Submitted by Luanna Matias (lua_matias@yahoo.com.br) on 2015-02-04T19:08:20Z No. of bitstreams: 3 Tese - Pablo Santana Santos - 2014 - Parte 01.pdf: 5282585 bytes, checksum: fab627afa4b6a3b55752f51b90659610 (MD5) Tese - Pablo Santana Santos - 2014 - Parte 02.pdf: 3067324 bytes, checksum: d46d29a129169e109e2f94a8068ec633 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-02-05T09:54:10Z (GMT) No. of bitstreams: 3 Tese - Pablo Santana Santos - 2014 - Parte 01.pdf: 5282585 bytes, checksum: fab627afa4b6a3b55752f51b90659610 (MD5) Tese - Pablo Santana Santos - 2014 - Parte 02.pdf: 3067324 bytes, checksum: d46d29a129169e109e2f94a8068ec633 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2015-02-05T09:54:10Z (GMT). No. of bitstreams: 3 Tese - Pablo Santana Santos - 2014 - Parte 01.pdf: 5282585 bytes, checksum: fab627afa4b6a3b55752f51b90659610 (MD5) Tese - Pablo Santana Santos - 2014 - Parte 02.pdf: 3067324 bytes, checksum: d46d29a129169e109e2f94a8068ec633 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-05-15 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / The agricultural expansion in the Brazilian Cerrado represents nowadays more than half of the total biome area, where conversion of the natural vegetation to pasturelands is the main dynamics imposed by the productive sector along the relatively recent historical occupation process. Such transformations tend to create distinct spatial patterns regarding the biophysical behavior of the main existent vegetation formations, which can be identified and discriminated through a variety of available remote sensing products. This study, focused on the rio Vermelho watershed, a representative unit of the Cerrado biome, and considering a variety of satellite data for the 2001 – 2011 period, pursued a detailed analysis of the biophysical responses in face of the historical processes that determined and shaped the landscape transformations. Specifically, the following datasets were utilized: MODIS (vegetation index, evapotranspiration and primary productivity) and TRMM (Tropical Rainfall Measurement Mission) precipitation. Our results indicated that climatic factors, such as seasonality, have a direct influence on biomass levels of key vegetation formations, particularly those with shallow root systems, for which reductions in radiometric values, as high as 50%, could be observed during the dry season. In fact, natural vegetation areas, comparatively to areas dominated by cultivated pastures, show very distinct and significant biophysical behavior (p < 0.05). Likewise, two major landscapes could be identified, i.e. “Region 1” and “Region 2”, where converted and remnant vegetation areas predominate, respectively. The distribution of natural and cultivated pastures seems to be related to local edafoclimatic factors, such as soil (depth/lithic content) and water availability, which explain the occurrence of most grass species. Based on field biomass, it is possible to say: 1) cultivated pastures found in “Region 1” are slightly more productive comparatily to those from “Region 2” (for both dry- and wet-seasons) and 2) there is a correspondence between “natural” and “cultivated” green biomass during the dry season, as opposed to the wet season. However, and based on the seasonal moderate spatial resolution MODIS images, it is not possible to separate between natural and cultivated pastures. In fact, such separation can be accomplished via the supervised classification (Support Vector Machine) of medium spatial resolution imagery (Landsat). Based on high spatial resolution (5m) RapidEye/BlackBridge images, it was produced a land cover / land use map for the entire basin at the 1:50.000 scale, in which it was possible to discriminate the major converted and natural physiognomies, and distinct grass species, in particular (Overall Accuracy ~ 90% and Kappa = 0.83). / A expansão da atividade agropecuária no Cerrado brasileiro representa hoje mais da metade da área total deste bioma, onde a conversão das áreas naturais em pastagens cultivadas foi a principal dinâmica imposta pelo setor produtivo ao longo de um processo histórico de ocupação relativamente recente. Tais transformações tendem a resultar em padrões espaciais distintos quanto ao comportamento biofísico das principais formações vegetais existentes, os quais podem ser identificados e discriminados através dos vários produtos de sensoriamento remoto disponíveis. O presente trabalho, ao utilizar a bacia hidrográfica do rio Vermelho como unidade experimental do bioma Cerrado, teve como objetivo principal realizar uma análise detalhada das respostas biofísicas frente aos processos históricos que condicionaram as transformações na paisagem, considerando o período entre 2001 a 2011, e uma ampla base de dados satelitária, obtida a partir dos produtos MODIS (índice de vegetação, evapotranspiração, produtividade primária) e TRMM (Tropical Rainfall Measurement Mission/precipitação). Os nossos resultados evidenciam que fatores climáticos, a exemplo da sazonalidade, tem uma influência direta na biomassa das principais formações vegetais, principalmente àquelas que apresentam sistemas radiculares superficiais, com reduções nos valores radiométricos de até 50% durante o período da seca. De forma significativa, as áreas de vegetação natural, comparadas às áreas de pastagens cultivadas, apresentaram comportamentos distintos do ponto de vista biofísico (p < 0,05). Em fato, dois macroambientes puderam ser definidos para a área de estudo, onde predominam a ocupação antrópica (“Região 1”) e a vegetação natural remanescente (Região 2), respectivamente. A distribuição das pastagens cultivadas e naturais está associada a fatores edafoclimáticos locais, como características de solo (profundidade/pedregosidade) e disponibilidade hídrica, os quais explicam a ocorrência da maioria das espécies forrageiras. Com base nos dados de biomassa coletados em campo, é possível afirmar: 1) as pastagens cultivadas encontradas na “Região 1” são ligeiramente mais produtivas do que as encontradas na “Região 2”, tanto no período seco quanto chuvoso, e 2) há uma correspondência entre a biomassa verde encontrada no período seco para as duas categorias de pastagens, ao contrário do observado no período chuvoso. Entretanto, e tendo por base as imagens biofísicas sazonais de resolução espacial moderada (MODIS), não é possível separar entre pastagens nativas e cultivadas. Por sua vez, esta separação se mostra possível através da classificação supervisionada (Support Vector Machine) de imagens de resolução espacial média (Landsat). Com base em imagens RapidEye/BlackBridge, com resolução espacial de 5m, foi produzido um mapa de cobertura e uso da terra à escala de 1:50.000, no qual foi possível separar as áreas de pastagens quanto à sua tipologia, bem como individualizálas em outras formas de uso e fito-fisionomias remanescentes (Acurácia Total ~ 90% e Kappa = 0,83).

2'-5'-oligoadenylate synthetases (OAS) are interferon-stimulated proteins that act in the innate immune response to viral infection. Upon binding to viral double-stranded RNAs, OAS enzymes produce 2'-5'-linked oligoadenylates that stimulate RNase L and ultimately slow viral propagation. Studies have linked mutations in the OAS1 gene to increased susceptibility to West Nile virus (WNV) infection, highlighting the importance of the OAS1 enzyme. Here I report that the 5'-terminal region (5'-TR) of the WNV genome, comprising both the 5'-untranslated region (5'-UTR) and initial coding region, is capable of OAS1 activation in vitro. This region contains three RNA stem loops (SLI, SLII, and SLIII), whose relative contribution to OAS1 binding affinity and activation were investigated using electrophoretic mobility shift assays and enzyme kinetics experiments. Stem loop I (SLI) is dispensable for maximum OAS1 activation, as a construct containing only SLII and SLIII was capable of enzymatic activation. Mutations to the RNA binding site of OAS1 confirmed the specificity of the interaction. Solution conformations of both the 5'-TR RNA of WNV and OAS1 were then elucidated using small-angle x-ray scattering. I also report that the 3' terminal region (3'-TR) is able to mediate specific interaction with and activation of OAS1. Binding and kinetic experiments identified a specific stem loop within the 3'-TR that is sufficient for activation of the enzyme. The solution confirmation of the 3'-terminal region was determined by small angle X-ray scattering, and computational models suggest a conformationally restrained structure comprised of a helix and short stem loop. Structural investigation of the 3'-TR in complex with OAS1 is also presented. Finally, we show that genome cyclization by base pairing between the 5'- and 3'-TRs, a required step for replication, is not sufficient to protect WNV from OAS1 recognition. The purity, monodispersity and homogeneity of all samples subjected to SAXS analysis were evaluated using dynamic light scattering and/or analytical ultra-centrifuge. These data provide a framework for understanding recognition of the highly structured terminal regions of a flaviviral genome by an innate immune enzyme. / October 2015

Dans un contexte de changement climatique global et d'évolution locale de l'usage des terres, le devenir des paysages culturels des Alpes françaises, façonnés au cours des siècles par les interactions mutuelles entre sociétés et environnement, apparaît incertain. Dans le même temps, les écosystèmes qui les constituent abritent une biodiversité riche et sont à l'origine de nombreuses ressources naturelles et fonctions écologiques dont bénéficient les populations humaines. Ces ressources et fonctions sont conceptualisées sous le terme de « services écosystémiques » et font aujourd'hui l'objet d'une attention accrue dans la gestion et la protection des ressources environnementales, au même titre que la biodiversité. L'identification des facteurs liés à leur maintien, en termes écologiques, socio-culturels et politiques, est une étape nécessaire à leur gestion durable, bien qu'encore insuffisamment explorée. Mon projet de thèse visait à accroître la compréhension des interactions positives (synergies) et négatives (antagonismes) entre services écosystémiques et biodiversité via une approche multidimensionnelle du socio-écosystème des Alpes françaises. - Le Chapitre I propose une approche biophysique quantitative et spatialisée de la multifonctionnalité des écosystèmes. Suite à une étape de modélisation, les patrons spatiaux de synergie et d'antagonisme entre services et biodiversité ont été explorés statistiquement et reliés à des enjeux de gouvernance actuels à différentes échelles. Ce travail a permis d'identifier les bouquets de services écosystémiques représentatifs des différentes conditions biogéographiques, de gestion et de d'hétérogénéité du paysage représentées dans le massif. - Cette approche est complétée dans le Chapitre II par une représentation qualitative des relations d'influence entre services écosystémiques et biodiversité, ainsi que de leurs liens avec d'autres variables écologiques et sociales. Nous avons considéré explicitement les dimensions multiples englobées par le concept de service écosystémique (leurs ‘facettes') et proposons un cadre conceptuel pour en cartographier les réseaux d'influence. Ce cadre a servi de base à l'analyse d'un processus consultatif que nous avons mené auprès d'acteurs du territoire. Les analyses ont mis en lumière leur perception globale des relations d'influence importantes au sein du socio-écosystème. - Afin de mieux comprendre les régulations sociales appliquées à la gestion environnementale, nous testons dans le Chapitre III une méthodologie d'analyse de l'efficacité environnementale d'instruments de gouvernance. Notre analyse a privilégié un nombre restreint d'instruments qui encadrent actuellement les interactions entre agriculture, tourisme et biodiversité. L'utilisation d'un ensemble d'indicateurs de performance et d'adéquation avec le cadre socio-culturel et de gouvernance a souligné l'articulation complexe des instruments entre eux et a abouti à la production d'une synthèse pour les décideurs (‘policy brief'). - Le Chapitre IV explore enfin certains enjeux conceptuels et éthiques de la recherche dans le domaine des services écosystémiques. Après une réflexion générale sur les relations entre science et société, je propose une évaluation réflexive et personnelle des projets de recherche auxquels j'ai contribué. Pour conclure, je propose une vision transversale du socio-écosystème alpin mettant en lumière les enjeux majeurs identifiés par les différentes analyses. / In the context of global climate change and local land use changes, the future of the French Alps cultural landscapes, shaped through long-lasting and mutual interactions between human and their environment, appears uncertain. Simultaneously, the ecosystems constituting alpine landscapes host a rich biodiversity and provide the many natural resources and ecological functions that benefit to human societies. These resources and functions are conceptualised as “ecosystem services” and currently attract an increasing attention for the management and the conservation of environmental resources, along with biodiversity. Identifying the variables linked to their maintenance, in ecological, socio-cultural and political terms, is a necessary step of their sustainable management, and yet is still under-explored. My PhD project aimed at increasing the understanding of positive (synergies) and negative (trade-offs) interactions among ecosystem services and biodiversity through a multi-dimensional approach of the French Alps social-ecological system. - In Chapter I, I present a quantitative and spatially explicit biophysical assessment of ecosystem multifunctionality. After a modelling step, we explored spatial patterns of trade-offs and synergies among ecosystem services and biodiversity using a series of statistical analyses of increasing complexity. Results were structured to provide insights for sound environmental governance at multiple scales. We identified various bundles of ecosystem services representative of the different conditions across the French Alps massif in terms of biogeography, management and landscape heterogeneity. - This approach is complemented in Chapter II by a qualitative representation of influence relationships among ecosystem services and biodiversity that also accounts for additional ecological and social variables. We explicitly considered the multiple dimensions encompassed by the ecosystem service concept (their ‘facets') and proposed an innovative conceptual framework to represent their influence networks. This framework was applied to analyse a consultative process that we carried out with stakeholders of regional expertise. This analysis highlighted their general perception of important influence relationships in the alpine social ecological system. - In order to better understand social regulations linked to environmental governance, we test in Chapter III a methodology for assessing the environmental effectiveness of policy instruments. We concentrated on a restricted set of instruments regulating the interactions between biodiversity, agriculture and outdoor tourism. The consideration of multiple indicators assessing the performance and the fit with the socio-cultural and governance setting highlighted the complex articulation of instruments within the broader policy mix. Results were synthesised in a policy brief targeting regional decision-makers. - Chapter IV is conceived as my personal exploration of the conceptual and ethical issues linked to research on ecosystem services. Following some general thinking on the relations between environmental sciences and society, I conducted a personal reflexive assessment of the research projects I contributed to. To conclude, I propose a synthetic vision of the alpine social-ecological system and discuss the major issues revealed throughout the analyses.

Dans un contexte de changement climatique global et d'évolution locale de l'usage des terres, le devenir des paysages culturels des Alpes françaises, façonnés au cours des siècles par les interactions mutuelles entre sociétés et environnement, apparaît incertain. Dans le même temps, les écosystèmes qui les constituent abritent une biodiversité riche et sont à l'origine de nombreuses ressources naturelles et fonctions écologiques dont bénéficient les populations humaines. Ces ressources et fonctions sont conceptualisées sous le terme de « services écosystémiques » et font aujourd'hui l'objet d'une attention accrue dans la gestion et la protection des ressources environnementales, au même titre que la biodiversité. L'identification des facteurs liés à leur maintien, en termes écologiques, socio-culturels et politiques, est une étape nécessaire à leur gestion durable, bien qu'encore insuffisamment explorée. Mon projet de thèse visait à accroître la compréhension des interactions positives (synergies) et négatives (antagonismes) entre services écosystémiques et biodiversité via une approche multidimensionnelle du socio-écosystème des Alpes françaises. - Le Chapitre I propose une approche biophysique quantitative et spatialisée de la multifonctionnalité des écosystèmes. Suite à une étape de modélisation, les patrons spatiaux de synergie et d'antagonisme entre services et biodiversité ont été explorés statistiquement et reliés à des enjeux de gouvernance actuels à différentes échelles. Ce travail a permis d'identifier les bouquets de services écosystémiques représentatifs des différentes conditions biogéographiques, de gestion et de d'hétérogénéité du paysage représentées dans le massif. - Cette approche est complétée dans le Chapitre II par une représentation qualitative des relations d'influence entre services écosystémiques et biodiversité, ainsi que de leurs liens avec d'autres variables écologiques et sociales. Nous avons considéré explicitement les dimensions multiples englobées par le concept de service écosystémique (leurs ‘facettes') et proposons un cadre conceptuel pour en cartographier les réseaux d'influence. Ce cadre a servi de base à l'analyse d'un processus consultatif que nous avons mené auprès d'acteurs du territoire. Les analyses ont mis en lumière leur perception globale des relations d'influence importantes au sein du socio-écosystème. - Afin de mieux comprendre les régulations sociales appliquées à la gestion environnementale, nous testons dans le Chapitre III une méthodologie d'analyse de l'efficacité environnementale d'instruments de gouvernance. Notre analyse a privilégié un nombre restreint d'instruments qui encadrent actuellement les interactions entre agriculture, tourisme et biodiversité. L'utilisation d'un ensemble d'indicateurs de performance et d'adéquation avec le cadre socio-culturel et de gouvernance a souligné l'articulation complexe des instruments entre eux et a abouti à la production d'une synthèse pour les décideurs (‘policy brief'). - Le Chapitre IV explore enfin certains enjeux conceptuels et éthiques de la recherche dans le domaine des services écosystémiques. Après une réflexion générale sur les relations entre science et société, je propose une évaluation réflexive et personnelle des projets de recherche auxquels j'ai contribué. Pour conclure, je propose une vision transversale du socio-écosystème alpin mettant en lumière les enjeux majeurs identifiés par les différentes analyses. / In the context of global climate change and local land use changes, the future of the French Alps cultural landscapes, shaped through long-lasting and mutual interactions between human and their environment, appears uncertain. Simultaneously, the ecosystems constituting alpine landscapes host a rich biodiversity and provide the many natural resources and ecological functions that benefit to human societies. These resources and functions are conceptualised as “ecosystem services” and currently attract an increasing attention for the management and the conservation of environmental resources, along with biodiversity. Identifying the variables linked to their maintenance, in ecological, socio-cultural and political terms, is a necessary step of their sustainable management, and yet is still under-explored. My PhD project aimed at increasing the understanding of positive (synergies) and negative (trade-offs) interactions among ecosystem services and biodiversity through a multi-dimensional approach of the French Alps social-ecological system. - In Chapter I, I present a quantitative and spatially explicit biophysical assessment of ecosystem multifunctionality. After a modelling step, we explored spatial patterns of trade-offs and synergies among ecosystem services and biodiversity using a series of statistical analyses of increasing complexity. Results were structured to provide insights for sound environmental governance at multiple scales. We identified various bundles of ecosystem services representative of the different conditions across the French Alps massif in terms of biogeography, management and landscape heterogeneity. - This approach is complemented in Chapter II by a qualitative representation of influence relationships among ecosystem services and biodiversity that also accounts for additional ecological and social variables. We explicitly considered the multiple dimensions encompassed by the ecosystem service concept (their ‘facets') and proposed an innovative conceptual framework to represent their influence networks. This framework was applied to analyse a consultative process that we carried out with stakeholders of regional expertise. This analysis highlighted their general perception of important influence relationships in the alpine social ecological system. - In order to better understand social regulations linked to environmental governance, we test in Chapter III a methodology for assessing the environmental effectiveness of policy instruments. We concentrated on a restricted set of instruments regulating the interactions between biodiversity, agriculture and outdoor tourism. The consideration of multiple indicators assessing the performance and the fit with the socio-cultural and governance setting highlighted the complex articulation of instruments within the broader policy mix. Results were synthesised in a policy brief targeting regional decision-makers. - Chapter IV is conceived as my personal exploration of the conceptual and ethical issues linked to research on ecosystem services. Following some general thinking on the relations between environmental sciences and society, I conducted a personal reflexive assessment of the research projects I contributed to. To conclude, I propose a synthetic vision of the alpine social-ecological system and discuss the major issues revealed throughout the analyses.