Puerto Rico has the highest prevalence of type 2 diabetes, low birth-weight, and the second highest prevalence of preterm-birth in all the U.S. and its non-incorporated territories. These conditions are related. Birth-weight at both ends of the spectrum and preterm-birth are associated with an increased risk for developing type 2 diabetes and immune-inflammatory dysregulations. Maternal psychosocial stressors during pregnancy have also been recognized as potential risk factors for type 2 diabetes, and have been consistently associated with preterm-birth and low birth-weight across populations. Current evidence points toward epigenetic fetal metabolic-programming as the mechanism that underlies the increased risk for the previously mentioned morbidities. However, the particular psychosocial stressors that may contribute to the high prevalence of low birth-weight and preterm-birth in the population of Puerto Rico have not been well studied. The present study assesses the relationships between particular psychosocial stressors, socioeconomic status, food insecurity, and birth outcomes. The results of this study show that low-risk pregnancy women were more likely to have babies with a higher ponderal index if they were exposed to stressors during gestation months 5, 6, and 7, or if exposed to "relationship stress" at any time during pregnancy. Women exposed to "financial difficulties" at any time during pregnancy were more likely to deliver babies at an earlier gestational age. Differences in birth outcomes between the exposed and non-exposed women were independent of maternal anthropometric measurements, maternal age at birth, number of previous births, and sex of the baby. Significant differences in birth outcomes were found between categories of father's self-identified and identified by others ethnicity, but sample size within categories was small. Although mothers with children at home had higher levels of food insecurity, and the level of food insecurity was correlated with higher levels of stress, no birth outcome measure was associated with food insecurity. Some results are atypical in comparison with other populations, and therefore these findings may contribute to the understanding of population differences in the relationship between maternal stress during pregnancy and birth outcomes. The relatively small sample size and strict exclusion criteria of this study may limit the generalizability of the findings. Epidemiological similarities between Puerto Rico and other populations, and the possibility of a higher ponderal index increasing the risk for type 2 diabetes in the population of Puerto Rico need to be examined in future research.

H1 linker histone facilitates the formation of higher order chromatin structure and is essential for mammalian development. Mice have 11 H1 variants which are differentially regulated and conserved in human. Previous research indicates that H1 regulates the expression of specific genes in mouse embryonic stem cells (ESCs). However, whether individual variants have distinct functions and how H1 participates in gene regulation remain elusive. An investigation of the precise localization of individual H1 variants in vivo would facilitate the elucidation of mechanisms underlying chromatin compaction regulated gene expression, while it has been extremely difficult due to the lacking of specific antibodies toward H1 variants. In this dissertation, I have generated a knock-in system in ESCs and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts in vivo. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H10 displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d ,and H1e causes pericentric chromocenter clustering and de-repression of major satellites. Collectively, these results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and demonstrate significant changes at pericentric heterochromatin upon depletion of this epigenetic mark.

Epigenetic control of gene expression by histone post-translational modifications (PTMs) is a complex process regulated by proteins that can 'read', 'write' or 'erase' these PTMs. The histone lysine demethylase (KDM) family of epigenetic enzymes remove methyl modifications from lysines on histone tails. The Jumonji C domain (JmjC) family is the largest family of KDMs. Investigating the scope and mechanisms of the JmjC KDMs is of interest for understanding the diverse functions of the JmjC KDMs in vivo, as well as for the application of the basic science to medicinal chemistry design. The work described in this thesis aimed to biochemically investigate the inhibitor and substrate diversity of the JmjC KDMs, it led to the identification of new inhibitors and substrates and revealed a potential combinatorial dependence between adjacent histone PTMs. Structure-activity relationship studies gave rise to an n-octyl ester form of IOX1 with improved cellular potency and selectivity towards the KDM4 subfamily. This compound should find utility as a basis for the development of JmjC inhibitors and as a tool compound for biological studies. The rest of this thesis focused on the biochemical investigations of potential substrates and inhibitors for KDM3A, a JmjC demethylase with varied physiological functions. Kinetic characterisation of reported KDM3A substrates was used as the basis for evaluations of novel substrates and inhibitors. Further studies found TCA cycle intermediates to be moderate co-substrate competitive inhibitors of KDM3A. Biochemical investigations were carried out to study potential protein-protein interactions of KDM3A with intraflagellar transport proteins (IFTs), non-histone proteins involved in the formation of sperm flagellum. Work then addressed the exploration of novel in vitro substrates for KDM3 (KDM3A and JMJD1C) mediated catalysis, including: methylated arginines, lysine analogues, acetylated and formylated lysines. KDM3A, and other JmjC KDMs, were found to catalyse novel arginine demethylation reaction in vitro. Knowledge gained from studies with unnatural lysine analogues was utilised to search for additional novel PTM substrates for KDM3A. These results constitute the first evidence of JmjC KDM catalysed hydroxylation of an Nε-acetyllysine residue. The H3 K4me3 position seems to be required for acetyllysine substrate recognition, implying a combinatorial effect between PTMs. Preliminary results provide evidence that JMJD1C, a KDM3 protein previously reported to be inactive, may catalyse deacetylation in vitro. An additional novel reaction, observed with both KDM3A and JMJD1C, is deformylation of N^ε-formyllysine residues on histone H3 fragment peptides. Interestingly, H3 K4 methylation was also observed to enhance the apparent deformylation of both KDM3A and JMJD1C catalysed reactions. Overall, findings in this thesis suggest that the catalytic activity of JmjC KDMs extends beyond lysine demethylation. In a cellular context, members of the KDM3 subfamily might provide a regulatory link between methylation and acylation marks. Such a link will further highlight the complex relationships between histone PTMs and the epigenetic enzymes that regulate them. The observed dependency of H3 K9 catalysis on H3 K4 methylation adds another layer of complexity to the epigenetic regulation by histone PTMs.

La Bronchopneumopathie Chronique Obstructive (BPCO) associe inflammation et hypoxie, vraisemblablement à l’origine d’altérations du tissu musculaire des patients dont l'état est corrélé au pronostic vital. Bien que justifiée, la réhabilitation par l'exercice n'est pas efficace dans 1/3 des cas, sans que les mécanismes à son origine n’aient été identifiés. Cette non-réponse pourrait impliquer un contrôle épigénétique de l'expression des gènes en lien avec la croissance musculaire via leurs profils d'acétylation. Pour étudier les effets de l'exercice sur le muscle BPCO, nous avons développé un modèle murin d'hypertrophie musculaire induite utilisé dans un contexte d'hypoxie (HC) et d'inflammation pulmonaire chronique (IP). Dans ce contexte, en comparant soléaire et plantaire, il apparaît que l’hypertrophie du soléaire est altérée par l’IP alors que celle du plantaire est fortement inhibée par l’HC. L'administration d'un inhibiteur des Bromodomaines et domaines Extra-Terminaux (i-BET), éléments impliqués dans la lecture des niveaux d’acétylations des histones, restaure leurs capacités d'hypertrophie. Cette altération de la croissance musculaire est associée à des perturbations des voies de protéosynthèse (Akt, S6k1, Erk) et de protéolyse (MuRF-1) muscles dépendantes. Dans le soléaire, l’acétylation des lysines des histones H3 et H4 est augmentée par l’IP ainsi que la transcription d’Histones Déacétylases (HDAC) est diminuée. Ces modifications associées à la restauration de l’hypertrophie du soléaire par l’i-BET malgré la présence d’une IP, suggèrent fortement l’implication des mécanismes épigénétiques dans l‘inhibition de la croissance musculaire. L’augmentation de l’acétylation des histones H3 et H4 du plantaire soumis à une HC tend à confirmer l'implication de mécanismes épigénétiques dans l’altération de la réponse de ce muscle. Toutefois des travaux supplémentaires seraient nécessaires pour confirmer cette hypothèse. Pour finir, les mesures de paramètres hémodynamiques cardiaques nous ont montrés que l’i-BET était également à l’origine d’une diminution de l’Hypertension Artérielle Pulmonaire (HTAP), de l’hypertrophie du ventricule droit et de l’hématocrite lors de l’exposition de nos animaux à une HC.Ces travaux suggèrent que la non-réponse au réentrainement d’un tiers des patients BPCO pourrait être liée à la présence d’une IP associée à une hypoxémie. La restauration des capacités adaptatives du muscle par un traitement à l’iBET pourrait constituer une perspective thérapeutique prometteuse, permettant à ces patients de retirer les importants bénéfices d’une telle prise en charge. Toutefois, la réduction de l’hématocrite de nos animaux traités avec l’i BET en HC, implique une prise en charge parallèle à, ce traitement pour maintenir l’adaptation à l’HC des patients BPCO hypoxémiques. / The Chronic Obstructive Pulmonary Disease (COPD) associates inflammation with hypoxia, likely causing deterioration of muscle tissue whose status is tightly correlated to vital prognosis. Although justified due by its anabolic effects, rehabilitation through exercise which progressively became a key medical care in COPD is inefficient in 1/3 of the patients. This non-response could involve epigenetic control of gene expression via alterations of the acetylation profile induced by pulmonary Inflammation (PI) and Chronic Hypoxia (CH). To study this, we used a murine model of either soleus or plantaris muscle hypertrophy induced by a functional overload, in PI and CH conditions. Results show that soleus hypertrophy is diminished by PI while plantaris hypertrophy is inhibited by CH. These specific responses are associated with alterations in proteosynthesis (Akt, S6k1, Erk) and proteolysis (MuRF-1) in a muscle-dependent manner. With PI, acetylation of lysines of histones H3 and H4 is increased in soleus muscle while transcription of Histone Deacetylases (HDACs) is decreased. Inhibiting the proteins in charge of reading the acetylations (BET) is able to restore the hypertrophic capacities of the soleus when exposed to PI, reinforcing the hypothesis of an involvement of epigenetic regulatory mechanisms in the problem of muscle response to a hypertrophic stimulus. Moreover, the use of the BET inhibitor (i-BET) prevents the development of pulmonary arterial hypertension, of the right ventricle hypertrophy and the increase in hematocrit in animals exposed to CH. Restoring the muscle adaptive capacities using i-BET led us to consider new promising therapeutic perspectives in COPD patients who present limited or no response to exercise rehabilitation.

Les cellules tumorales circulantes (CTCs) sont des cellules tumorales provenant de la tumeur primaire et/ou des métastases que l’on retrouve dans la circulation sanguine. Les plus agressives d’entre elles peuvent envahir les organes distants pour former des métastases. Leur faible nombre parmi la multitude de cellules sanguines rend difficile leurs détections et leurs études. C'est pourquoi, le challenge actuel est de pouvoir mettre en culture ces cellules.Dans le cadre de l’éude clinique nationale COLOSPOT, notre laboratoire a pu recueillir des échantillons de patients atteints d’un cancer colorectal métastatique. Grâce à ces prélèvements sanguins, 9 lignées dérivées de CTCs ont pu être établies : CTC-MCC-41, CTC-MCC-41.4, CTC-MCC-41.5A-G.Dans ce projet de thèse, les 9 lignées cellulaires ont été caractérisées au niveau du génome, du transcriptome, du protéome, du sécrétome et fonctionnel, et comparées à des lignées cellulaires tumorales primaires et métastatiques connues, comme effectuée précédemment sur la lignée CTC-MCC-41 (Cayrefourcq et al. 2015)Cette analyse très complète a montré malgré des profils génétiques très différents, toutes les lignées CTCs ont les caractéristiques d’un phénotype intermédiaire épithélial/mésenchymal, des propriétés de cellules souches, la mutation BRAFV600E et la capacité d’éviter divers processus de lutte contre les cellules tumorales comme la résistance à l’anoïkis et l’échappement au système immunitaire. Les études fonctionnelles ont montré que les CTC-MCC pouvaient induire rapidement la formation de tubes avec des cellules endothéliales in vitro, signe d'un potentiel angiogénique.La seconde partie de ce travail de thèse a été d’étudier la transition épithélio-mésenchymateuse (EMT) in vitro. Ce phénomène est une étape clé du processus métastatique des CTCs et implique diverses transformations des cellules à divers niveaux : morphologique, protéique et transcriptomique. Trois méthodes différentes ont été testées pour induire l’EMT au sein des lignées CTCs impliquant deux différents modes d’induction et deux modes de culture. Ces changements ont pu être observés dans les lignées témoins, validant les expérimentations effectuées. Cependant, l’EMT n’a pas été clairement observée sur les lignées CTCs.En conclusion, ces analyses suggèrent que les CTC coliques cultivés à partir de biopsies liquides séquentielles, effectuée durant le traitement d’un même patient, ont des caractéristiques communes. Mais la sélection des clones, avec un phénotype distinct, résistant au traitement, a été observée. D'autres études avec ces lignées CTC-MCC sont en cours, évaluant leur capacité à induire des tumeurs résistantes à des médicaments spécifiques ou à analyser la contribution épigénétique. Ces données peuvent fournir des indications pour la découverte de nouveaux biomarqueurs permettant d'identifier les sous-populations de CTC les plus agressives et pour la mise au point de nouveaux médicaments pour inhiber les CTCs initiatrices de métastases dans le cancer du côlon. / Circulating tumor cells (CTCs) are tumor cells that have been shed from the primary tumor and/or metastases into the bloodstream. The most aggressive ones can invade distant organs to form metastases. Their low number among the multitude of blood cells makes difficult their detection and study. This is why the current challenge in this field of expertise is to be able to culture them ex vivo.In the national COLOSPOT clinical study, our team was able to collect samples of patients with metastatic colorectal cancer. From blood samples of only one patient, 9 cancer cell lines derived from CTCs could be established: CTC-MCC-41, CTC-MCC-41.4, CTC-MCC-41.5A-G.In this project, the 9 CTC-MCC lines have been characterized at the genome, transcriptome, proteome, secretome and functional levels, and compared with primary and metastatic commercial colon cancer cell lines, as previously done on the CTC-MCC-41 line (Cayrefourcq et al., Cancer Res. 2015)These analyses have shown that despite their very different genetic profiles, all CTCs have the characteristics of an epithelial/mesenchymal intermediate phenotype, stemcell like characteristics, with BRAFV600E mutation, and the ability to avoid biological processes such as the resistance to anoïkis and the escape to the immune system. Moreover, functional studies have shown that all CTC-MCC lines can rapidly induce tubes formation with endothelial cells in vitro, a sign of an angiogenic potential.The second part of this thesis work was to study the epithelial-to-mesenchymal transition (EMT) in vitro. This phenomenon is a key step in the metastatic process and involves several cell transformations at various levels: morphological, proteomic and transcriptomic. Three different methods have been tested to induce EMT within these CTC-MCC lines involving two different induction and culture modes. These changes could be observed in the control lines, validating the experiments carried out. However, EMT has not been clearly observed yet on the CTC-MCC lines.In conclusion, this longitudinal study suggest that colorectal CTCs cultured from sequential liquid biopsies, performed during treatment of the same patient, have common characteristics. However, our results strongly suggest that no clonal selection, with a distinct phenotype, resistant to treatment, has occurred. Further studies with these CTC-MCC lineages are in process, evaluating their ability to induce in vivo drug-resistant tumors or to analyze the epigenetic contribution. These data may provide guidance for the discovery of new biomarkers to identify the most aggressive CTC subpopulations and for the development of novel drugs to inhibit metastases-competent CTCs in colon cancer.

DNA methylation entails the addition of a methyl group to the 5-carbon of the cytosine base of the DNA. This modification is important during many biological processes such as imprinting, X-chromosome inactivation, cell differentiation as well as silencing of transposable elements (TEs). DNA methylation is dynamic during early mammalian development, despite being a more static mark in somatic cells. Global hypomethylation is a hallmark of epigenetic reprogramming in mammalian primordial germ cells (PGCs), the early embryo and in naïve embryonic stem cells (ESCs). Genome integrity is crucial during early development, as the germline DNA needs to be protected for future generations. Therefore, epigenetic reprogramming presents a critical phase for TE defence since presumably alternative silencing pathways need to be employed to limit their activity. In this thesis, I investigate the role of small RNAs to control TEs during global waves of DNA demethylation in cellular reprogramming, naïve pluripotency as well as early mammalian development. Following an introduction to the research questions, in chapter 3 I investigate the mechanism of TE regulation in an in vitro model of Dnmt1 deletion in mouse ES cells to recapitulate in vivo epigenetic reprogramming. I find that certain classes of TEs become transcriptionally upregulated and subsequently resilenced by a mechanism independent of DNA methylation. I identify ARGONAUTE 2 (AGO2) bound siRNAs as the prominent mechanism to control certain classes of TEs, while others appear to be regulated by redistribution of repressive histone modifications. In chapter 4, I construct Dicer constitutive and conditional KO ESCs in the background of the Dnmt1f l/f l ESCs using CRISPR-Cas9. I dissect the role of DNA methylation and of DICER dependent small RNAs on transcriptional changes of ESCs. Additionally, I find that DICER dependent small interfering RNAs (siRNAs) re-silence transcriptionally active TE classes. Finally, in chapter 5, I examine the role of small RNAs in TE silencing in different models of global hypomethylation in vivo and in vitro PGCs, during iPSC reprogramming and in a transition from serum to 2i culturing of mouse ESCs.

Les longs ARN non codants (lncRNAs) sont définis comme des transcrits de plus de 200nt et n'ayant pas de potentiel codant. Des études récentes ont démontré que les lncRNAs pouvaient être impliqués dans la régulation de la transcription, de la traduction, de la différenciation cellulaire, de l'expression génique, du cycle cellulaire et des modifications de la chromatine. De plus, il a été montré un impact fonctionnel de certains lncRNAs dans le processus de cancérogenèse mais nos connaissances actuelles sur ces molécules dans le cancer, et plus particulièrement dans la leucémie, restent extrêmement limitées. Au cours de cette étude, nous avons analysé l'expression des lncRNAs par RNA-sequencing sur 40 patients atteints de leucémie aiguë myéloblastique (LAM) à caryotype normal. Parmi les 11065 lncRNAs exprimés dans nos échantillons, nous avons identifié une signature de lncRNAs associée à la mutation de NPM1. Afin de mettre en évidence les fonctions putatives des lncRNAs sélectionnés, nous avons utilisé un algorithme de prédiction d'interaction protéine/ARN. De manière intéressante, plus de la moitié des lncRNAs présentent des sites d'interactions potentiels à SUZ12, une sous unité du complexe PRC2 (Polycomb repressive complex 2), connu pour être recruté par des lncRNAs pour la régulation épigénétique de gènes cibles. Par RNA immunoprécipitation (RIP) de SUZ12, nous avons pu démontrer que le lncRNA XLOC_087120 interagissait avec SUZ12. De plus, son expression est anti-corrélée avec celle des gènes voisins codants des histones, suggérant un rôle dans la régulation négative des histones par ce lncRNA. L'impact de la dérégulation de XLOC_087120 sur les histones a été confirmé par des expériences de surexpression et d'inhibition de ce lncRNA dans des lignées de LAM. De plus, même si la mutation NPM1 ne semble pas affecter directement l'expression de ce lncRNA, des expériences d'infection de la forme mutée de NPM1 dans une lignée LAM ont montré que NPM1 pourrait réguler la localisation nucléaire/cytoplasmique de XLOC_087120 et moduler sa fonction de répresseur. En conclusion, ces données suggèrent que les lncRNAs sont des facteurs clés dans la pathogenèse des LAMs. / Long noncoding RNAs (lncRNAs) are defined as RNA transcripts that are larger than 200 nt but do not appear to have protein- coding potential. Recent studies have demonstrated that lncRNAs regulate many processes such as transcription, translation, cellular differentiation, gene expression regulation, cell cycle regulation, and chromatin modification. Cumulative evidence points towards an important role of lncRNAs in cancer initiation, development, and progression. However, our overall knowledge of lncRNAs in cancer, including leukemia, remains extremely limited. In this study, we investigated lncRNA expression by RNA-sequencing in 40 acute myeloid leukemia (AML) patients with normal karyotype. Among 11065 lncRNA expressed in our samples, we identified specific lncRNA signature associated with the presence of NPM1 mutation. To go further into the putative function of these lncRNAs, we used catRAPID Omics algorithm to predict potential protein partners. Interestingly, the majority of the selected lncRNAs contains putative SUZ12 binding sites, a PRC2 (Polycomb Repressive Complex 2) component known to be linked to lncRNAs and to epigenetically regulates target genes. By using SUZ12 RNA Immunoprecipitation, we identify one lncRNA named XLOC_087120 linked to SUZ12. XLOC_087120 is located in a region enriched in histone genes. Pearson correlation showed a significative anti-correlation between XLOC_087120 and histone neighboring coding gene expression suggesting a role of this lncRNA in the regulation of histone genes. The impact on histone genes expression was confirmed by overexpression and inhibition of XLOC_087120 in AML cell lines. Overexpression of NPM1 mutant in an AML cell line showed that NPM1 modulates the nuclear/cytoplasmic localization of XLOC_087120 and consequently its repressive function. Altogether, these data suggest that lncRNAs should be considered as key players in the pathogenesis of acute myeloid leukemias.

Les ARN messagers (ARNm) fonctionnels sont produits au cours d'un mécanisme complexe qui allie la transcription, qui permet la synthèse d'un pré-ARNm, la maturation de ce transcrit et son export. De plus, ces différentes machineries vont devoir faire face à la structure compacte de la chromatine, nécessitant une activité de décondensation/recondensation de la chromatine qui est notamment régulée par les mécanismes épigénétiques. Un très grand nombre de facteurs sont donc requis pour la production des ARNm fonctionnels . Parmi ces facteurs, les protéines Spt6 et Iws1 sont impliquées dans le mécanisme général de la transcription, dans la modulation de la structure de la chromatine et la maturation et l'export des ARNm. Ces travaux de thèse ont permis de caractériser biochimiquement, structuralement et fonctionnellement ces deux protéines, leur complexe et leur interaction avec d'autres effecteurs de la transcription. Ces travaux ont notamment permis de comprendre en termes moléculaires et fonctionnels (i) comment Spt6 est recrutée par l'ARN polyméraseII au cours de la transcription et (ii) comment le complexe Spt6/Iws 1 est formé. Ils ont également permis d'identifier de nouveaux interactants potentiels de Spt6, et notamment le facteur d'élongation de la transcription TFIIS. Ces travaux ont ainsi permis de révéler le rôle essentiel et extrêmement complexe joué par Spt6 et Iws1 lors de la production d'un ARNm, mais également de permettre l'étude future de leur interaction avec d'autres facteurs transcriptionnels. / Production of functional messenger RNA (mRNA) requires a complex mechanism that couples transcription with maturation and export of the mRNA. In addition to this mechanism, chromatin needs to be unwound to allow the transcription machinery access the DNA, this unwinding being also highly regulated. Thus, production of a functional mRNA requires a huge number of factors implicated in these different processes. Among these proteins Spt6 and Iws1 are participating in the mechanism of transcription, chromatin unwinding, and maturation and export of the mRNA. The work carried out during this thesis has enabled the biochemical, structural and functional characterization of these proteins, their complex and their interaction with other effectors of transcription. This work has specifically enabled the molecular and functional characterization (i) of the recruitment of Spt6 by RNA polymerase II and (ii) of the formation of the Spt6/Iws1 complex. Moreover, this work has identified putative new partners of Spt6, not ably the elongation factor TFIIS. Thus, our work has highlighted the essential and complex role of Spt6 and Iws1 during the production of functional mRNA, and has also enabled future studies of the complexes formed by these two proteins with other transcriptional factors.

O Distrito Mineiro de Artigas, no Uruguai, compreende uma das maiores jazidas de ametista e ágata de que se tem conhecimento e é comparável às jazidas da região do Alto Uruguai, próximas ao município de Ametista do Sul, Brasil. A mineralização ocorre em geodos parcialmente preenchidos por ágata, quartzo incolor, ametista e ± calcita, que ocorrem nesta seqüência, da borda para o centro das cavidades. As rochas hospedeiras da mineralização são basaltos andesíticos da Formação Arapey, equivalente à Formação Serra Geral, no Brasil. Na área de estudo ocorre uma seqüência de seis derrames, de composição entre basalto e andesito. As estruturas de resfriamento são dos tipos I e II, que diferem pela ausência e presença de disjunção colunar, respectivamente, na porção interna do derrame. Destes seis derrames dois são do tipo I (maciço na zona central) e portadores de minério. Com base em observações de campo de estruturas rúpteis associadas às zonas mineralizadas, foi elaborado um modelo epigenético para a mineralização de ametista em geodos em basalto. Neste modelo, os geodos são formados após a solidificação da lava, por deformação ou dissolução do basalto, depois de alterado para argilominerais do grupo da esmectita pela interação com fluidos hidrotermais. O preenchimento ocorre após a abertura e pelo mesmo fluido que abriu a cavidade. O fluido é meteórico, de baixa salinidade e tem composição próxima a de água pura. A temperatura do fluido é < 200°C, com base na mineralogia de alteração da rocha hospedeira. A temperatura de cristalização dos minerais no interior dos geodos não ultrapassa 70°C. Esta temperatura foi calculada com base nos coeficientes de partição do oxigênio entre quartzo e água e entre calcita e água para um fluido com assinatura isotópica de T18O de -5 ‰. A intensa alteração hidrotermal nas rochas portadoras do minério e nos derrames, no âmbito do Distrito Mineiro de Artigas, corrobora para eventos epigenéticos relacionados com a mineralização. Isótopos de T34S nas encaixantes do minério indicam percolação de fluido em grande escala, e assinatura isotópica compatível com as unidades sedimentares subjacentes ao pacote vulcânico. A integração dos dados obtidos sugere que os geodos de ametista foram formados após a solidificação da lava e os minerais que preenchem os geodos cristalizadados por um fluido de origem meteórica. / The Artigas Mining District, in Uruguay, is a world-class amethyst deposit, and is comparable with those in Alto Uruguai region, Brazil (Ametista do Sul). The mineralization occurs as geodes partially filled by agate, colorless quartz and amethyst, ± calcite, which occur in this sequence from the rim to the inner part of the cavities. The host rocks are andesitic basalts from the Arapey Formation. The study area comprises a sequence of six lava flows, including basaltic to andesitic composition. The cooling structure of the flows is type I and type II; those are differentiated by the inner part of the flow. Type II has columnar joints, whereas type I is massive. Two out of six flows are mineralized and structured as type I flows. Based on field observations of brittle failures associated with the geode zone, an epigenetic model is elaborated for the mineralization of amethyst in geodes hosted by basalts. In this model, the geodes are formed after the flow solidifies. The cavities are formed by deformation or dissolution, after the basalt was altered to clay minerals (smectite group) by hydrothermal fluids. The filling occurred after the cavity was formed by the same fluid. The fluid is close to pure water in composition, of meteoric origin, with low salinity. The temperature is <200°C, based on alteration mineralogy in the host rock. The crystallization temperature is <70°C. The temperature is calculated based on fractionation coefficient of oxygen isotopes between quartz and water and between calcite and water. The value of T18O of the mineralized fluid is assumed to be -5 ‰. The intensive alteration in the host rocks and in lava flows within the mining district, favors the epigenetic hypothesis related to the mineralization processes. T34S isotopes on the host rock, agree with large scale hydrothermal fluid percolation. The data obtained suggest that the amethyst geodes were formed after the lava solidified and was filled by meteoric hydrothermal fluids.

A central concept in Evolutionary theory is the character trait. It provides a context in which to explore differences and similarities among taxa, both extant and extinct. It is expanded in scope in Evolutionary Developmental theory to functional units with a biological role, "evolutionarily stable configurations." The talo-crural joint is such a configuration, a highly canalized structural unit in primates forming the interface between organism, and foot and substrate. It is a microcosm in which to examine the relationship of shape with environment and function and the interplay of genetics, ontogeny, and use. Geometric Morphometric analysis of landmark data was employed in studying the articular surfaces of the talus in a diverse sample of adult specimens in nine catarrhine taxa. The influence of four factors on talar shape was examined: superfamily, a proxy for phylogeny; size and mass, a proxy for physical attributes; and substrate preference, a proxy for behavior. All significantly affected shape, and substrate preference was unrelated to the others. Appositional articular morphology, the shape of the subchondral bone surfaces of the talo-crural joints in an expanded sample of 12 taxa, showed a significant effect of the four proxies on the tibial and talar components, and substrate preference was weakly related to the other proxies in each. Singular Warp analysis of the cross-covariance matrices of the joints demonstrated sorting of taxa by substrate use and signals of convergent and divergent evolution among hominoids and cercopithecoids in joint shape. The ontogeny of the appositional articular shape was examined using adult and subadult specimens grouped by molar eruption. Singular Warp analysis demonstrated a genetic signal in the subadults, strongest in the slowly maturing African hominoids, and an epigenetic signal across taxa to substrate use in the adults. The talo-crural joint, a highly canalized, modular, and integrated "evolutionarily stable configuration," provides a model for the study of the evolution of shape. The epigenetic signal observed is consistent with plasticity or developmental plasticity in response to the interaction of the joint complex with the environment due to a behavioral effect, substrate use. This dissertation included previously unpublished, co-authored material.