Les éléments transposables (ETs) sont des éléments génétiques mobiles capables de se déplacer et de se multiplier au sein d’un génome. Identifiés dans la plupart des espèces vivantes incluant les bactéries, mais longtemps considérés comme de l’ADN poubelle, aujourd’hui les ETs sont indéniablement des acteurs majeurs impliqués dans l’évolution des gènes, des génomes et des organismes. Si à l’échelle des individus les ETs peuvent avoir des effets délétères pouvant entrainer des maladies, à plus grande échelle ils sont de puissants agents évolutifs impliqués dans la plasticité génomique. Ces « parasites » peuvent également être sources de nouveaux matériels génétiques comme des promoteurs ou même de nouveaux gènes avec de nouvelles fonctions pour l’hôte. Les objectifs majeurs de mon travail de thèse ont été de déterminer les différentes familles d’ETs présentes dans les génomes de poissons, la part que chacune d’entre elles occupe dans ces génomes et enfin de comprendre l’histoire évolutive des familles d’ETs dans les génomes de poissons en comparaison avec les autres génomes de vertébrés. Cette comparaison à grande échelle permettra de comprendre les différentes stratégies évolutives des ETs. D’autre part, j’ai étudié deux gènes de vertébrés, Gin-1 et Gin-2 dérivés d’ETs, dans le but de comprendre leurs origines et évolution au sein des vertébrés ainsi que d’émettre des hypothèses quant à leur fonction moléculaire potentielle encore inconnue. Pour cela, des analyses in silico ont permis de mieux comprendre les origines de ces gènes. Gin-1, présent chez les amniotes, et Gin-2, absent uniquement des mammifères placentaires, dérivent tous deux de transposons GIN. / Transposable elements (TEs) are mobile genetic elements - able to move and to multiply within genomes - identified in almost all living organisms including bacteria. Considered as junk DNA for long, nowadays they are undeniably major players of gene, genome and host evolution. TEs can be deleterious causing diseases but these “parasites” can also be source of new genetic materials as promoters or even new genes bringing new functions for hosts. The objectives of my thesis was to determine the presence or not of the different TE families in vertebrate genomes, as well as their respective content to understand their evolutionary history. I performed a large-Scale comparative analysis to highlight the various evolutionary strategies of TEs. I showed that TE content is highly variable in vertebrate genomes, the smallest and the largest being found in fish, and may contribute to their genome sizes especially in fish. These superfamilies underwent differential waves of activity in vertebrate species highlighting TE dynamics. On another hand, I focused on the study of a vertebrate-Specific TE-Derived gene, named Gin-2, to understand its origin, evolution, and its potential function in vertebrates. In silico analyses showed that Gin-2 is a very ancient gene (500 My, only absent from placentals) derived from GIN transposons. Further analyses present a particular expression in brain and gonads during adulthood, while a strong expression during gastrulation suggests a potential role of Gin-2 in zebrafish development. All together, the different analyses contribute to a better view of TE evolution and their evolutionary impacts in vertebrate genomes.

Molecular aspects of nitrogen metabolism in vertebrates is an interesting area of physiology and evolution to explore due to the different ways in which animals excrete nitrogenous waste as they transition from an aquatic to a terrestrial lifestyle. Two main products of nitrogen metabolism in fishes are ammonia and urea. Ammonia is produced during protein catabolism and build up of ammonia is toxic. Some aquatic vertebrates convert ammonia into a less toxic compound urea via de novo synthesis through the ornithine-urea cycle (O-UC). Five enzymes are involved in the O-UC: carbamoyl phosphate synthetase (CPS), ornithine carbamoyl transferase (OCT), argininosuccinate synthetase (ASS), argininosuccinate lyase (ASL), and arginase (ARG). An accessory enzyme, glutamine synthetase (GS) also participates in the "fish-type" O-UC. Teleosts excrete ammonia passively over their gills into the aquatic environment. The teleost, Opsanus beta, has been shown to increase urea production after 48 hours of crowding. This thesis explored how crowding stress affected nitrogen metabolite levels of ammonia and urea and O-UC gene expression and enzyme activity in O. beta. Lungfishes while in an aquatic environment avoid ammonia toxicity by releasing excess ammonia across their gills, but when stranded on land they produce urea through the O-UC. Urea production via the O-UC has a metabolic cost of at least four ATP molecules. This thesis explored the response of a lungfish, Protopterus annectens, to six days of aerial exposure and re-immersion conditions by measuring concentrations of O-UC mRNA expression and enzyme activity and nitrogen metabolites ammonia and urea. CPS acts as the entry point to the O-UC and based on enzymatic studies, most aquatic vertebrates utilize one isoform of this enzyme (CPSIII) while terrestrial vertebrates utilize a different isoform of this enzyme (CPSI). Lungfishes are a particularly interesting group of air-breathing fishes, not only because of their link to the origins of tetrapods, but also because CPS I may have originated within this group. Both CPS III and CPS I have been enzymatically described within this group. This thesis uses phylogenetics to investigate how CPS nucleotide sequences in lungfishes evolved compared to other vertebrates.

During zebrafish gastrulation, highly coordinated cellular rearrangements lead to the formation of the three germ layers, ectoderm, mesoderm and endoderm. Recent studies have identified silberblick (slb/wnt11) as a key molecule that regulates gastrulation movement through a conserved pathway, which shares significant similarity with a signalling pathway that establishes epithelial planar cell polarity (PCP) in Drosophila (Heisenberg et al., 2000; Veeman et al., 2003), suggesting a role for cell polarity in regulating gastrulation movements. However, the cellular and molecular mechanisms by which slb/wnt11 functions during zebrafish gastrulation are still not fully understood. In the first part of the thesis, the three-dimensional movement and morphology of individual cells in living embryos during the course of gastrulation were recorded and analysed using high resolution confocal microscopy. It was shown that in slb/wnt11 mutant embryos, hypoblast cells within the forming germ ring display slower, less directed migratory movements at the onset of gastrulation, which are accompanied by defects in the orientation of cellular processes along the individual movement directions of these cells. The net movement direction of the cells is not changed, suggesting that slb/wnt11-mediated orientation of cellular processes serves to facilitate and stabilize cell movements during gastrulation. By using an in vitro reaggregation assay on mesendodermal cells, combined with an analysis of the endogenous expression levels and distribution of E-cadherin in zebrafish embryos at the onset of gastrulation, E-cadherin mediated adhesion was found to be a downstream mechanism regulating slb/wnt11 function during gastrulation. Interestingly, the effects of slb/wnt11 on cell adhesion appear to be dependent on Rab5-mediated endocytosis, suggesting endocytic turnover of cell-cell contacts as one possible mechanism through which slb/wnt11 mediates its effects on gastrulation movements. - Die Druckexemplare enthalten jeweils eine CD-ROM als Anlagenteil: QuickTimeMovies (ca. 23 MB)- Übersicht über Inhalte siehe Dissertation S. 92 - 93"

The Lower Permian Admiral Formation redbeds in north-central Texas are famous for their well-studied vertebrate fauna. Taphonomical and paleoecological aspects, however, are inadequately understood. The prerequisite for taphonomical interpretations is an analysis of the depositional environments. Low relief and low regional dip expose extensive paleoslopes in western Archer County. Three major depositional systems may be recognized: a fine-grained meanderbelt, a low sinuosity fine-grained fluvial system, and a tidal flat. The small scale of the sedimentation (average sandstone thickness 1. 5 m) is remarkable. Four types of vertebrate occurrences can be distinguished: Type 1: Mass death bonebeds are situated in a floodbasin facies comprised of gray and red mudstones with abundant Psaronius roots (a swamp-dwelling tree fern) which is associated with the fluvial systems. Such basins were covered by a dense swamp forest with a high diversity of vertebrates. This type is exemplified by the Geraldine Bonebed, which has yielded at least 45 partly articulated skeletons representing 4 genera of tetrapods, and remains of another 8 vertebrate taxa. The bones were found on a layer of fern, seed fern, and conifer foliage and wood. This occurrence was formed by a single catastrophic event, possibly a forest fire, which drove the animals of the swamp forest into a pond, where they died of suffocation and were concentrated into a bonebed by physical processes (wind). Type 2: Lag bonebeds, situated on the landward margin of tidal flat environments, are represented by the Rattlesnake Canyon Bonebed which consists mainly of a calcareous concretion conglomerate, which contains fragmentary bone, serpulid worm colonies (brackish water!), and calamitelean wood. The diversity of forms represented by articulated material is low. The ubiquitous predator Dimetrodon and an amphibian, Trimerorachis, which tolerates brackish water, are common. This type was deposited as lag in a storm washover deposit. Type 3: Ponds (abandoned channels, etc.) which contained a fauna dominated by aquatic forms (the fishes Xenacanthus and Ectosteorachis, and the amphibian Archeria) were gradually filled by fine-grained sediment and organic debris (vertebrates, plants). These oxbow lakes were probably rimmed by stands of Calamites. Four examples are described. Type 4: Single, complete skeletons examplified here by Diadectes are occasionally found in red floodplain mudstones. / text

The object of this thesis was to study plant community structure, especially in relation to vertebrate herbivory, in an altitudinal gradient in the Fennoscandian mountain chain. A sowing experiment in a high alpine Ranunculus glacialis population showed that seeds germinated better in cleared microsites than under established individuals. This is contrasted with a hypothesis that predicts positive plant-plant interactions in high alpine environments. It was concluded that plant-plant interactions in die studied population varied from neutral to negative, whereas no indications for positive interactions were found. An exclosure experiment in a snow-bed showed that a lemming population consumed 33 % of the available graminoids and 66 % of the mosses from August to June during a population peak. The results shows that grazing needs to be considered as a structuring factor in snow-bed vegetation. The vegetation in exclosures in another snow-bed changed from a graminoid-dominated to a herb-dominated plant community during a long-term (six years) experiment No changes of the same magnitude were seen in a tall herb meadow on a lower altitude. Survival of transplanted adult shoots from the tall herb meadow was equally high in the snow-bed as on the meadow, and germination was also high on bare ground in the snow-bed. Grazing seemed to be a more important structuring factor in the snow-bed than in the more productive tall herb meadow. Raising the grazing pressure during one growing season by introducing microtine rodents into enclosures did not cause any large short-term effects on plant community structure in a tall hob meadow or in a snow-bed. Marked shoots showed that some preferred plant species had a high shoot mortality, but biomass for pooled categories of plants was not significantly affected. It was predicted that the tall herb meadow would be more grazing sensitive than die snow-bed, but productivity on the meadow seemed to be sufficiently high for the plants to compensate for the grazing during the growing season. A greenhouse experiment showed that voles, when grazing freely, have the potential to deplete productive field layer vegetation contrary to predictions from plant defence theories. A nitrogen-based defence did not prevent heavy shoot mortality for toxic tall herbs. / <p>Diss. (sammanfattning) Umeå : Umeå universitet, 1993, härtill 5 uppsatser.</p> / digitalisering@umu.se

Une question fondamentale de la biologie évolutive porte sur la compréhension des mécanismes sous-tendant les processus évolutifs et l'évolution des compromis entre les traits d'histoire de vie. Parmi ces mécanismes, les télomères suscitent un intérêt particulier. Les télomères sont localisés à l'extrémité des chromosomes eucaryotes et participent à la sénescence cellulaire et au vieillissement des individus. La longueur des télomères est susceptible de donner des indications sur le mode de vie et l'état physiologique des organismes. Le but de cette thèse a été de comprendre quels sont les facteurs déterminant la longueur des télomères et leur implication dans les compromis évolutifs, ceci en établissant : si la taille des télomères est-elle héritable? Le taux de perte des télomères est-il affecté par des facteurs environnementaux? Quel lien entre les télomères, la maintenance individuelle et la qualité des individus? Il résulte de ce travail que la longueur des télomères est partiellement déterminée par les facteurs génétiques, elle semble aussi influencée par les facteurs environnementaux. En effet, le coût de la reproduction, ainsi que la modification des trajectoires de croissance, ont des effets néfastes sur la longueur des télomères. L'effet de la manipulation expérimentale de l'activité télomérase indique un lien entre les télomères et la maintenance individuelle, suggérant que les télomères sont susceptibles de donner des indications sur la qualité des individus. Ce travail de thèse montre que la dynamique des télomères est un mécanisme sous-jacent des compromis évolutifs, et présente un intérêt considérable pour la compréhension des processus évolutifs.

Thesis (Ph. D.)--University of Alabama at Birmingham, 2008. / Title from first page of PDF file (viewed Feb. 12, 2009). Includes bibliographical references (p. 136-146).

Fundação de Amparo a Pesquisa do Estado de Minas Gerais / ABSTRACT - CHAPTER I Actomyosin from rat testis was obtained by freezing the soluble fraction and myosin II was isolated from this actomyosin. Testis was homogenized in a buffer extract, centrifuged, and the 40,000g x 40 supernatant frozen at -20°C for 48 hours. The supernatant was thawed at 4°C, centrifuged at 45.000g x 45 and the precipitate washed twice with imidazole buffer (pH 7.0 and 9.0, respectively). The resulting precipitate was enriched in 3 polypeptides: p205, p43 and one that migrated together with the front of the gel. These polypeptides were solubilized in pH 10.8 buffer at 27°C. When isolated in a Sephacryl S-400 column, p205 cosedimented with F-actin in the absence, but not in the presence, of ATP and was marked with anti-myosin II. Although the testis preparation expressed low K/EDTA-ATPase activity, a similar preparation obtained from skeletal muscle exhibited high K/EDTA-ATPase activity. In this study, myosin II was isolated from an actomyosin preparation obtained by freezing the soluble fraction of testis. ABSTRACT - CHAPTER II Actomyosin from swine, bovine and chicks brain was obtained by freezing the soluble fraction and myosin II and V was precipitate together, and myosin II from swine brain was partially isolated from this actomyosin. Brain was homogenized in a buffer extract, centrifuged, and the 40,000g x 40 supernatant frozen at -20°C for 48 hours. The supernatant was thawed at 4°C, centrifuged at 45.000g x 45 and the precipitate washed twice with imidazole buffer (pH 7.0 and 10.0, respectively). The resulting precipitate was enriched in 3 polypeptides: p205, p53, p43 and own high Mg2+-ATPase activity. These polypeptides were solubilized in pH 10.2 buffer at 27°C, with addition of ATP, Mg and NaCl. The p205 from swine brain was partially isolated in a Sephacryl S-500 column. This polypeptide of 205 kDa was marked with antibody anti-myosin II and V. Although the brain preparation expressed low K/EDTA-ATPase activity, we observed Co2+- ATPase activity and a stimulation of the Mg2+-ATPase activity by Tween 20. In this study, showed a precipitation together of myosin II and V, and partially isolated this myosin from swine brain from actomyosin preparation obtained by freezing the soluble fraction of brain. / RESUMO GERAL - Miosinas são proteínas motoras que translocam sobre filamentos de actina e atualmente constituem uma superfamília com 20 classes. Algumas são conhecidas apenas a estrutura primária através de seqüência gênica, outras já estão bem caracterizadas bioquimicamente, como as miosinas I, II e V. São amplamente distribuídas em todas as células eucarióticas. Apresentam como características bioquímicas: alta atividade ATPase na presença de EDTA e alta concentração de potássio (atividade K/EDTA-ATPase) e uma baixa atividade Mg2+-ATPase, que é estimulada por F-actina. Preparação de actomiosina é obtida a partir da precipitação de fração solúvel de cérebro tanto em baixa quanto em alta força iônica e esse processo de precipitação constitui um passo importante para purificar e caracterizar miosina II e V a partir de fração solúvel de cérebro. Miosina II é precipitada quando a fração solúvel de cérebro é dializada contra tampão de baixa força iônica, enquanto que, miosina V é precipitada seletivamente em relação à miossina II, quando a fração solúvel de cérebro é tratada com alta força iônica, sendo postulado que essa precipitação de miosina (II e V) seja resultado de sua interação com actina e vesículas. Recentemente temos obtido a precipitação de actomiosina a partir do congelamento de fração solúvel de cérebro ou testículo de rato. Neste trabalho mostramos a purificação de miosina II de testículo de rato e a obtenção de actomiosina de cérebro de suino, bovino e pintainho através do congelamento de fração solúvel de cérebro e testículo. RESUMO - CAPÍTULO I Actomiosina de testículo de rato foi obtida através do congelamento de fração solúvel e miosina II foi isolada a partir dessa actomiosina. Testículos foram homogeneizados em tampão de extração, centrifugado e o sobrenadante 40.000g x 40 foi congelado a -20oC por 48 horas. O sobrenadante foi descongelado a 4oC, centrifugado a 45.000g x 45 e o precipitado foi lavado duas vezes com tampão imidazol (pH 7,0 e 9,0, respectivamente). O precipitado resultante é enriquecido em três polipeptídeos: p205, p43 e um que migra junto com a frente do gel. Esses polipeptídeos foram solubilizados em tampão pH 10,8 a 27oC. O p205, isolado em Sephacryl S-400, co-sedimenta com F-actina na ausência, mas não na presença, de ATP e foi marcado com anti-miosina II. Embora a preparação de testículo, praticamente, não expressou atividade K/EDTA-ATPásica, uma preparação similar obtida a partir de músculo esquelético apresentou alta atividade K/EDTA-ATPásica. Nesse trabalho, miosina II foi isolada a partir de uma preparação de actomiosina obtida pelo congelamento de fração solúvel de testículo. RESUMO - CAPÍTULO II Actomiosina de cérebro de suino, bovino e pintainho foi obtida através do congelamento de fração solúvel e miosina II e V foram precipitadas conjuntamente, sendo que miosina de cérebro de suino foi parcialmente isolada a partir dessa actomiosina. Os cérebros foram homogeneizados em tampão de extração, centrifugado e o sobrenadante 40.000g x 40 foi congelado a -20oC por 48 horas. O sobrenadante foi descongelado a 4oC, centrifugado a 45.000g x 45 e o precipitado foi lavado duas vezes com tampão imidazol (pH 7,0 e 10, respectivamente). O precipitado resultante é enriquecido em três polipeptídeos: p205, p53, p43 e possui alta atividade Mg2+-ATPase. Esses polipeptídeos foram solubilizados em tampão pH 10,2 a 27oC, com adição de ATP, Mg e NaCl. O p205 de cérebro de suino foi parcialmente isolado em Sephacryl S-500. Esse polipeptídeo de 205 kDa foi marcado com anticorpos anti-miosina II e V. Embora a preparação de cérebro, praticamente, não expressou atividade K/EDTAATPásica, apresentou atividade Co2+-ATPase e uma estimulação da atividade Mg2+-ATPase por Tween 20. Nesse trabalho mostramos a precipitação conjunta de miosina II e V e o isolamento parcial dessas miosinas de cérebro de suino a partir de uma preparação de actomiosina obtida pelo congelamento de fração solúvel de cérebro. / Mestre em Genética e Bioquímica

This work is mainly based on the collection of Neogene (Miocene-Pliocene) odontocetes (toothed whales) from the area of Antwerp (northern Belgium, southern margin of the North Sea Basin) preserved at the Institut royal des Sciences naturelles de Belgique (IRSNB). <p> The systematic revision of members of the long-snouted dolphin family Eurhinodelphinidae leads to the description/re-description of five species in the genera Eurhinodelphis (E. cocheteuxi and E. longirostris), Schizodelphis (S. morckhoviensis), and Xiphiacetus n. gen. (X. cristatus and X. bossi). Furthermore, the systematic status of several eurhinodelphinid species from other localities in the world is revised. A cladistic analysis with the parsimony criterion is undertaken to highlight the phylogenetic relationships of several eurhinodelphinid taxa with other fossil and extant odontocetes. Eurhinodelphinids are more closely related to the beaked whales; the latter are distinctly separated from the sperm whales. A second analysis, with a likelihood criterion, reaches nearly identical results. Then a separate parsimony analysis investigates the relationships within the family Eurhinodelphinidae; the results suggest sister-group relationships between Schizodelphis + Xiphiacetus and Ziphiodelphis + (Mycteriacetus + Argyrocetus) and a more stemward position for Eurhinodelphis. After that, anatomical, palaeogeographic, and phylogenetic data allow several suggestions about the ecological features of the eurhinodelphinids. The extinction of this family, before the end of the Miocene, is commented, related to the changes in the biodiversity of other odontocete groups and to a contemporary major sea level drop. <p>\ / Doctorat en sciences, Spécialisation biologie animale / info:eu-repo/semantics/nonPublished

La segmentation de l’axe antéro-postérieur en somites est une caractéristique majeure des Vertébrés. Ce processus est basé sur un oscillateur, l’« horloge de segmentation ». Cette thèse cherche à comprendre la dynamique de signalisation régulant ce processus. Nous avons étudié la régulation transcriptionnelle de Mesp2 et nous avons montré que Tbx6 contrôle son expression chez le poulet. Nous présentons également un système d’étude ex vivo présentant des oscillations stables du gène cyclique Lfng. Nous avons mis en évidence un effet de population régulant la génération de ces oscillations et reposant sur la voie Notch et des facteurs mécaniques que nous interprétons avec un modèle d’oscillateur excitable. De plus, nous avons démontré un effet dose-dépendant de la voie Fgf sur la différenciation cellulaire, remettant ainsi en question le modèle actuel de segmentation. Par ailleurs, ce système d’étude nous a permis d’identifier un rôle du taux de traduction dans le contrôle de la période de l’horloge. Enfin, nous présentons des travaux, où nous cherchons à reconstituer l’horloge de segmentation in vitro à partir de cellules souches murines différenciées. / The segmentation of the anteroposterior axis in somites is a major feature of Vertebrates. This process relies on an oscillator, the “segmentation clock”. The present thesis addresses the signaling dynamics regulating this process. We studied the transcriptional regulation of Mesp2 and showed that Tbx6 controls its expression in chicken. We established an ex vivo experimental system with stable oscillations of the cyclic gene Lfng. We demonstrated the existence of a population behavior that controls the generation of oscillations and involves the Notch pathway and mechanical factors. We interpreted these observations in the framework of an excitable oscillator. Moreover, we evidenced a dose-dependent effect of Fgf signaling on cell determination that challenges current models of segmentation. Furthermore, this experimental system has enabled us to identify a role of the translation rate on the clock period. Last, we showed ongoing work aiming to recapitulate the segmentation in vitro using differentiated mouse embryonic stem cells.