Stable isotope composition of bulk leaf water is a useful proxy for geochemical and biological processes and is, thus, appreciated in ecological research and global modelling. The mechanisms determining the abundance of different isotopes in leaf water are not fully understood. The research presented in this thesis aimed to describe variability in leaf water isotopes which occurs under natural conditions and to distinguish which factors generate such variability. For that purpose, field sampling, water extraction, stable isotope analysis and measurements of several additional environmental and physiological characteristics were carried out at one sampling site during three subsequent growing seasons. The results obtained point out that oxygen isotopes rather then hydrogen isotopes have greater potential to be used in higher scale applications. Apart from that, several interesting ecophysiological interpretations of isotopic data have been made.

The thesis is focused on the comparison of several types of microclimates in enclosed places of livestock production, aimed at beef-raising. The goal is a making the comparison of final results of microclimate elements at two sorts of stabling. Stanchion housing versus opened housing.

Alzheimer’s disease (AD) is the most prevalent form of dementia affecting the elderly, and as the aging population increases the social and economic burden of AD grows substantially. Pathological hallmarks of AD include the accumulation of extracellular amyloid plaques and intracellular neurofibrillary tangles (NFTs), as well as significant neuron loss. Amyloid plaques consist of aggregated amyloid beta (Aβ) peptide, which is generated from the proteolytic processing of amyloid precursor protein (APP) in addition to several other peptides. While the processing of APP has been characterized, its primary physiological function and its involvement in AD pathology are poorly understood. Developing a greater understanding of the function of APP, and the molecular and cellular functions it is involved in or other proteins it is associated with, could provide insight into its role in AD pathology. To investigate the function of APP695, the neuronal isoform of APP, we used mass spectrometry to compare changes in protein expression and phosphorylation between APP-null B103 and APP695-expressing B103-695 rat neuroblastoma cells. Mass spectrometry-based proteomics has become a powerful technique for the unbiased identification of proteins from complex mixtures. Quantitative proteomics using labeling techniques, such as stable isotope labeling by amino acids in cell culture (SILAC), allow relative quantitation of multiple samples at once. More recently, with advances in mass spectrometer technology, label-free quantitation has become a reliable quantitative proteomics approach. Additionally, mass spectrometry can be used for the analysis of post-translational modifications, such as phosphorylation, a dynamic modification involved in the regulation of many cellular processes. Phosphoproteomics identifies site-specific phosphorylation and surrounding sequence information, which can be used for consensus motif analysis to provide further information about potential changes in kinase activity. Identifying changes in phosphorylation and kinase activity also provides information about signaling pathways and functions that may be affected by APP695 expression. Comprehensive proteomic and phosphoproteomic datasets can be used to gain insight into the molecular mechanisms that may be regulated by APP695 expression, or involved in AD progression and pathology, leading to the development of novel therapeutic and preventative strategies for AD. Proteomic and phosphoproteomic analysis of B103 and B103-695 cells identified several significant protein expression and phosphorylation changes that may be mediated by APP695-expression. Global-scale proteomic analysis identified increased expression of Ras and ƴ-synuclein in B103-695 cells, which was further validated in human AD brain tissue. Phosphoproteomic analysis showed increased phosphorylation of Histone H4 at Ser47, and led to the investigation of PCTAIRE-2 (Cdk17), and PCTAIRE-3 (Cdk18) expression, which were all shown to be increased in AD transgenic mouse tissue, culture primary rat neurons treated with Aβ, as well as mild cognitive impairment (MCI) and AD human brain tissue. Label-free quantitative proteomics was used for the analysis of human brain tissue from the cortex of individuals affected by AD, MCI, Parkinson’s disease (PD), and progressive supranuclear palsy (PSP) compared to cognitively normal, control samples. A number of differentially expressed proteins were identified in AD, MCI, PD, and PSP tissue. Bioinformatic analysis of the comprehensive proteomic datasets from AD, MCI, PD, and PSP human brain tissue identified several proteins consistent with corresponding disease pathology and neurodegeneration, such as inflammatory proteins. While some of the molecular and cellular functions were unique among neurodegenerative diseases, there also appears to be overlap of affected functions, suggesting there may be a more common mechanism of neurodegeneration.

A utilização de traçadores como os isótopos estáveis de carbono e nitrogênio, é crescente e complementa as técnicas convencionais nos estudos referentes à dieta em animais silvestres. Isso é possível pois o valor isotópico dos itens utilizados na alimentação é refletido nos tecidos. A diferença isotópica resultante chamada de fator de discriminação ou fracionamento, está associada aos processos metabólicos necessários para que ocorra a incorporação de nutrientes. O estudo teve como objetivo medir o tempo de incorporação dos isótopos no plasma e nas células sanguíneas, componentes de \"tecido\" não mortal reamostrável, e determinar o fator de discriminação em cinco espécies de quelônios de água doce: Podocnemis expansa (tartaruga-da-Amazônia), Podocnemis unifilis (tracajá), Phrynops geofroanus (cágado-de-barbicha), Trachemys scripta (tartaruga-de-orelha-vermelha) e Trachemys dorbigni (tigre-d\'água). Os animais foram mantidos em cativeiro e as diferenças isotópicas dos 10 indivíduos adultos de cada espécie, foram medidas a partir da troca de dietas com valores isotópicos distintos. Com a mudança da dieta, o turnover do carbono e nitrogênio foram estimados entre 7 e 185 dias por meio de regressão exponencial não linear, quando os novos fatores de fracionamento foram estimados. O tempo de turnover para as espécies de quelônios variou de 72 a 337 dias para o carbono, e de 29 a 270 dias para o nitrogênio no plasma. Nas células sanguíneas o turnover variou de 3 a 373 dias para o carbono, e de 51 a 216 dias para o nitrogênio. Os fatores de discriminação que eram em média próximos a zero para o carbono, e entre 3-4‰ para o nitrogênio, variaram de 1,01 a 3,28‰ para o 13C e -0,76 a 0,49‰ para o 15N no plasma, e de 1,49 a 3,98‰ para o 13C e 0,99‰ a 4,69 para o 15N nas células sanguíneas, com a diminuição de 3,7‰ e aumento de 6,2‰, respectivamente para carbono e nitrogênio, na nova dieta. A diferença encontrada entre os fatores de discriminação calculados anteriormente a troca da dieta e após a troca, mostraram que provavelmente a incorporação dos isótopos estáveis se dá de forma heterogênea nos tecidos. De acordo com a literatura foi possível analisar que fatores como a memória isotópica, as rotas metabólicas e elementos característicos dos répteis possivelmente estão ligados ao turnover mais lento, diferente dos animais endotérmicos em que esse processo é mais rápido. / The use of tracers such as stable carbon and nitrogen isotopes is crescent and complements the conventional techniques used in the studies referring to the diet in wild animals. This is possible because the isotopic value of the items used in the diet reflects their isotopic values on the tissues. The resulting isotopic difference called the discrimination factor or fractionation is associated with the metabolic processes required for nutrient incorporation to occur. The object of the study was to measure the incorporation time of isotopes into plasma and blood cells, components of re-portable non-lethal \"tissue\", and to determine the discriminant factor of five species of freshwater chelonians: Podocnemis expansa (Amazonia tortoise), Podocnemis unifilis (tracajá), Phrynops geofroanus (geoffroy´s side necked turtle), Trachemys scripta (red-eared slider turtle) and Trachemys dorbigni (d\'orbigny\'s slider). The isotopic differences of 10 adult individuals of each species kept in captivity were measured through shifting diets with different isotopic values. With the diet variation, carbon and nitrogen turnover was estimated between 7 and 185 days by non-linear exponential regression, when the new fractionation factors were estimated. The turnover time for the chelonians species varied from 72 to 337 days for carbon, and from 29 to 270 days for the plasma nitrogen. In blood cells, the turnover ranged from 3 to 373 days for carbon, and from 51 to 216 days for nitrogen. Discrimination factors that were, in average, close to zero for carbon and between 3 and 4‰ for nitrogen ranged from 1.01 to 3.28‰ for 13C and -0.76 to 0.49‰ for 15N in plasma, and from 1.49 to 3.98‰ for 13C and 0.99 to 4.69 for 15N in blood cells, with a decrease of 3.7‰ and an increase of 6.2‰, respectively for carbon and nitrogen in the new diet. The difference found between the discrimination factors calculated before and after the diet shift, showed that stable isotopes incorporation probably occurs in a heterogenous way in tissues. According to the literature it was possible to analyze that factors such as isotopic memory, metabolic routes and reptiles characteristic elements are possibly linked to slower turnover, different from endothermic animals in which this process is faster.

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O objetivo desta dissertação é estudar grafos com pesos nos vértices como um invariante global das aplicações de Gauss estáveis de superfícies compactas e orientadas. Apresentaremos também alguns invariantes locais que são importantes no estudo de aplicações estáveis. Abordaremos o problema de realização de grafos por aplicações de Gauss estáveis, considerando também um destes invariantes, o número de cúspides destas aplicações. Finalmente, usaremos matrizes para representar estes invariantes e definiremos classes de equivalências para estes representantes. Esta foi uma ideia que surgiu no final deste trabalho de mestrado. / The propose of this work is to study graphs with weights at the vertices as a global invariant of stable Gauss applications on compact and oriented surfaces. We also present some local invariants that are important to the study of stable applications. We approach the problem of realization of graphs by stable Gauss applications, also emphasizing one of these invariants, the number of cusps of these applications. Finally, we use matrices to represent these invariants and define equivalence classes for these representatives. This idea appeared at the end of this master\'s thesis.

O delta do rio Tubarão, situado na costa centro-sul catarinense entre os municípios de Tubarão, Jaguaruna e Laguna, constitui raro exemplo de delta lagunar ativo no Brasil. Sua planície deltaica cobre área aproximada de 250km2, onde são encontradas evidências de migração de canais fluviais dadas por séries de truncamentos de antigos distributários, alguns ainda ativos. Dez testemunhos foram obtidos junto aos principais canais distributários do rio Tubarão, a partir dos quais foram realizadas análises de fácies, granulométrica, de minerais pesados, de teor de matéria orgânica e de relações químio-isotópicas, além de datações 14C. Também foram levantados acervos históricos de fotografias aéreas e de dados de prospecção mineral de subsuperfície. Cerca de 5000 anos atrás, na região de seu ápice, próximo ao rio tributário Capivari de Baixo, o delta do rio Tubarão ingressou numa antiga baía lagunar e ramificou-se em sete distributários principais que, desde seus momentos iniciais de migração, foram controlados por avulsões autogênicas rumo a antigas depressões do fundo da bacia receptora. Tais avulsões progradaram o delta inicialmente para SW, depois para ENE, e então para NNE, favorecendo a fragmentação da antiga baía lagunar em uma série de lagos e lagunas menores. Diante deste cenário dinâmico, sambaquis foram erigidos no entorno do sistema lagunar, constituindo importantes registros arqueológicos de interação entre evolução sedimentar e ocupação humana pré-histórica. O resultado das análises granulométricas indicou que a sedimentação deltaica, nas proximidades de encostas de morros, foi misturada com colúvio e/ou depósitos de fluxos gravitacionais, como evidenciado pela presença de intervalos texturalmente muito imaturos em alguns testemunhos. Em relação à análise de minerais pesados, o principal fator de controle nas variações da assembleia em depósitos de delta e de bacia é a proveniência sedimentar. Em termos mediatos, essa proveniência reflete fontes plutônicas e metamórficas (médio a alto grau) do Batólito de Florianópolis (e xenólitos associados) e do Complexo Granito-Gnáissico, e rochas arenáceas alteradas da Bacia do Paraná. Em termos imediatos, depósitos deltaicos destacam-se pela afinidade mineralógica com as areias do rio Tubarão, inferida sobretudo a partir da presença mútua de grãos alterados de cianita e estaurolita, enquanto que depósitos da bacia lagunar destacam-se por sua similaridade mineralógica com areias dos rios tributários Braço do Norte e Capivari de Baixo, neste caso principalmente pela presença de zircão. A matéria orgânica presente nos depósitos do delta e de sua bacia receptora resulta do aporte de fontes terrestres (fornecido pelos rios) e marinhas (trazido via desembocaduras lagunares), fato que é evidenciado pelos resultados de \'delta\'\'POT.13 C\', \'delta\'\'POT.15 N\' e razão \'C IND.ORG\'/\'N IND.TOTAL\'. Particularmente, nos sedimentos da bacia, variações entre diferentes tipos de matéria orgânica têm ocorrido ao longo do Holoceno, as quais são atribuídas tanto ao isolamento físico progressivo do sistema lagunar em relação ao mar aberto como por mudança climática regional (aumento destacado de precipitação). A análise isotópica de oxigênio (\'delta\'\'POT 18 O\') de conchas de moluscos em depósitos da bacia indicou enriquecimento relativo em \'ANTPOT.16 O\' durante o Holoceno. Este resultado, a exemplo daquele dos isótopos de carbono e de nitrogênio dos sedimentos, sugere isolamento gradual das águas lagunares em relação às de mar aberto. / The Tubarão river delta, located on the centre-south coast of Santa Catarina State, among the municipalities of Tubarão, Jaguaruna and Laguna, is rare example of active lagoonal delta in Brazil. Its delta plain covers an area of about 250km2, where there are evidences of migration of fluvial channels in a set of truncations of ancient distributaries, some of these still in activity. Ten cores were acquired adjacent to the main distributary channels of the Tubarão river, from which analyses of facies, grain size, heavy minerals, organic matter, chemistry-isotope ratios, and radiocarbon datings were performed. Also, aerial photographies and data of subsurface mining were surveyed from historical collections. Thereabout 5,000 years ago, in the region of its apex, near Capivari de Baixo tributary river, the Tubarão river delta entered an ancient lagoonal bay and branched seven main distributaries. Since the beginning of its migration, these distributaries were controlled by autogenic avulsions towards ancient depressions in the bottom of the basin. Initially, these avulsions prograded the delta towards SW, afterwards to ENE, and then to NNE, favoring the fragmentation of the ancient lagoonal bay in a set of smaller lakes and lagoons. Faced with this dynamical scenario, shellmounds were erected surrounding the lagoon system, composing important archaeological records of the interaction between sedimentary evolution and prehistoric human occupation. The results of the grain size analysis showed that the deltaic sedimentation, in the vicinity of slopes of hills, was mixed with colluvium and/or gravity flow deposits, that is evidenced by the presence of texturally very immature intervals in some cores. The analysis of heavy minerals, by its turn, showed that the main controlling factor in the variations of its assemblage in deposits of delta and basin is the sedimentary provenance. In terms of mediate sources, this provenance reflects plutonic and metamorphic (medium to high grade) rocks of the Florianópolis batholith (including its xenoliths) and of the Granite-Gneiss Complex, and weathered sedimentary sandstones of the Palaeozoic Paraná basin. Regarding immediate sources, deltaic deposits stand out by its mineralogical affinity with sands of the Tubarão river, mainly by the mutual presence of weathered grains of kyanite and staurolite, whereas deposits of the lagoon have mineralogical similarity with the sands of Braço do Norte and Capivari de Baixo tributary rivers, especially in relation to the presence of zircon. The origin of the organic matter found in the deposits of the delta and in its lagoonal basin is both from sedimentary input of terrestrial sources (provided by rivers) and marine (brought via inlets), fact evidenced by results of \'delta\'\'POT.13 C\', \'delta\'\' POT.15 N\', and \'C IND.ORG\'/\'N IND. TOTAL\' ratio. Particularly, in the sediments of the basin, variations between different types of organic matter have occurred during the Holocene, and are attributed both to the progressive physical isolament of the lagoon system from the open sea, and by local climate change (pronounced augment of precipitation). The isotope analyses of oxygen (\'delta\'\'POT.18 O\') of molluskan shells from the deposits of the basin present relative enrichment in \'ANTPOT.16 O\' during the Holocene. This result, as well as the one from isotope analyses of carbon and nitrogen of sediments, suggests gradual isolation of the lagoonal waters of influence of waters from the open sea.

Nearshore marine habitats provide critical nursery grounds for juvenile fishes, but their functional role requires the consideration of the impacts of spatial connectivity. This thesis examines nursery function in seagrass habitats through a marine landscape (“seascape”) lens, focusing on the spatial interactions between habitats, and their effects on population and trophic dynamics associated with nursery function to rockfish (Sebastes spp.). In the temperate Pacific Ocean, rockfish depend on nearshore habitats after an open-ocean, pelagic larval period. I investigate the role of two important spatial attributes, habitat adjacency and complexity, on rockfish recruitment to seagrass meadows, and the provision of subsidies to rockfish food webs. To test for these effects, underwater visual surveys and collections of young-of-the-year (YOY) Copper Rockfish recruitment (summer 2015) were compared across adjacent seagrass, kelp forest, and sand habitats within a nearshore seascape on the Central Coast of British Columbia. Recruitment was positively influenced by the structural complexity of seagrass and adjacency to kelp forest sites, however a negative interaction between seagrass complexity and kelp forest adjacency suggests that predation modifies Copper Rockfish recruitment densities. In addition, using δ13C and δ15N isotopes to determine the basal contributions to seagrass food webs, kelp-derived nutrients were on average 47% ± 0.4 of YOY Copper Rockfish diets, which was 3x and 67x greater than the contribution of autochthonous seagrass production (seagrass epiphyte and seagrass blades, respectively). YOY Copper Rockfish diets in seagrass adjacent to sand habitats had the greatest amounts of kelp-derived nutrients and harpacticoid copepods, and concurrently had lower body condition compared to rockfish in the seagrass kelp edges and interior, feeding predominantly on seagrass epiphytes and calanoid copepods. This thesis provides further evidence that temperate seagrasses are nurseries for rockfish and that spatial elements of seascapes, including connectivity via habitat adjacency and variability in habitat structure, alter the recruitment and diets of rockfish in seagrass habitats. These seascape nursery effects are important considerations for marine planning, especially given the global decline of nearshore habitats. / Graduate

Feeding ecology of organisms has a critical influence on ecosystem structure, function, and stability, but how feeding ecology of a single organism varies over multiple spatial and temporal scales in nature is unknown. Here, I characterize the factors driving and the implications of variability in feeding ecology of juvenile Chinook Salmon (Oncorhynchus tshawytscha) over multiple spatial and temporal scales using stable isotopes and stomach contents. Significant variation in juvenile Chinook salmon feeding ecology at the individual-level was found to occur off of the west coast of Vancouver Island (WCVI) (British Columbia, Canada). This variation is correlated with a diet shift from feeding on invertebrates to feeding on fish, as the salmon increase in size. I developed a novel Bayesian stable isotope method to model this shift while taking into account the time-lag associated with isotopic turnover. I found that this model was able to replicate patterns seen in a simplified coastal food web, and that resource-use estimates from this stable isotope model somewhat diverged from a compilation of stomach content data. Next, I compared the feeding ecology of Chinook Salmon in one season and year along nearly their entire North American range. I found considerable spatial variation in ontogeny and feeding ecology, with individuals of the same size from different geographic regions having different δ13C, δ15N, and trophic levels. These differences likely corresponded to regional variability in sea surface temperature, ocean entry date and size, and growth rates. Subsequently, I quantified temporal shifts in the feeding ecology of Chinook Salmon from WCVI. I found that feeding ecology over winter was different from feeding ecology in the fall, and that this likely corresponds to shifts in the prey field. Finally, I found that WCVI juvenile Chinook Salmon showed significant interannual variability in feeding ecology, and that the interannual variability in the δ13C value of juvenile salmon (indicative of primary productivity or nutrient source) predicts their smolt survival. In turn, large-scale climate variability determines the δ13C values of salmon—thus mechanistically linking climate to survival through feeding ecology. These results suggest that qualities propagated upwards from the base of the food chain have a cascading influence that is detectable in salmon feeding ecology. I conclude that the feeding ecology of juvenile Chinook Salmon varies on individual, spatial, season and interannual scales, and that this variability has impacts on survival rates. These findings have implications for the understanding of ontogeny in natural systems in general, allowing for modelling of ontogeny in previously intractable ecological systems. Furthermore there may also be implications for Chinook Salmon management, considering that feeding ecology showed utility as a mechanistic leading indicator of survival rates. / Graduate

PANcreatic DERived factor (PANDER, FAM3B) is a member of a superfamily of FAM3 proteins that are uniquely structured and strongly expressed from the endocrine pancreas and co-secreted with insulin. Unique animal models available to our lab have indicated that PANDER can induce a selective hepatic insulin resistant (SHIR) phenotype whereby insulin signaling is blunted yet lipogenesis is increased. The complexity of the biological networks involved with this process warranted the logical approach of employing quantitative mass spectrometry based proteomic analysis using stable isotope labeling of amino acids in cell culture (SILAC) to identify the global proteome differences between the PANDER transgenic (TG) overexpressing murine model to matched wild-type mice under three metabolic states (fasted, fed and insulin stimulated). Additionally, this technique was used to compare the hepatic proteome of mice on a high fat diet to elucidate early and late mechanisms of disease progression. The “spike-in” process was employed by equal addition of lysate obtained from livers of heavy L-Lysine (13C6, 97%) fed mice to the mice liver protein lysate (PANTG and WT) for relative quantitative analysis. Upon acquisition of the dataset by use of liquid chromatography tandem mass spectrometry (LC-MS/MS, LTQ Orbitrap), geometric means and Uniprot Protein identification numbers were uploaded to Ingenuity Pathway Analysis (IPA) to reveal the effect of PANDER on hepatic signaling. IPA identified lipid metabolism and fatty acid synthesis as top cellular functions differentially altered in all metabolic states. Several molecules with a role in lipid metabolism were identified and include FASN, ApoA1, ApoA4, SCD1, CD36, CYP7A1 and ACC. Furthermore, central to the differentially expressed proteins was the revealed activation of the liver X receptor (LXR) pathway. In summary, our SILAC proteomic approach has elucidated numerous previously unidentified PANDER induced molecules and pathways resulting in increased hepatic lipogenesis. In addition, we have demonstrated strong utility of this approach in comprehensively phenotyping animal models of hepatic insulin resistance. PANDER may potentially propagate pro-hepatic lipogenic effects by LXR activation in contrast to increased LXRα expression. This can be evaluated through the use of LXR agonists (T0901317) antagonists (GSK 2033). LXR activity can be measured by luciferase assays using an LXRE response plasmid. Our central hypothesis is that PANDER induces activation of LXR and is measured and predicted in our line of experiments. In general, PANDER induced LXR activation will be enhanced by T0901317 and diminish effects of GSK 2033 along with direct correlation of downstream metabolic effects such as increased hepatic lipogenesis and fatty acid metabolism. Taken together, PANDER strongly impacts hepatic lipid metabolism and may induce a SHIR phenotype via the LXR pathway. Additionally, phosphoproteomic analysis uncovered large-scale differences in protein phosphorylation states as PANDER impacts insulin signaling. A notable finding was the increased phosphorylation of glycogen synthase (GSK), possibly responsible for the decreased hepatic glycogen content in the PANTG mouse. In an effort to map out critical molecules involved in non-alcoholic fatty liver disease (NAFLD) pathogenesis, the same proteomic approach was carried out, providing a unique dataset of differentially expressed hepatic proteins due to a high at diet.