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It is argued that if theories of rationality are to avoid logical difficulties (i.e., self referential inconsistencies or logical paradoxes), then these theories require a minimal dogmatism, that is, some basic presuppositions that are unjustifiable without intuitions, vicious circularity, or infinite regress. Thus, it is argued that if rationality is characterized as the search for justifications then a comprehensive rationality is in the end an impossible and self -contradictory task; while if rationality is characterized by the criticizability of any position, then a rationality that intends to be comprehensive leads to self-referential logical paradox. It is also argued that there are logical limits to the justifiability of the most basic scientific methodological rules and aims, that is, it is argued that to justify our various scientific methods and aims we are required to assume without a bona fide justification (i.e., dogmatically) some basic cognitive methods and goals. These conclusions are illustrated by exploring the theories of rationality of the Popperian tradition and the theories of scientific method of various naturalised scientific meta-methodologies, in particular, by critically examining the alleged justification of our scientific methods provided by 'evolutionary epistemology' and Laudan's normative naturalism.

Les anomalies congénitales de la glycosylation (CDG) sont des maladies génétiques rares caractérisées par une glycosylation aberrante des protéines. Récemment, un sous-groupe de CDG dues à des perturbations de l'homéostasie de l’appareil de Golgi a fait son apparition. En 2012, notre équipe a identifié TMEM165 comme étant une protéine golgienne impliquée dans les CDG, mais dont les fonctions biologiques et cellulaires demeurent inconnues. Au cours de mon doctorat, nous avons montré que l'homéostasie golgienne du Mn2+ était altérée en absence de TMEM165. Alors que de forts défauts de glycosylation, en particulier des défauts de galactosylation, ont été observés dans des cellules déficientes en TMEM165, nous avons découvert que la supplémentation en Mn2+ était suffisante pour rétablir une glycosylation normale. De façon intéressante, nous avons également démontré que ce défaut de glycosylation pouvait également être supprimé par une supplémentation en galactose. Fort de cette observation, la supplémentation orale en galactose a été testée chez des patients déficients en TMEM165 et il a été prouvé que ce traitement améliorait significativement les paramètres biochimiques et cliniques. De plus, nous avons mis en évidence que la stabilité de TMEM165 était altérée en présence d'une concentration élevée de Mn2+. En effet, nous avons montré que l'exposition à des concentrations élevées de Mn2+ entraînait une dégradation lysosomale rapide de TMEM165. Dans l'ensemble, notre étude montre que TMEM165 est (i) un acteur clé de la glycosylation golgienne en régulant finement l'homéostasie du Mn2+ et (ii) une nouvelle protéine de l’appareil de Golgi sensible au manganèse. / Congenital Disorders of Glycosylation (CDG) are severe inherited diseases in which aberrant protein glycosylation is a hallmark. From this genetically and clinically heterogeneous group, a significant subgroup due to Golgi homeostasis defects is emerging. Our team previously identified TMEM165 as a Golgi protein involved in CDG. But despite strong efforts, the biological and cellular functions of TMEM165 were not known so far. During my thesis, we highlighted that Golgi Mn2+ homeostasis was impaired due to TMEM165 deficiency. While strong glycosylation defects, especially galactosylation defects, were observed in TMEM165 depleted cells, we discovered that Mn2+ supplementation was sufficient to fully restore a normal glycosylation. Interestingly, we also demonstrated that the observed glycosylation defects in mammalian cells could be overcome by galactose supplementation. Strong of this observation, oral galactose supplementation in TMEM165 deficient patients was assayed and this treatment was proven to significantly improve biochemical and clinical parameters. Moreover, we highlighted TMEM165 as a novel Golgi protein whose stability is altered in the presence of high manganese concentration. Indeed, we showed that exposure to high Mn2+ concentrations led to a rapid lysosomal degradation of TMEM165. Altogether, our study points TMEM165 as (i) a key player in Golgi glycosylation by finely regulating Golgi Mn2+ homeostasis and (ii) a novel Golgi protein sensitive to manganese.

This thesis is about dialetheism and the problem of revenge. More broadly, it is about truth and what the logical paradoxes tell us about the logical behaviour of truth. One of the driving forces behind the contemporary study of truth and paradox is the problem of revenge: that many, perhaps all, available theories of truth, give rise to further paradoxes, invoking central notions of those theories, which demonstrate that the theory cannot express those notions. This sort of expressive limitation, especially if it involves the very notion invoked to diagnose what goes wrong in paradoxical sentences, would normally be thought a decisive point against a given theory of the paradoxes, were it not for the fact that the problem is so pervasive that every currently available theory has, at some point, been argued to suffer from it. Dialetheism, the view that some contradictions are true, has often been thought to be the only view which has a reasonable chance of avoiding the problem. Indeed, the surge of interest in the view since the first publication of Priest’s In Contradiction, in 1987, defending dialetheism, is probably due in large part to the seeming immunity to the revenge problem that Priest’s view possesses. Its virtue, in respect of revenge, is that its ability to accept, without collapse into incoherence, contradictions, allows it to accept any further revenge paradoxes as merely giving more sound arguments for dialetheia (true contradictions). This thesis argues that this appearance of revenge-immunity is mistaken. Dialetheism, too, has its revenge problems. The seeming virtue of dialetheism, that it can accept the contradictions generated by revenge paradoxes without incoherence, also has its drawbacks. This is because dialetheists are not only able, but compelled to accept the contradictions arising from the semantic paradoxes. This means that contradictions can arise in certain areas where they are undesirable. In particular, there are notions which seem to require consistency in order to be expressible. If we can demonstrate, using revenge paradoxes, that, on dialetheism, predicates putatively representing these notions would have to behave inconsistently, then we can demonstrate that dialetheists cannot express the notions. There are many ways one might wish to carve up the different varieties of dialetheism available. I have separated the view into two broad kinds: metatheoretically paraconsistent dialetheism, on the one hand, and metatheoretically consistent dialetheism, on the other. This distinction decides to which variety of revenge problem the version of dialetheism in question is subject. I take each in turn, and argue that they are each subject to expressive limitations brought about by revenge paradox.

Includes bibliographical references (p. 31-33).

A conversão de áreas de florestas da Amazônia em áreas agrícolas e pastoris desregula processos relacionados ao estoque de carbono, sendo considerada depois da queima de combustíveis fósseis a atividade que mais contribui com a emissão de gases do efeito estufa, dentre os quais se encontra o metano. A produção de metano é intermediada pelas arquéias metanogênicas, que atuam na decomposição anaeróbia da matéria orgânica. Portanto, para compreender as alterações do fluxo desse gás no ecossistema amazônico, é necessário que as comunidades microbianas envolvidas nesse processo sejam estudadas. Dessa forma, o presente estudo teve por objetivo monitorar e caracterizar comunidades de arquéias metanogênicas, por análises de enriquecimento destas comunidades, em amostras de solo provenientes de floresta primária, floresta secundária e pastagem da região amazônica. As amostras de solo foram colocadas em meio enriquecido com a adição de acetato, metanol ou H2:CO2, separadamente, para estimular os metabolismos aceticlástico, metilotrófico e hidrogenotrófico. O monitoramento desses cultivos foi realizado por análises de emissão de metano por cromatografia gasosa, quantificação do gene mcrA pela técnica de PCR quantitativo (qPCR) e caracterização da comunidade metanogênica por meio de microscopia e sequenciamento da região V4-V5 do gene 16S rRNA. Analisando a emissão de metano entre os três tipos de fontes de carbono para as três amostras de solo, os enriquecimentos com metanol apresentaram uma produção maior de metano em relação as amostras com o acetato e muito superior aos cultivos com atmosfera de H2:CO2. A maior média de produção de metano ocorreu nos enriquecimentos com metanol, indicando que a via metilotrófica embora considerada alternativa, pode ser importante na produção de metano no solo amazônico. Por meio da técnica de qPCR foi possível quantificar o gene mcrA das amostras de pastagens logo no tempo inicial da incubação, o que não foi possível para as amostras florestais. No tempo final, o número de cópias desse gene foi similar para os três perfis de solo. Foi possível observar pela caracterização fenotípica dos enriquecimentos agregados de células característicos do gênero Methanosarcina, gênero que foi identificado posteriormente pelo sequenciamento do gene 16S rRNA, além de células em formatos de bastonetes e cocos. Os resultados do sequenciamento permitiram identificar 7 grupos distintos de arqueias metanogênicas, afiliados aos filos Euryarchaeota e Bathyarchaeota. Nas amostras iniciais de pastagens foram identificadas sequências que se afiliaram a todos esses grupos, enquanto as amostras florestais apresentaram sequencias afiliadas apenas ao gênero Methanosarcina. A composição final da comunidade das amostras de pastagens foi similar a inicial, porém mais abundante. Os enriquecimentos de amostras de solo de floresta primária e secundária apresentaram uma composição distinta, devido ao enriquecimento de grupos que não foram identificados no início da incubação. Os resultados obtidos mostraram que embora as arqueias metanogênicas estejam em baixa abundância nos solos florestais, podem ser enriquecidos quando submetidos a condições favoráveis, atingindo produção de metano e alcançando composição similar as amostras de pastagens. / Amazonian forest conversion into agricultural and livestock areas disrupts processes related to carbon stock, being considered, after the fossil fuels burning, the activity contributes most to greenhouse gases emission, of which is methane. Methane production is mediated by methanogenic archaea, acting in organic matter anaerobic decomposition. Therefore, to understand the changes in the flow of this gas in the Amazonian ecosystem, it is necessary to study microbial communities involved in this process. This study aims to monitor and characterize methanogenic archaeal communities by population enrichment from soil samples collected in primary, secondary and pasture of the Amazon region. Soil samples were placed into an enriched medium and received separately acetate, methanol, and H2:CO2 to stimulate the three metabolism types: acetoclastic, methylotrophic and hydrogenotrophic. Monitoring was performed by methane emission analysis by gas chromatography, mcrA quantification by the quantitative PCR and the community characterization was performed by microscopy and sequencing of the V4-V5 region of the 16S rRNA gene. Analyzing the methane emission by the three types of carbon sources in the three soil samples, methanol enrichments presented a higher methane yield than the acetate samples and much larger than cultures with H2:CO2. These results indicate that methylotrophic pathway, although considered as an alternative, may be important in methane production in the Amazonian soil. Was possible to quantify the mcrA gene by qPCR from pasture samples at the initial incubation time, which was not possible for forest samples. In incubation final time, copies number of this gene was similar for the three soil profiles. The phenotypic characterization of enrichments revealed aggregated cells, characteristic of the genus Methanosarcina, later identified by 16S rRNA sequencing. The cells in rod-shaped and cocci formats were also observed. Was identify by sequencing 7 different methanogenic archaeas groups affiliated with Euryarchaeota and Bathyarchaeota phylum. In the initial pasture samples, were identified sequences affiliated with all these groups, while forest samples presented sequences affiliated with only a Methanosarcina genus. Pasture samples showed a final community composition similar to initial, however more abundant. Soil samples enrichment from primary and secondary forest presented a distinct composition due to groups enrichment that was not identified at incubation beginning. These results showed that although methanogenic archaeas are in low abundance in forest soils, they can be enriched when submitted to favorable conditions, archive methane production and reaching similar composition pasture samples.

Benjamin Lax, W.P. Allis, Sanborn C. Brown. / "June 30, 1950." / Bibliography: p. 16. / Army Signal Corps Contract No. W36-039-sc-32037 Project No. 102B Dept. of the Army Project No. 3-99-10-022

A conversão de áreas de florestas da Amazônia em áreas agrícolas e pastoris desregula processos relacionados ao estoque de carbono, sendo considerada depois da queima de combustíveis fósseis a atividade que mais contribui com a emissão de gases do efeito estufa, dentre os quais se encontra o metano. A produção de metano é intermediada pelas arquéias metanogênicas, que atuam na decomposição anaeróbia da matéria orgânica. Portanto, para compreender as alterações do fluxo desse gás no ecossistema amazônico, é necessário que as comunidades microbianas envolvidas nesse processo sejam estudadas. Dessa forma, o presente estudo teve por objetivo monitorar e caracterizar comunidades de arquéias metanogênicas, por análises de enriquecimento destas comunidades, em amostras de solo provenientes de floresta primária, floresta secundária e pastagem da região amazônica. As amostras de solo foram colocadas em meio enriquecido com a adição de acetato, metanol ou H2:CO2, separadamente, para estimular os metabolismos aceticlástico, metilotrófico e hidrogenotrófico. O monitoramento desses cultivos foi realizado por análises de emissão de metano por cromatografia gasosa, quantificação do gene mcrA pela técnica de PCR quantitativo (qPCR) e caracterização da comunidade metanogênica por meio de microscopia e sequenciamento da região V4-V5 do gene 16S rRNA. Analisando a emissão de metano entre os três tipos de fontes de carbono para as três amostras de solo, os enriquecimentos com metanol apresentaram uma produção maior de metano em relação as amostras com o acetato e muito superior aos cultivos com atmosfera de H2:CO2. A maior média de produção de metano ocorreu nos enriquecimentos com metanol, indicando que a via metilotrófica embora considerada alternativa, pode ser importante na produção de metano no solo amazônico. Por meio da técnica de qPCR foi possível quantificar o gene mcrA das amostras de pastagens logo no tempo inicial da incubação, o que não foi possível para as amostras florestais. No tempo final, o número de cópias desse gene foi similar para os três perfis de solo. Foi possível observar pela caracterização fenotípica dos enriquecimentos agregados de células característicos do gênero Methanosarcina, gênero que foi identificado posteriormente pelo sequenciamento do gene 16S rRNA, além de células em formatos de bastonetes e cocos. Os resultados do sequenciamento permitiram identificar 7 grupos distintos de arqueias metanogênicas, afiliados aos filos Euryarchaeota e Bathyarchaeota. Nas amostras iniciais de pastagens foram identificadas sequências que se afiliaram a todos esses grupos, enquanto as amostras florestais apresentaram sequencias afiliadas apenas ao gênero Methanosarcina. A composição final da comunidade das amostras de pastagens foi similar a inicial, porém mais abundante. Os enriquecimentos de amostras de solo de floresta primária e secundária apresentaram uma composição distinta, devido ao enriquecimento de grupos que não foram identificados no início da incubação. Os resultados obtidos mostraram que embora as arqueias metanogênicas estejam em baixa abundância nos solos florestais, podem ser enriquecidos quando submetidos a condições favoráveis, atingindo produção de metano e alcançando composição similar as amostras de pastagens. / Amazonian forest conversion into agricultural and livestock areas disrupts processes related to carbon stock, being considered, after the fossil fuels burning, the activity contributes most to greenhouse gases emission, of which is methane. Methane production is mediated by methanogenic archaea, acting in organic matter anaerobic decomposition. Therefore, to understand the changes in the flow of this gas in the Amazonian ecosystem, it is necessary to study microbial communities involved in this process. This study aims to monitor and characterize methanogenic archaeal communities by population enrichment from soil samples collected in primary, secondary and pasture of the Amazon region. Soil samples were placed into an enriched medium and received separately acetate, methanol, and H2:CO2 to stimulate the three metabolism types: acetoclastic, methylotrophic and hydrogenotrophic. Monitoring was performed by methane emission analysis by gas chromatography, mcrA quantification by the quantitative PCR and the community characterization was performed by microscopy and sequencing of the V4-V5 region of the 16S rRNA gene. Analyzing the methane emission by the three types of carbon sources in the three soil samples, methanol enrichments presented a higher methane yield than the acetate samples and much larger than cultures with H2:CO2. These results indicate that methylotrophic pathway, although considered as an alternative, may be important in methane production in the Amazonian soil. Was possible to quantify the mcrA gene by qPCR from pasture samples at the initial incubation time, which was not possible for forest samples. In incubation final time, copies number of this gene was similar for the three soil profiles. The phenotypic characterization of enrichments revealed aggregated cells, characteristic of the genus Methanosarcina, later identified by 16S rRNA sequencing. The cells in rod-shaped and cocci formats were also observed. Was identify by sequencing 7 different methanogenic archaeas groups affiliated with Euryarchaeota and Bathyarchaeota phylum. In the initial pasture samples, were identified sequences affiliated with all these groups, while forest samples presented sequences affiliated with only a Methanosarcina genus. Pasture samples showed a final community composition similar to initial, however more abundant. Soil samples enrichment from primary and secondary forest presented a distinct composition due to groups enrichment that was not identified at incubation beginning. These results showed that although methanogenic archaeas are in low abundance in forest soils, they can be enriched when submitted to favorable conditions, archive methane production and reaching similar composition pasture samples.

This master thesis discusses current legislation in the field of supported and renewable energy sources. At the beginning of the thesis are defined renewable energy sources from the perspective of Czech legislation and of professional view. The second part is focused on legislation regarding renewable energy sources in the European Union and the Czech Republic. Follows an overview of the support tools and legislation regarding renewable energy sources in other member states of the European Union and the current status of the set objectives related to the share of energy from renewable sources in gross final energy consumption, which have been established by Directive 2009/28/EC. At the end is summary, along with an overview of the most successful and least successful countries in terms of achieving the objective.