In the growing field of proteomics identification of proteins by tandem mass spectrometry (MS/MS) is performed by matching experimental mass spectra against calculated spectra of all possible peptides in a protein database. One problem with this approach is the false-positive identifications. MS-based proteomics experiments are further affected by a rather poor efficiency typical in the range of 10-15%, implicating that only a low percentage of acquired mass spectrometric data is significantly identified and assigned a peptide sequence. In this thesis improvement in spectrum specificity is accomplished by using a combination of high-accuracy mass spectrometry and techniques that will yield complementary sequence information. Performing collision-activated dissociation (CAD) and electron capture dissociation (ECD) upon the same peptide ion will yield such complementary sequence information. Implementing this into a proteomics approach and showing the advantages of using complementary fragmentation techniques for improving peptide identification is shown. Furthermore, a novel database-independent score is introduced (S-score) based upon the maximum length of the peptide sequence tag derived from complementary use of CAD and ECD. The S-score can be used to separate poor quality spectra from good quality spectra. An-other aspect of the S-score is the development of the ‘reliable sequence tag’ which can be used to recover below threshold identifications and for a reliable backbone for de novo sequencing of peptides. A novel proteomics-grade de novo sequencing algorithm has also been developed based upon the RST, which can retrieve peptide identification with the highest reliability (>95%). Furthermore, a novel software tool for unbiased identifications of any post-translational modifications present in a peptide sample is introduced (ModifiComb). Combining all the tools described in this thesis increases the identification specificity (>30 times), recovers false-negative identifications and increases the overall efficiency of proteomics experiements to above 40%. Currently one of the highest achieved in large-scale proteomics.

The central nervous system (CNS) melanocortin signaling pathway plays a critical role in the regulation of metabolism. However, the regulatory effects of CNS melanocortin signaling on hepatic lipid metabolism and fatty liver disease have not been well established. Although the activity of the CNS melanocortin system is regulated by metabolic signals, the mechanism for this regulation is not fully understood. Variants of the FTO (fat mass and obesity-associated) gene are associated with obesity and FTO is expressed in the hypothalamic neurons including proopiomelanocortin (POMC) neurons. Therefore, it is hypothesized that hypothalamic FTO plays a role in the regulation of metabolism by mediating the effect of metabolic signals on hypothalamic melanocortinergic neurons, and that impairments in this regulation may cause metabolic impairments including obesity and fatty liver disease. Intracerebroventricular (i.c.v.) treatment with SHU9119, a melanocortin antagonist, increased hepatic lipid accumulation and the expression of genes encoding lipogenic enzymes in lean mice. Conversely, i.c.v. treatment with MTII, a melanocortin agonist, reduced the expression of hepatic lipogenic genes in association with reduction in body weight in ob/ob mice, a mouse model of fatty liver disease. Immunohistochemical analysis demonstrated that Fto is co-expressed in both POMC and agouti-related protein (AgRP) neurons in the mouse hypothalamus. Fto mRNA and protein expression was reduced by fasting and increased by glucose treatment in nutritionally important hypothalamic nuclei. Fasting-induced reduction in hypothalamic Fto expression was observed in both lean wild-type and obese ob/ob mice, while the stimulatory effect of glucose on hypothalamic Fto expression was absent in ob/ob mice. These findings support the hypothesis that central melanocortin signaling regulates hepatic lipid metabolism in part by regulating de novo lipogenesis. Impairments in the central melanocortin signaling lead to the development of hepatic steatosis, while enhanced melanocortin signaling may be beneficial in reversing abnormal hepatic lipid metabolism in fatty liver disease (Poritsanos et al., 2008). These findings also support the hypothesis that Fto is expressed in the hypothalamic melanocortinergic neurons and is regulated by metabolic signals involving changes in CNS glucose availability and/or glucose action. Impairments in this regulation may cause metabolic impairments including obesity and fatty liver disease.

The ratio of auxin to cytokinin determines de novo organogenesis in plants. Relatively little is known about the effect of genetically altered auxin signaling on in vitro organogenesis. Here, callusogenesis, shoot, and root formation were studied in loss- (LOF) and gain-of-function (GOF) alleles in two phylogenetically related Auxin Response Factors (ARFs), MONOPTEROS (MP/ARF5) and NON-PHOTOTROPHIC HYPOCOTYL 4 (NPH4/ARF7). Reduced MP activity greatly diminished shoot regeneration, and partially diminished callusogenesis and root formation. LOF in NPH4 strongly decreased callusogenesis, and mildly decreased shoot and root regeneration in particular categories of explants. By contrast, organogenesis responses were strongly increased in aerial explants carrying the GOF transgene dMP. Thus, both MP and NPH4 seem to act as positive regulators of certain organogenesis processes and the GOF dMP transgene may be of interest for stimulating organogenesis in plant species with poor regeneration properties. Also, organogenesis in vitro may reveal unknown developmental ARF functions.

The ratio of auxin to cytokinin determines de novo organogenesis in plants. Relatively little is known about the effect of genetically altered auxin signaling on in vitro organogenesis. Here, callusogenesis, shoot, and root formation were studied in loss- (LOF) and gain-of-function (GOF) alleles in two phylogenetically related Auxin Response Factors (ARFs), MONOPTEROS (MP/ARF5) and NON-PHOTOTROPHIC HYPOCOTYL 4 (NPH4/ARF7). Reduced MP activity greatly diminished shoot regeneration, and partially diminished callusogenesis and root formation. LOF in NPH4 strongly decreased callusogenesis, and mildly decreased shoot and root regeneration in particular categories of explants. By contrast, organogenesis responses were strongly increased in aerial explants carrying the GOF transgene dMP. Thus, both MP and NPH4 seem to act as positive regulators of certain organogenesis processes and the GOF dMP transgene may be of interest for stimulating organogenesis in plant species with poor regeneration properties. Also, organogenesis in vitro may reveal unknown developmental ARF functions.

Cette thèse concerne le développement de complexes de lanthanide et leur utilisation pour résoudre les structures de macromolécules biologiques par diffraction des rayons X, en particulier celles de protéines membranaires et de complexes protéiques de grande taille. Les complexes de lanthanide sont formés d'un atome de lanthanide et d'un ligand chimique qui assure une liaison non-covalente avec les surfaces protéiques. Introduits dans les cristaux de protéine, ces derniers constituent une sous-structure qui, déterminée par les méthodes de phasage de novo courantes, permet de résoudre la structure de la macromolécule d'intérêt. La première partie de ce travail de thèse est une étude menée sur la grande famille des complexes picolinates de lanthanide, complexes luminescents dont la fixation au sein des cristaux est aisément décelable. En premier lieu, nous avons défini les conditions dans lesquelles le complexe tris-dipicolinate de lanthanide peut être utilisé ainsi que ses éventuelles capacités à promouvoir la cristallisation (effet supramoléculaire). En second lieu, un nouveau complexe, dérivé du précédent, a été développé au cours de cette thèse : le tris-hydroxymethyltriazoledipicolinate de lanthanide (" [Ln(TDPA)3]3- "). Il nous a permis de réaliser un phasage de novo très précis conduisant à la détermination des structures du lysozyme de blanc d'œuf de poule et de la thaumatine de Thaumatococcus daniellii à haute résolution. Par ailleurs, différents ligands pour ce nouveau complexe ont été synthétisés par chimie-click, nous permettant de créer une panoplie de complexes uniques et des complexes hybrides. Nous avons montré que cette nouvelle famille de complexes présente une meilleure affinité pour les protéines permettant leur utilisation à de faibles concentrations. Les essais menés avec ces LnTDPA ont aussi permis d'entrevoir l'importance de la charge globale pour expliquer l'effet supramoléculaire. En troisième lieu, un tripicolinate cagé, le LnTNTPA, a également été évalué. Constitué d'une cage chimique de charge globale nulle, nous avons montré que ce nouveau complexe luminescent est le seul de cette famille picolinate qui puisse être utilisé en présence d'ions divalents. Dans la seconde partie de cette thèse, nous décrivons l'utilisation des complexes de lanthanide pour le phasage de protéines multimériques de grandes tailles par les méthodes de phasage de novo. Premièrement, la structure de l'aminopeptidase dodécamérique PhTET1-12s de 480 kDa a été déterminée à 4 Å de résolution à l'aide du tris-dipicolinate d'europium. Ceci nous a permis de démontrer que les complexes de lanthanide peuvent être utilisés pour obtenir un phasage précis, même à basse résolution. Deuxièmement, les complexes de lanthanide issus de l'imagerie médicale ont aussi permis de déterminer la structure de trois nouvelles enzymes homotétramériques de la famille des malate déshydrogénases. Ces structures permettent d'apporter de nouveaux éclaircissements sur l'adaptation halophile. Enfin, en utilisant ces enzymes en tant que bibliothèque de fonctions chimiques, nous avons pu mettre en place une nouvelle approche méthodologique pour comprendre finement les modes d'interaction des complexes de lanthanide.

L'information géographique et ses outils informatiques avec les Systèmes d'Informations Géographiques font figure aujourd'hui d'éléments incontournables pour l'aménagement et la gestion des territoires. Le travail mené s'applique à interroger leur place dans les modalités de gouvernement des territoires et de définition des politiques d'action publique dans les villes des pays des Suds. A partir d'une étude de cas menée sur la région urbaine littorale du Bénin, dans un contexte de présence accrue des agences internationales de développement, on analyse les jeux d'acteurs et les imbrications d'échelles (internationale, nationale, régionale, communale et locale) suscités par la production, l'accès et l'utilisation pratique de cette information et ses outils. Les intérêts de cette recherche se situent au croisement des problématiques de gestion des territoires à l'ère de la mondialisation avec l'essor et la vulgarisation des techniques professionnelles et d'accès à l'information et de la décentralisation et municipalisation censée encourager le rôle des pouvoirs locaux dans le processus de développement des territoires. Cette étude questionne cependant l'adaptabilité de modèles du Nord vers le Sud et leurs possibilités d'appropriations locales : capacité de résistance, de cohabitation et de résilience des valeurs culturelles et des pratiques locales avec les encadrements techniciens et astreignants liés à la diffusion de l'information géographique et ses outils.

The central nervous system (CNS) melanocortin signaling pathway plays a critical role in the regulation of metabolism. However, the regulatory effects of CNS melanocortin signaling on hepatic lipid metabolism and fatty liver disease have not been well established. Although the activity of the CNS melanocortin system is regulated by metabolic signals, the mechanism for this regulation is not fully understood. Variants of the FTO (fat mass and obesity-associated) gene are associated with obesity and FTO is expressed in the hypothalamic neurons including proopiomelanocortin (POMC) neurons. Therefore, it is hypothesized that hypothalamic FTO plays a role in the regulation of metabolism by mediating the effect of metabolic signals on hypothalamic melanocortinergic neurons, and that impairments in this regulation may cause metabolic impairments including obesity and fatty liver disease. Intracerebroventricular (i.c.v.) treatment with SHU9119, a melanocortin antagonist, increased hepatic lipid accumulation and the expression of genes encoding lipogenic enzymes in lean mice. Conversely, i.c.v. treatment with MTII, a melanocortin agonist, reduced the expression of hepatic lipogenic genes in association with reduction in body weight in ob/ob mice, a mouse model of fatty liver disease. Immunohistochemical analysis demonstrated that Fto is co-expressed in both POMC and agouti-related protein (AgRP) neurons in the mouse hypothalamus. Fto mRNA and protein expression was reduced by fasting and increased by glucose treatment in nutritionally important hypothalamic nuclei. Fasting-induced reduction in hypothalamic Fto expression was observed in both lean wild-type and obese ob/ob mice, while the stimulatory effect of glucose on hypothalamic Fto expression was absent in ob/ob mice. These findings support the hypothesis that central melanocortin signaling regulates hepatic lipid metabolism in part by regulating de novo lipogenesis. Impairments in the central melanocortin signaling lead to the development of hepatic steatosis, while enhanced melanocortin signaling may be beneficial in reversing abnormal hepatic lipid metabolism in fatty liver disease (Poritsanos et al., 2008). These findings also support the hypothesis that Fto is expressed in the hypothalamic melanocortinergic neurons and is regulated by metabolic signals involving changes in CNS glucose availability and/or glucose action. Impairments in this regulation may cause metabolic impairments including obesity and fatty liver disease.

Dissertação (Mestrado) - Universidade Federal de Santa Catarina, Centro de Filosofia e Ciências Humanas. / Made available in DSpace on 2012-10-17T01:47:52Z (GMT). No. of bitstreams: 0Bitstream added on 2016-01-08T21:35:23Z : No. of bitstreams: 1 139907.pdf: 20688659 bytes, checksum: 502c0acd624d6914f3e7ec52c30c0d62 (MD5)

Conselho Nacional de Desenvolvimento Científico e Tecnológico / A presente pesquisa do Corpus Hermeticum IV.3-6a trata de um objeto da História do Mundo Contemporâneo do Novo Testamento, da História das Antigas Religiões Mediterrâneas e da História da Filosofia. Sendo assim, objetiva-se analisar a concepção de βαπτίζω [baptizō] em Ὁ Κρατήρ (Corpus Hermeticum IV.3-6a), levando em consideração sua intertextualidade e sua correlação histórico-religiosa. Especificamente, analisa-se a concepção de βαπτίζω neste texto, com o intuito de examinar sua correlação com o hino da Aparição Onírica de Háthor (Estela Wien 8390) e sua intertextualidade, por meio da Alegoria da Cratera, com Timaeus 41D, De somniis II. 183, 190, 249, e Provérbios 9.1-6 (LXX). Em particular, esta pesquisa demonstra que o Corpus Hermeticum IV.3-6a descreve um banquete ou um simpósio (symposium). Ademais, ao cotejar frases em que ocorrem os verbos ϰεράννυμι e μίγνυμι em relação ao ϰρατήρ, percebe-se que a acepção do verbo βαπτίζω, na frase βάπτισον σεαυτὴν ἡ δυναμένη εἰς τοῦτον τὸν ϰρατῆρα (do Corpus Hermeticum IV.4a), significa misturar. Por último, a presente pesquisa afirma que o verbo βαπτίζω, nessa frase, com sentido de misturar, tem influência egípcia e correspondência com a palavra jʻj e a palavras tḫ e suas derivações. / The current inquiry into the Corpus Hermeticum IV.3-6a deals with an object of the History of the Contemporary World of the New Testament, the History of the Ancient Mediterranean Religions and the History of Philosophy. As such, it aims to analyze the conception of βαπτίζω [baptizo] in Ὁ Κρατήρ (Corpus Hermeticum IV.3-6a), taking into account its intertextuality and its religious-historical correlation. Specifically, the conception of βαπτίζω is analyzed in this text, with the intention of examining its correlation with the hymn of the Dreamlike Apparition of Hathor (Stela Wien 8390) and its intertextuality, through the Allegory of the Crater, with Timaeus 41D, De Somniis II. 183, 190, 249, and Proverbs 9.1-6 (LXX). In particular, this inquiry demonstrates that the Corpus Hermeticum IV.3-6a describes a banquet or symposium. Moreover, comparing sentences in which the verbs ϰεράννυμι and μίγνυμι take place in connection with ϰρατήρ, one perceives that the sense of the verb βαπτίζω, in the sentence βάπτισον σεαυτὴν ἡ δυναμένη εἰς τοῦτον τὸν ϰρατῆρα (of the Corpus Hermeticum IV.3-6a), means to mix. Finally, the present inquiry asserts that the verb βαπτίζω, in this sentence, with the sense of mixing, has Egyptian influence and correspondence with the word jʻj and the word tḫ and its derivations.

Submitted by Johnny Rodrigues (johnnyrodrigues@ufcg.edu.br) on 2018-09-12T18:06:44Z No. of bitstreams: 1 PEDRO PEREIRA LEMOS - DISSERTAÇÃO PPGERR 2003..pdf: 28952758 bytes, checksum: df8ecb426b59c6b5466e978c5859fbab (MD5) / Made available in DSpace on 2018-09-12T18:06:44Z (GMT). No. of bitstreams: 1 PEDRO PEREIRA LEMOS - DISSERTAÇÃO PPGERR 2003..pdf: 28952758 bytes, checksum: df8ecb426b59c6b5466e978c5859fbab (MD5) Previous issue date: 2003 / O problema da má distribuição de terras no Brasil sempre serviu de motivação para movimentos sociais, pesquisadores e para a promoção de políticas no sentido de solucioná-lo ou, pelo menos, amenizá-lo. Em 1998 o governo brasileiro lançou um programa inovador de reforma agrária: o Fundo de Terras e da Reforma Agrária - Banco da Terra, que propõe a compra de terra através de negociação direta entre beneficiários e o proprietário. E a chamada reforma agrária de mercado. O problema central deste trabalho é o estudo desse novo instrumento de reforma agrária, destacando-se alguns aspectos de seu funcionamento no Estado da Paraíba. Para isto realizamos pesquisas bibliográficas em livros, artigos, relatórios e sites da Internet, participamos de reuniões de sindicatos, fizemos visitas e entrevistas na secretaria do Banco da Terra e do INCRA na Paraíba. Verificamos que a luta pela terra é histórica no Brasil e apresenta novos elementos ao longo do tempo, enriquecendo a discussão. De fato, pouco se tem avançado no sentido de superar a má distribuição de terras no Brasil. O Banco da Terra surge dentro do contexto macroeconômico neoliberal do governo Fernando Henrique Cardoso, delegando ao mercado a tarefa de resolver um problema histórico. Na Paraíba o Programa foi implantado em 2000, e podemos perceber alguns problemas em sua atuação: contribui para o encarecimento do preço da terra; juntamente com outros instrumentos, desmobiliza os movimentos de luta pela terra; além disso, tudo leva a crer que os beneficiários, na sua maioria, não terão condições de pagar os financiamentos contraídos. Contudo, esse ainda não é o principal instrumento de reforma agrária na Paraíba como suspeitava-se. Nos moldes atuais o Banco da Terra não é uma boa alternativa, principalmente para regiões com dificuldades climáticas como a Nordeste e não visa corrigir uma exclusão histórica nem assegurar a subsistência dos beneficiários. É um programa regido e direcionado para o mercado. / In Brazil the unfair land distribution has been a reason of social struggle, which focuses on the attempt of sorting it out. Researchers have been committed in promoting policies to either solve the matter, or reduce it. In 1998, the Brazilian Government initiated a new land reform program The "Fundo de Terras e da Reforma Agrária - Banco da Terra" (Land Fund and Land Reform) is intended to buying land through direct negotiations between proprietors and beneficiaries This is known as the Market-Assisted Land Reform. The main goal of this work is to study this new land reform tool, highlighting some of its operating aspects in the State of Paraíba. In order to do so, we had to do reserches on books, textbooks, articles, reports, internet sites, etc. We also attended meetings at local labor syndicates, visited some locations where the program is in place, and interviewed personnel concerned, at Secretaria do Banco da Terra e do INCRA, in Paraiba. We noticed that the unfair land distribution system is a historical issue in Brazil but, along time, it has shown new elements, enhancing the subject under discussion. As a matter of fact, when it comes to solving the land distribution point, very little concrete measure have been achieved to overcome the situation. Banco da Terra comes up from a macroeconômica!and neoliberal context by the government of President Fernando Henrique Cardoso. In brief, it hands over to the market the task of solving this historical problem. In Paraíba, the program was implemented in 2000. However, we could detect some negative results in its performance. The land price has become more expensive, and, in cooperation with other instalments, it dismantles the organized struggle that the Landless have towards land. Moreover, everything indicates that most of the beneficiaries will not be able to pay off the acquired financing debts. Even though, in contrast to what we used to believe, this is still not the main concern regarding land distribution in Paraíba. At present, Banco da Terra does not seem to be a good alternative, especially for regions that suffer from weather difficulties, as the Northeast does It is not the goal of the Bank to either correct an unfair and historical process or ensure means of providing a better life to the beneficiaries. In other words, it is a program that is maintained, managed and directed to the market