts and also the complexity of the genetic content of giant viruses. Considering all these elements, we can support the hypothesis that giant viruses belong to a new domain of life, in complement to eukaryotes, bacteria and algae.

No / A laboratory-based experiment was carried out to examine the dissolution characteristics of testate amoebae (Protozoa: Rhizopoda) under acidic conditions. The results suggest a large degree of variability in the dissolution susceptibility of taxa and no straightforward distinction between the relative robustness of xenosomic and idiosomic test types. Individuals from the genus Euglypha have tests composed of thin-walled siliceous plates, which are prone to severe dissolution. Certain other taxa are relatively unaffected by low pH conditions, including Assulina muscorum, Amphitrema flavum and Trigonopyxis arcula type. Differential preservation of subfossil testate amoebae must be acknowledged as a particular problem for peat-based palaeoclimate studies.