O desmatamento se faz presente na história do Brasil desde a era colonial. Dados recentes evidenciam que o cenário só piorou nos últimos anos, especialmente no bioma da Mata Atlântica. No estado de São Paulo a cobertura por florestas decaiu de 80% para apenas 16,3% em um período de tempo relativamente curto. O processo de desmatamento resultou um grande arquipélago de pequenos fragmentos florestais sem conexão. Criou-se assim uma necessidade de se identificar os efeitos da fragmentação florestal e entender qual a relação existente entre esses remanescentes e o seu entorno. A importância dos efeitos da matriz circundante sobre os fragmentos tem implicação direta sobre as estratégias de conservação nas paisagens fragmentadas. Neste trabalho objetivou-se avaliar o efeito de borda de fragmentos florestais divididos em duas classes de tamanho e analisar como diferentes tipos de ocupação antrópica influenciam no estado de manutenção da biodiversidade e nos estoques de carbono, partindo do pressuposto de que diferentes tipos de matrizes influenciam o efeito de borda de maneira distinta. Foram analisadas as seguintes situações de interface: 1. cana-de-açúcar, 2. pastagem e 3. eucalipto, presentes no entorno de fragmentos de floresta Estacional Semidecidual localizados no município de Piracicaba-SP. O intuito desta pesquisa foi verificar quais situações são mais ou menos favoráveis à proteção do fragmento, verificando as alterações de estrutura, composição florística e estoques de carbono e biomassa. No contexto, analisou-se os principais mapeamentos existentes de uso e ocupação do solo do município de Piracicaba, verificando a porcentagem de áreas de floresta, cana-de-açúcar, pastagens e plantios monoculturais de eucalipto. Os fragmentos avaliados apresentaram claros indícios de efeito de borda até os 50 m. A interface de eucalipto apresentou maior riqueza de espécies e maior estabilidade de estoque de carbono na borda e no centro. Quanto à composição da paisagem, há a predominância do componente agropecuário no município de Piracicaba. A quase totalidade destes remanescentes estão circundados por estas ocupações, havendo pouca ou nenhuma conexão entre eles. Procura-se assim verificar a possibilidade de se utilizar as áreas de produção também como forma de preservação. / Deforestation is present in Brazil\'s history since colonial era. Recent data shows that the scenario has worsened in the last years, especially in the Atlantic Forest biome. In São Paulo the coverage by forests declined from 80% to only 16,3% over a relatively short time. The deforestation process resulted in a large archipelago of small forest fragments with no connection. Thus, has created a need to identify the effects of forest fragmentation and understand which is the relationship between these remains and their surrounding. The importance of the effects of the surrounding matrix on the fragments have direct implications on strategies for conservation in fragmented landscapes. This study aimed to evaluate the effect of edge of forest fragments divided into two size classes and analyze how different types of anthropic occupation influence in maintenance of biodiversity and carbon stocks, on the assumption that different types of matrices influence the effect of edge differently. The following interface situations was analyzed: 1. sugar cane, 2. grassland and 3. eucalyptus, present in around of seasonal semideciduous forest fragments, located in Piracicaba-SP. The purpose of this research was to verify which situations are more or less favorable to the protection of the fragment, checking the structural alterations, floristic composition and carbon and biomass\' stocks. In addition, was analyzed the main mapping of land use and occupation of the municipality of Piracicaba, verifying the percentage of areas of forest, sugarcane, pasture and monoculture eucalyptus plantations. The fragments evaluated presented clear signs of edge effect up to 50 m. The eucalyptus interface presented greater species richness and greater stability of carbon stock at the edge and at the center. Regarding the composition of the landscape, there is predominance of the agricultural component (sugar cane and pasture) in the municipality of Piracicaba. Almost all of these remnants are surrounded by these occupations, with little or no connection between them. This study seeks to verify the possibility of using the production areas also as a way of preservation.

Master of Science / Department of Physics / Itzhak Ben-Itzhak / Ultrafast lasers allow us to study molecular dynamics on their natural timescale. The electronic dynamics can be studied using attosecond pulses, while the vibrational and rotational dynamics can be probed using tens of femtosecond and picosecond laser pulses, respectively. This capability has led to a broad understanding of the electronic dynamics in atoms and molecules as well as vibrational and rotational dynamics of molecules, which is one of the important goals in basic science. Moreover, it is possible to control quantum mechanical processes using ultrafast intense lasers. In this thesis, we focus on a couple of experiments. The first involves quantum control of the formation of neutral molecular fragments while the second focuses on three-body fragmentation of molecules employing the native-frames analysis method, which was recently introduced by our group [J. Rajput et al., Phys. Rev. Lett. 120, 103001 (2018)]. Experimental studies focused on the formation of excited neutral D fragments from D2 molecules are presented. We show that by manipulating the chirp of the intense laser pulses, i.e. the “time order” of the frequency components within the pulse, the formation of these fragments is controlled. To achieve this control we implement a single-prism compressor to manipulate the chirp of the laser pulses. Three-body fragmentation of CO₂ resulting in C+ + O+ + O+ is also studied. We show that if the two bonds break in a two-step process, i.e. a sequential breakup, the pathways from which the two identical O+ fragments originate can be separated using the native-frames analysis method. In contrast, the two O+ fragments cannot be distinguished if the two C-O bonds break simultaneously.

A partir do novo século, dinâmicas de dispersão urbana diferenciadas, relacionadas com os avanços da econômica capitalista, alteram os padrões de ocupação do tecido urbano ao longo do vetor noroeste paulista, eixo São Paulo-Campinas. Esse histórico e produtivo corredor, cuja evolução se estrutura em redes de infraestruturas e sobrepõe temporalidades históricas fragmentadas, transformou-se no mais importante vetor econômico do país. Tempos de globalização e reestruturação produtiva avançada configuram novos territórios metropolitanos, que na sua dispersão se integram, redefinindo conceitos e limites instituídos. Com olhar empírico para municípios com formação recente e predomínio de ocupações ligadas à economia moderna, evidenciou-se o impacto destas no tecido urbano deste eixo regional. Formas mais avançadas de urbanização em processo de constituição, extensas, fragmentadas, superpostas, contínuas, dispersas e porosas, apresentam contornos mais nítidos, mas são complexas do ponto de vista dos seus fluxos espaciais. Devido à ausência de planos e políticas públicas mais abrangentes capazes de atuar em novas dimensões, compreendendo a totalidade das relações que este território metropolitano estabelece, elabora-se uma matriz que sistematiza hierarquias e conhecimento, para uma atuação territorial integradora e em múltipla escala. / From the new century, new dynamics of urban sprawl, related to the progress of the capitalist economy, are changing the land use patterns along the northwest vector of São Paulo state capital, São Paulo -Campinas axis. This historical and productive axis, whose evolution is structured in infrastructure networks and overlaps fragmented historical temporalities, has become the most important economic vector of the country. Times of globalization and advanced productive restructuring have shaped new metropolitan territories which, in their sprawl are integrated, redefining concepts and set limits. With focus on small cities, due to their recent formation, the research observed the impact of the greater intensity of tertiary sector occupations linked to the advanced economies in this regional productive axis. More advanced forms of urbanization in the process of constitution, extensive, fragmented, overlapping, continuous, sprawl or diffuse, have more visible boundaries, but are complex from the point of view of their spatial relationships. Based on this and due to the lack of metropolitan and regional public policies that may have a comprehensive and integrated impact on this scattered metropolitan territory, a matrix is elaborated that systematizes hierarchies and knowledge, for an integrative and multiple scale territorial action.

Lyme disease is one of the most common vector-borne diseases around the world, and the numbers of reported cases are quickly rising. Ixodes ticks are the principal vectors, while Borrelia burgdorferi sensu lato genospecies are the etiological agents of the disease. Climate change, namely global warming, and habitat modification, namely forest fragmentation, are hypothesized to play an active role in this rise in reported cases. An analysis of the primary literature, specifically of studies focused on North America and Europe, was conducted in order to investigate these hypotheses. These studies show that global warming has precipitated a growth in tick populations as well as a northward tick migration, thereby increasing the risk of Lyme disease in emergent and endemic areas alike, for Borrelia spirochetes quickly infect naïve tick populations. Furthermore, published studies support the idea that forest fragmentation near human population centers has also increased the risk of Lyme disease in North America, for edge habitats provide suitable conditions for ticks and provide edible vegetation for the animals on which ticks feed, animals which also serve as hosts for B. burgdorferi sensu lato. In contrast, a decrease in fragmentation was found to facilitate tick invasion and establishment in Europe. These studies demonstrate that anthropogenic habitat modifications of varying types can affect ticks and their host populations and increase the risk of Lyme disease near human population centers. However, more research needs to be done to truly understand the different factors that are precipitating the rising number of cases of Lyme disease since there are significant interactions between climate change, habitat modification, and other drivers not examined here. Furthermore, understanding how these drivers function in specific geographic locations can help scientists and public officials tailor local public health measures appropriately. Finally, researchers and pharmaceutical companies must develop a safe, long-lasting, and effective vaccine against the Lyme disease spirochete, for there is not one currently available. Although easily treatable if diagnosed early, Lyme disease can progress to debilitating disease. Unfortunately, the risk of contracting this illness is currently rising and will continue to rise unless effective preventative measures are employed.

Mitochondria are important cellular organelles whose functions include generation of ATP, sequestration and release of pro-apoptotic molecules and calcium buffering. Mitochondria function is tightly linked to organelle morphology, which exits in a dynamic spectrum between a highly interconnected/fused mitochondria network to a punctate/fragmented scattering of individual mitochondrion. A family of large GTPase enzymes modulates this spectrum, with fusion catalyzed through the actions of mitofusin 1 and 2 (Mfn1/2) on the outer mitochondria membrane (OMM) and optic atrophy 1 (Opa1) causing fusion of the inner mitochondria membrane (IMM). On the other end of the spectrum, fragmentation is catalyzed through the actions of dynamin-related protein 1 (Drp1). Drp1 is recruited from the cytosol to binding partners at the OMM, organizes into concentric spiral rings, undergoes GTP hydrolysis to constrict the ring and pinches mitochondrion in two. While fragmentation is achieved through the action of only one GTPase enzyme, the mechanisms behind the complex regulation of Drp1 remain relatively obscure. In order to expand upon known Drp1 regulatory mechanisms, an examination of how both Drp1 splicing and Drp1 recruitment to the OMM contributes to protein regulation is necessary. Drp1 contains three alternatively spliced exons, resulting in the potential generation of eight protein isoforms. Each of these isoforms is capable of inducing mitochondrial fragmentation, however one exon arrangement (termed Drp1-x01) can also bind to microtubules within the cell. Characterization of the Drp1-x01 isoform at both the RNA and protein level indicate an important, yet incompletely characterized, role in immune system biology. Drp1 is capable of interacting with several proteins localized at the OMM. Among these, mitochondria fission factor (Mff) has been implicated in the formation of Drp1 spirals and the eventual fragmentation process. Mff contains four alternatively spliced exons as well as several phosphorylation sites identified through nonbiased phosphoproteomic screens. Inclusion of alternative exons to the Mff structure decreases its ability to recruit Drp1 from the cytosol, while phosphomimetic substitutions to conserved serine residues enhances the Drp1::Mff interaction. Taken together, this suggests that regulation of mitochondrial fragmentation occurs at the pretranslational (alternative splicing) and the posttranslational (phosphorylation) level is critical for maintaining the complex, yet essential, balance between mitochondrial fission and fragmentation.

The primary objective of the studies described in this thesis was to improve the cryopreservation success of koala spermatozoa for the purpose of establishing a genome resource bank for this species. A defining feature of the studies in this thesis was the implementation of an organelle-specific approach to better understand the causes of koala sperm cryo-injury. The functional attributes of spermatozoa, such as mitochondrial function, plasma membrane fluidity, membrane lipid asymmetry and DNA integrity were assessed as an indication of cryo-injury. Sperm mitochondrial function and plasma membrane integrity were examined by cryomicroscopy using the fluorescent probes JC-1 and propidium iodide (PI) respectively in a dual staining technique. Cooling and re-warming koala spermatozoa were more detrimental to mitochondrial function than to plasma membrane integrity. Mitochondrial membrane potential (MMP) was suppressed by freezing and thawing treatments; after thawing, MMP declined significantly during rewarming (from 5ºC to 35ºC). The distribution of GM1 ganglioside was examined using fluorescent-labelled cholera toxin B. No significant redistribution of GM1 was observed after chilling or cryotreatment. The externalisation of phosphatidylserine (PS) was examined using fluorescent-labelled annexin V. There was no significant increase in translocation of PS after chilling or cryopreservation. These observations imply that cryotreatment had little effect on plasma membrane lipid asymmetry. Koala spermatozoa were incubated in a range of anisotonic media to investigate whether nuclear swelling was caused by osmotic flux during the cryopreservation process. Although the most hypotonic solution tested (64 mOsm/kg) induced the highest incidence of nuclear relaxation (mean ± SEM; 12 ± 3%), this was not as severe as that previously documented following cryopreservation. Chromatin relaxation is a phenomenon observed in koala spermatozoa, where the sperm nucleus expands due to the result of structural changes in the natural conformation of the sperm DNA/protamine complex. DNA fragmentation was not a primary cause of cryopreservation-induced sperm chromatin relaxation, although in situ nick translation of putative DNA breaks indicated that these increased as the sperm head became progressively more relaxed. Using a Sperm Chromatin Dispersion test (SCDt) specifically developed and validated for koala spermatozoa, a continuum of nuclear morphotypes was observed, ranging from no apparent DNA fragmentation to spermatozoa with highly dispersed and degraded chromatin. A double comet assay was also developed to investigate DNA fragmentation in the koala spermatozoa. Conducted under neutral followed by alkaline conditions, this assay was able to differentiate between single- (SSB) and double-stranded (DSB) DNA damage in an effort to refine the interpretation of DNA damage in mature koala spermatozoa; the majority of the koala spermatozoa had nuclei with DNA abasic-like residues. The ubiquity of these residues suggested that constitutive alkali-labile sites are part of the structural configuration of the koala sperm nucleus. Spermatozoa with “true” DNA fragmentation exhibited a continuum of comet morphologies, ranging from a more severe form of alkaline-susceptible DNA, to nuclei that exhibited both SSB and DSB. Swelling of koala sperm chromatin following cryopreservation has largely been attributed to the absence of inter-molecular disulphide cross-linkages in the marsupial sperm nucleus. Fish spermatozoa also lack disulphide bonds within their chromatin, but nevertheless, have been successfully cryopreserved. To examine the hypothesis that the cryoprotectants used for fish sperm cryopreservation will confer a similar degree of protection on koala spermatozoa, various concentrations of five cryoprotectants (dimethyl sulphoxide, methanol, propylene glycol, ethylene glycol and dimethylacetamide) were evaluated. Each treatment was compared against an established koala sperm cryopreservation protocol that uses 14% glycerol. Dimethylacetamide at a concentration of 12.5% (v/v) was found to be comparable to glycerol in the successful cryopreservation of koala spermatozoa although high inter-male variability was observed. However, when the new protocol was subsequently validated for a larger population of captive koalas (n = 22), glycerol emerged the better cryoprotectant with respect to all sperm viability parameters assessed except for that of the incidence of chromatin relaxation, which was not affected by the cryoprotectant. Significant difference was also observed in the post-thaw survival of spermatozoa from different animals, which was independent of pre-freeze semen quality. Based on post-thaw semen viability parameters, the koalas could be divided into two distinct groups, where one group had significantly higher sperm viability compared to the other group, regardless of cryoprotectant used. Positive correlation between motility and MMP was observed before and after cryopreservation. However, cryopreservation significantly reduced the dependency between these variables (P < 0.001), suggesting that cryopreservation reduced the dependency between mitochondrial function and motility.

The primary objective of the studies described in this thesis was to improve the cryopreservation success of koala spermatozoa for the purpose of establishing a genome resource bank for this species. A defining feature of the studies in this thesis was the implementation of an organelle-specific approach to better understand the causes of koala sperm cryo-injury. The functional attributes of spermatozoa, such as mitochondrial function, plasma membrane fluidity, membrane lipid asymmetry and DNA integrity were assessed as an indication of cryo-injury. Sperm mitochondrial function and plasma membrane integrity were examined by cryomicroscopy using the fluorescent probes JC-1 and propidium iodide (PI) respectively in a dual staining technique. Cooling and re-warming koala spermatozoa were more detrimental to mitochondrial function than to plasma membrane integrity. Mitochondrial membrane potential (MMP) was suppressed by freezing and thawing treatments; after thawing, MMP declined significantly during rewarming (from 5ºC to 35ºC). The distribution of GM1 ganglioside was examined using fluorescent-labelled cholera toxin B. No significant redistribution of GM1 was observed after chilling or cryotreatment. The externalisation of phosphatidylserine (PS) was examined using fluorescent-labelled annexin V. There was no significant increase in translocation of PS after chilling or cryopreservation. These observations imply that cryotreatment had little effect on plasma membrane lipid asymmetry. Koala spermatozoa were incubated in a range of anisotonic media to investigate whether nuclear swelling was caused by osmotic flux during the cryopreservation process. Although the most hypotonic solution tested (64 mOsm/kg) induced the highest incidence of nuclear relaxation (mean ± SEM; 12 ± 3%), this was not as severe as that previously documented following cryopreservation. Chromatin relaxation is a phenomenon observed in koala spermatozoa, where the sperm nucleus expands due to the result of structural changes in the natural conformation of the sperm DNA/protamine complex. DNA fragmentation was not a primary cause of cryopreservation-induced sperm chromatin relaxation, although in situ nick translation of putative DNA breaks indicated that these increased as the sperm head became progressively more relaxed. Using a Sperm Chromatin Dispersion test (SCDt) specifically developed and validated for koala spermatozoa, a continuum of nuclear morphotypes was observed, ranging from no apparent DNA fragmentation to spermatozoa with highly dispersed and degraded chromatin. A double comet assay was also developed to investigate DNA fragmentation in the koala spermatozoa. Conducted under neutral followed by alkaline conditions, this assay was able to differentiate between single- (SSB) and double-stranded (DSB) DNA damage in an effort to refine the interpretation of DNA damage in mature koala spermatozoa; the majority of the koala spermatozoa had nuclei with DNA abasic-like residues. The ubiquity of these residues suggested that constitutive alkali-labile sites are part of the structural configuration of the koala sperm nucleus. Spermatozoa with “true” DNA fragmentation exhibited a continuum of comet morphologies, ranging from a more severe form of alkaline-susceptible DNA, to nuclei that exhibited both SSB and DSB. Swelling of koala sperm chromatin following cryopreservation has largely been attributed to the absence of inter-molecular disulphide cross-linkages in the marsupial sperm nucleus. Fish spermatozoa also lack disulphide bonds within their chromatin, but nevertheless, have been successfully cryopreserved. To examine the hypothesis that the cryoprotectants used for fish sperm cryopreservation will confer a similar degree of protection on koala spermatozoa, various concentrations of five cryoprotectants (dimethyl sulphoxide, methanol, propylene glycol, ethylene glycol and dimethylacetamide) were evaluated. Each treatment was compared against an established koala sperm cryopreservation protocol that uses 14% glycerol. Dimethylacetamide at a concentration of 12.5% (v/v) was found to be comparable to glycerol in the successful cryopreservation of koala spermatozoa although high inter-male variability was observed. However, when the new protocol was subsequently validated for a larger population of captive koalas (n = 22), glycerol emerged the better cryoprotectant with respect to all sperm viability parameters assessed except for that of the incidence of chromatin relaxation, which was not affected by the cryoprotectant. Significant difference was also observed in the post-thaw survival of spermatozoa from different animals, which was independent of pre-freeze semen quality. Based on post-thaw semen viability parameters, the koalas could be divided into two distinct groups, where one group had significantly higher sperm viability compared to the other group, regardless of cryoprotectant used. Positive correlation between motility and MMP was observed before and after cryopreservation. However, cryopreservation significantly reduced the dependency between these variables (P < 0.001), suggesting that cryopreservation reduced the dependency between mitochondrial function and motility.

Les forêts du Liban ont fait l'objet de nombreux travaux depuis le milieu du XIXéme siècle. En particulier, des cartes forestières ont régulièrement été réalisées depuis 1965. Nous proposons de reprendre l'ensemble de ces données, de les compléter par des images satellites récentes (MSS 1972, TM 1989, Spot5 2003) puis de développer des outils susceptibles de caractériser l'évolution des forêts du Liban durant ces 50 dernières années.<br />Une analyse critique de l'ensemble des sources qui prend en compte leur mode de constitution a permis de constituer un référentiel géographique et sémantique commun pour comparer les cartes et les images satellites. Une modélisation des paysages reposant sur plusieurs indices fondés sur la caractérisation de « patches » est utilisée pour évaluer l'emprise du développement urbain, les processus de dégradation/régénération, l'impact des facteurs abiotiques (topographie, pédologie, ...), les pratiques agricoles, le rôle des routes ... sur la fragmentation des îlots forestiers.<br />Les forêts du Liban apparaissent clivées en deux grandes entités : la zone côtière et la zone intérieure. En zone côtière, les peuplements de chênes sont denses et présentent une bonne régénération durant la période étudiée tandis qu'en zone intérieure, ils témoignent d'une importante dégradation due à la création de carrières ou à un déboisement laissant la place à des cultures et à des espaces herbacés. Les forêts de Genévriers semblent fortement dégradées sur l'ensemble du territoire bien que leur type de formation arborée lâche permette mal de quantifier leur évolution

Ce manuscrit présente une étude de la dynamique de la fragmentation de molécules diatomiques (CO) et triatomiques (CO2) induite par impact d'ions multichargés rapides, dans un régime de vitesse de collision où l'ionisation de la cible est le processus dominant. Réalisée au GANIL, cette étude a nécessité la mise en œuvre une technique dite de "Spectroscopie d'Impulsion d'Ions de Recul" consistant en l'association d'un spectromètre de masse par temps de vol et d'un détecteur à localisation multi-impact basé sur une anode à ligne à retard. La mesure à haute résolution des distributions d'énergie cinétique (KER) des fragments issus de la dissociation de la molécule CO a permis de séparer et d'identifier les états électroniques excités du dication (CO)2+ peuplés lors de la collision, confirmant ainsi les limitations du modèle de l'explosion coulombienne. Le rôle de l'orientation de l'axe intermoléculaire de la molécule CO par rapport à la direction du faisceau projectile incident sur les sections efficaces a été mesuré et comparé aux prédictions d'un modèle géométrique. Enfin, différents comportements de la dynamique plus complexe de la fragmentation de la molécule CO2 ont été mis en évidence. Notamment, la triple ionisation de CO2 conduit majoritairement à une fragmentation concertée synchrone. Néanmoins, un comportement minoritaire a pu être observé et identifié comme associé à une fragmentation séquentielle impliquant un état métastable de l'ion moléculaire (CO)2+. Par contre, la fragmentation de l'ion moléculaire (CO2)2+ présente un caractère de type concerté asynchrone interprété à l'aide d'un modèle simple, mettant en jeu un mode de vibration asymétrique de la molécule.

Le thème principal de cette thèse est l'étude des processus de Fragmentation et de Coalescence dit homogènes. Le premier chapitre se concentre sur les propriétés des fragmentations de masses, en particulier on établit une correspondance utile entre les fragmentations de masses et les fragmentations de partitions. La deuxième partie se concentre sur les fragmentations d'intervalles. On s'intéresse particulièrement aux ensembles de points ayant une vitesse de fragmentation anormale et on calcule explicitement la dimension de Hausdorff de tels ensembles. Enfin, dans le dernier tiers on définit et on étudie les processus de fragmentation-coalescence homogènes qui décrivent l'évolution de systèmes de particules dans lesquels le phénomènes de coalescences et de fragmentations sont présent simultanément. On montre que la condition d'homogénéité est suffisante pour assurer l'existence d'une mesure d'équilibre que l'on étudie.