Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-04-04T15:17:57Z No. of bitstreams: 1 leticiadesouzaresende.pdf: 5007991 bytes, checksum: c0a1fecad549d52bbbfdf63c8a99ca85 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-04-04T15:39:52Z (GMT) No. of bitstreams: 1 leticiadesouzaresende.pdf: 5007991 bytes, checksum: c0a1fecad549d52bbbfdf63c8a99ca85 (MD5) / Made available in DSpace on 2017-04-04T15:39:52Z (GMT). No. of bitstreams: 1 leticiadesouzaresende.pdf: 5007991 bytes, checksum: c0a1fecad549d52bbbfdf63c8a99ca85 (MD5) Previous issue date: 2008-02-27 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A escassez de informações em relação aos pequenos felinos neotropicais deve-se a sua atividade predominantemente noturna, ao uso de vegetação densa e as pressões causadas pela caça que vêem dizimando as populações naturais. Dessa forma, estudos em cativeiro podem fornecer informações, que são essenciais para o desenvolvimento de planos de manejo e estratégias efetivas de conservação. Este trabalho teve como objetivo estudar o comportamento de pequenos felinos, focalizando aspectos relacionados com orçamento de atividade e padrão temporal dos comportamentos, uso do ambiente cativo e a influência dos odores na alteração do padrão comportamental. Foram estudados 14 indivíduos (10 Leopardus tigrinus, 2 Leopardus wiedii, 2 Leopardus geoffroyi) presentes no Centro de Reprodução de Pequenos Felinos Neotropicais da Fundação RIOZOO. Inicialmente, cada recinto foi monitorado através de duas microcâmeras durante 72 horas contínuas no período de novembro de 2006 a fevereiro de 2007. Os comportamentos observados nas filmagens para os indivíduos e os respectivos locais de ocorrência foram registrados a cada cinco minutos em uma planilha. Esta etapa foi utilizada para estabelecer o orçamento de atividade, organização temporal e uso do espaço e serviu como linha de base para as duas condições experimentais envolvendo canela (Cinnamomum sp.) e catnip ou erva-de-gato (Nepeta catarina). Os odores foram introduzidos separadamente em cada recinto durante três dias consecutivos em dois montes de gravetos e alfafa. Após a adição do primeiro odor em um determinado recinto, este era monitorado por três dias consecutivos. As três espécies estudadas apresentaram um padrão similar de orçamento de atividade, sendo Descanso a categoria comportamental com o maior valor médio, seguido por Locomoção, Vigilância, Forrageio e Manutenção. Em relação à organização temporal, foram descritos ritmos circadianos para os comportamentos de L. tigrinus, com exceção de Interação social que apresentou ritmo ultradiano. Para L. geoffroyi foram encontrados ritmos ultradianos para os comportamentos. L. wiedii apresentou ritmo ultradiano para o comportamento de Locomoção com período de 8 horas. Entretanto Descanso, Vigilância e Manutenção apresentaram ritmicidade circadiana. Foram verificadas diferenças significativas entre as proporções de tempo gastos nas diferentes subdivisões do recinto, confirmando a idéia de que felinos não utilizam igualmente todas as áreas do ambiente cativo.“Caixa” foi o local mais utilizado por todas as espécies, principalmente para Descanso. “Grade” foi utilizada predominantemente para pacing com baixa ocorrência de outros comportamentos. A presença de canela não influenciou no orçamento de atividade/ repouso, entretanto houve uma redução significativa do comportamento de pacing quando comparado com a fase anterior ao enriquecimento. Para o catnip, não foram observadas diferenças significativas na freqüência média de comportamento estereotipado, entretanto esse odor influenciou a expressão de comportamentos naturais da espécie, como explorar e marcar território. Estes resultados foram discutidos considerando a flexibilidade comportamental dessas espécies, buscando contribuir para ampliação do conhecimento científico e oferecer informações que serão úteis em estudos comparativos e para a conservação desses indivíduos. / The lack of information concerning the small neotropical felids can be related to their predominant nocturnal activity, use of dense vegetation and hunting that threats natural populations. Therefore, research with captive animals may supply essential information for the development of effective conservation plans and strategies. The aim of this work was to study the behavior of small felids, with emphasis in the activity budget and patterns of behavior, and influence of the use of captive environment and odors in the change of behavior. Fourteen individuals (10 Leopardus tigrinus, 2 Leopardus wiedii, 2 Leopardus geoffroyi) were kept in the Center of Reproduction of Small Neotropical Felids, RIOZOO Zoological Park. The evaluation of the olfactory effect was carried out on eight individuals of L. tigrinus. Initially, each cage was monitored through two microcameras during 72 hours from November, 2006 to February, 2007. Each behavior and respective place of occurrence was registered every five minutes. This phase was used to establish the activity budget, behavior pattern, use of captive environment and worked as baseline for the two experimental conditions involving cinnamon (Cinnamomum sp.) and catnip (Nepeta catarina). The odors were introduced separately in each cage during three consecutive days between small trunks and alfalfa. At tree-days monitoring period followed the addition of the first odor. The three species studied showed a similar activity budget, Rest was the most frequent behavior, followed by Locomotion, Vigilance, Feeding and Maintenance. Concerning the patterns of behavior, circadian rhythms were observed for L. tigrinus with exception of Social Interation that presented ultradian rhythm. For L. geoffroyi ultradians rhythms were found for all classes of behavior. L. wiedii presented ultradian rhythm for a Locomotion (eight-hours period) and circadian rhythms for Rest, Viligilance and Maintenance. The amount of time spent in each subdivision of the cage was significantly different, confirming the idea that felids do not equally use the areas of a captive environment. "Box" was the most used place by all species, mainly for Rest. "Edge area" was used predominantly for "Pacing" with low occurrence of the other behaviors. The presence of Cinnamon did not influence the rest/activity balance, although it had a significant effect in the reduction of "Pacing" when compared with the previous phase (baseline). Significant differences were not found for catnip in the medium frequency of stereotypic pacing. However, this odor influenced the expression of natural behaviours, as exploring and marking territory. These results are discussed taking into consideration the behavioral flexibility of the species, contributing to the scientific knowledge and providing information that will be useful in comparative studies and conservation of these species.

Ce travail se place dans le contexte des problèmes de fluides présentant une couche limite. Nous explorons l'usage de méthodes éléments finis enrichies pour ce type de problèmes. En particulier, nous présentons un algorithme nouveau d'enrichissement adaptatif, où les fonctions d 'enrichissement sont construites sans connaissance a priori sur la solution. Nous comparons cette approche à l'adaptation de degré polynômial et à l'adaptation de maillage. Nous montrons qu'elle peut-être plus compétitive que la première et qu'elle peut être utilisée efficacement comme complément à laseconde. Des expérimentations numériques sont menées sur des problèmes 2D scalaires (advection -diffusion, Burgers) et de Navier-Stokes. / We are interested in fluid dynamics problems with a boundary layer. We investigate enriched finite elements methods for this kind of problems. A point of interest is the new adaptive enrichment algorithm that we propose, where enrichment functions are built without a priori knowledge on the solution. This approach is compared to both p-adaptivity and h-adaptivity. We show that it can replace the former with profit, and is a good complement to the latter. Numerical experiments are shown on scalar problems (advection-diffusion) and Navier-Stokes equations.

The physiological and behavioral responses can vary with the form of housing of the fish and the presence of anxiolytic drugs. The aim of this study was to evaluate the response to acute stress in isolated and grouped fish and the effect of fluoxetine, diazepam and environmental enrichment on behavioral and endocrine parameters. Six experiments were performed: 1. Acute stress test in isolated and groups zebrafish; 2. Transfer of isolated or group zebrafish to a new environment; 3. Effect of introducing grouped stressed fish in a resident zebrafish shoal; 4. Effect of introducing one stressed fish in a resident zebrafish shoal; 5. Effect of acute exposure to fluoxetine and diazepam on behavioral responses after acute stress protocol; 6. Response to acute stress in isolated and grouped fish and the modulation by fluoxetine, diazepam and environmental enrichment. Based on the results we concluded that the group is able to potentiate stress response, however, that response is reduced by exposure to fluoxetine and diazepam in water and environmental enrichment; acute exposure to fluoxetine and diazepam modulates behavior in zebrafish after acute stress. / As respostas fisiológicas e comportamentais podem variar de acordo com a forma de alojamento dos peixes e pela presença de fármacos ansiolíticos. O objetivo do estudo foi avaliar a resposta ao estresse agudo em peixes isolados e agrupados e o efeito da fluoxetina, diazepam e enriquecimento ambiental sobre parâmetros comportamentais e endócrino. Foram realizados 6 experimentos: 1. Teste de estresse agudo em peixes-zebra isolados e em grupos; 2. Transferência de peixes-zebra isolados ou em grupo para um ambiente novo; 3. Efeito da introdução de peixes agrupados estressados em um cardume de peixe-zebra residente; 4. Efeito da introdução de um peixe estressado em um cardume de peixe-zebra residente; 5. Efeito da exposição aguda à fluoxetina e diazepam sobre as respostas comportamentais após o protocolo de estresse agudo; 6. Resposta ao estresse agudo em peixes isolados, agrupados e a modulação por fluoxetina, diazepam e enriquecimento ambiental. Com base nos resultados concluímos que grupo é capaz de potencializar a resposta ao estresse, porém, essa resposta é reduzida pela exposição à fluoxetina e diazepam na água e pelo enriquecimento ambiental; a exposição aguda à fluoxetina e diazepam modula comportamentos em peixes-zebra após estresse agudo.

Estuarine systems are of crucial importance to the provision of goods and services on a global scale. High human population densities in coastal systems have caused an increasing input of pollutants, of which nutrient pollution is of major concern. Increasingly, these areas are also impacted by physical disturbance, which can originate from anthropogenic sources (e.g. bait digging, shipping) or climate change causing increasingly frequent and intense storms. The individual impacts of such stressors on ecosystems have been investigated however their combined impacts have received less attention. Cumulative impacts of multiple stressors are unpredictable and will likely result in non-additive effects. Further, the effect of local environmental context on multiple stressors is a relatively understudied topic. Work in this thesis compared the combined impact of nutrient enrichment and physical disturbance in Scotland and Australia, using a series of manipulative field experiments. Results demonstrate that response to stressors is highly context dependent, varying between and within geographic locations. While the background levels of stress may vary, by comparing these two locations it is possible to comment on the adaptations and response that communities within different parts of the world display when subjected to additional stress. This study demonstrates that environmental context must be considered when implementing future management practices. Further work demonstrated that the impact of multiple stressors varies depending on how the stress is applied –whether stressors are applied simultaneously or whether there is a delay between two stressors. This study was among the first of its kind, assessing the implications of how multiple stressors react with each other given the order and intensity in which stressors were applied. Results demonstrated that systems can become sensitised to stress making them increasingly vulnerable to additional stress. Future research should be focussed on incorporating ecologically relevant scenarios of how stressors will impact estuaries while considering how environmental context will mediate impacts.

Humans have transformed much of the earth’s surface through a wide range of activities of varying intensities and scales, shaping the landscape we see today. The combination of time and complex human-environment interactions within the Hakai Lúxvbálís Conservancy on the Central Coast of British Columbia has resulted in a landscape with many anthropogenically-generated modifications, such as shell middens which can be found at sites with histories of long-term habitation. Globally, shell middens (and in general, habitation sites) have been found to be factors in shaping site ecology. This thesis seeks to investigate this relationship between human activity and occupation and the landscape. The goal of this project is to examine the legacies from past land use, and subsidies from shell middens, within the present-day plant communities. I conducted an observational study to determine if species richness and overall plant communities on these habitation sites differed from sites without a history of intense occupation. To do this I selected ten habitation sites with known extensive shell middens and paired them with ten control sites with similar site conditions (but without the same site history or shell middens). I measured species abundances within 540 1 m x 1 m quadrats. I also surveyed a select group of culturally significant plant species and culturally modified trees within belt transects at each site. Data regarding the water table level and soil and foliar samples were also collected. A variety of environmental factors, along with the site history were evaluated as explanatory variables. Principal component analyses were used to describe how the gradients within the vegetation communities at three vegetation layers (ground, herb, shrub) to see if they respond differently to long-term site use. The habitation sites were found to be characterized by N-rich plant communities, which were significantly different from the plant communities on the control sites at the ground layer, herb layer, and with all layers combined, at both transect distances analysed, but the shrub layer was only significantly different when the entire transect was considered. The results show plant community composition is most strongly influenced by a combination of factors including site type, canopy cover, slope, topography, and distance from shore, with the weight of their importance depending on what vegetation layer is considered. The habitation sites had a lower average species richness at all layers, compared to the control sites, and their plant communities were shown to change differently with distance from the marine shoreline. Habitation sites also differed by having higher soil nutrient content, lower water table levels, and contained culturally important plant species that were absent on the control sites. This research highlights the influence that humans have had on landscapes in this region. This study shows how the patterns within the plant communities at the habitation sites differ from what is expected within the Coastal Western Hemlock zone. The research improves our understanding of the factors influencing vegetation patterns on the Central Coast of British Columbia with this examination of the complex intersection of historical practices and environmental changes. / Graduate

The impact of the relative richness or poverty of the external environment on development has been demonstrated in a variety of species and for a number of physical and cognitive processes. However, a dichotomy exists in the present literature, wherein the physical and social environments are compartmentalized. The present study investigated the potential longitudinal interaction between the social and physical environments on early cognitive development and emotional reactivity. Bobwhite quail (Colinus virginianus) were exposed to different part-time combinations of social and physical enrichment over the first 96 hours following hatch. Developmental trajectories were explored using repeated non-identical maze tasks. The experiment was inconclusive as to the effects of enrichment; however a distinct trend arose as a main effect of age. Chicks were significantly less willing to explore and solve the maze at 72 and 96 hours. Potential explanations concerning experience and physiological maturation are discussed along with sources of variability.

The development of species-typical perceptual preferences has been shown to depend on a variety of socially and ecologically derived sensory stimulation during both the pre- and postnatal periods. The prominent mechanism behind the development of these seemingly innate tendencies in young organisms has been hypothesized to be a domain-general pan-sensory selectivity process referred to as perceptual narrowing, whereby regularly experienced sensory stimuli are honed in upon, while simultaneously losing the ability to effectively discriminate between atypical or unfamiliar sensory stimulation. Previous work with precocial birds has been successful in preventing the development of species-typical perceptual preferences by denying the organism typical levels of social and/or self-produced stimulation. The current series of experiments explored the mechanism of perceptual narrowing to assess the malleability of a species-typical auditory preference in avian embryos. By providing a variety of different unimodal and bimodal presentations of a mixed-species vocalizations at the onset of prenatal auditory function, the following project aimed to 1) keep the perceptual window from narrowing, thereby interfering with the development of a species-typical auditory preference, 2) investigate how long differential prenatal stimulation can keep the perceptual window open postnatally, 3) explore how prenatal auditory enrichment effected preferences for novelty, and 4) assess whether prenatal auditory perceptual narrowing is affected by modality specific or amodal stimulus properties during early development. Results indicated that prenatal auditory enrichment significantly interferes with the emergence of a species-typical auditory preference and increases openness to novelty, at least temporarily. After accruing postnatal experience in an environment rich with species-typical auditory and multisensory cues, the effect of prenatal auditory enrichment rapidly was found to rapidly fade. Prenatal auditory enrichment with extraneous non-synchronous light exposure was shown to both keep the perceptual narrowing window open and impede learning in the postnatal environment, following hatching. Results are discussed in light of the role experience plays in perceptual narrowing during the perinatal period.

Human domination of global nutrient cycles is profoundly altering our planet. Yet on coral reefs, the effects of changing nutrient regimes have likely been over-simplified. This dissertation investigates the complexity of animal-nutrient interactions at the organismal level and explores how the outcomes of these interactions cascade through levels of biological organization. To do so, I examined the effects of nitrogen (N) and phosphorus (P) on corals and macroalgae, and how these effects in turn influenced reef communities and entire ecosystems. I show that P consistently increases coral growth rates while N has variable, often negative, effects on coral growth. The majority of this variability was explained by the contrasting responses of corals to ammonium, which had negligible effects on coral growth, versus nitrate, which consistently had negative effects on corals. Experimental manipulations of nutrient regimes revealed that these effects could be attributed, in part, to increased damage to the photosynthetic components of the corals’ endosymbionts. Nitrogen and P-enrichment also impacted macroalgae, increasing the nutrient content of algal tissue and in turn, consumption patterns of herbivorous fishes. Initial phase parrotfishes and juvenile surgeonfishes increased their feeding rates on algae rich in N and P respectively. However, adults from both species were irresponsive to algal nutrient content. At the community level, the effects of N and P on corals, algae and herbivory were linked to the development of distinct benthic communities. Algae cover was lower and coral growth rates higher around reef structures that were consistently enriched with N and P excreted by sheltering fishes. At the ecosystem level, I found that the responses of corals to N and P enrichment were similar to those of other nutrient-sharing mutualists. Across terrestrial and marine environments, I show that N and P enrichment consistently decouples mutualism performance, benefiting one partner at the expense of the other. Thus, collectively this dissertation demonstrates that the impacts of global nutrient loading resonate from single organisms through whole ecosystems.

La probabilité de défaillance d’une structure sous séisme est représentée à l’aide de « courbes de fragilité ». Pour les estimer, nous proposons d’enrichir une base de données pré-existante à l’aide du modèle de l’article de F. Poirion et I. Zentner, Stochastic model construction of natural hazards given experimental data, qui se fonde sur la représentation de Karhunen-Loève. Les signaux générés sont triés par classes d’indicateur de nocivité sismique à l’aide d’un algorithme de partitionnement de données. Malgré la ressemblance certaine que présentent plusieurs signaux simulés, et les conséquences que nous tirons de ce problème, ils sont soumis à la structure. Les signaux de réponses résultants sont eux aussi enrichis, en prenant en compte certaines incertitudes afin de construire un intervalle autour de la courbe. La méthode fonctionne pour tout indicateur de nocivité sismique, et permet de s’affranchir de plusieurs hypothèses simplificatrices courantes. Les caractéristiques du scénario sismique sont conservées lors de l’enrichissement, et le processus modélisant le mouvement du sol garde toute sa généralité. Notre démarche est validée d’abord sur un cas simple, puis sur un cas industriel. / The failure probability of a structure under earthquake is represented with « fragility curves ». To estimate them, we propose to enrich a pre-existing data basis using the model of the article Stochastic model construction of natural hazards given experimental data, written by F. Poirion et I. Zentner, which is based on the Karhunen-Loeve expansion. The generated signals are sorted by seismic indicator classes using a data partitioning algorithm. Despite the resemblance between some simulated signals, and the consequences we draw from this problem, the structure is submitted to them. The resulting response signals are also enriched, taking into account uncertainties to construct an interval around the curve. The method works for any seismic indicator, and overcomes several common simplifying assumptions. The characteristics of the seismic scenario are preserved during the enrichment, and the process modeling the ground motion retains its generality. Our approach is first validated on a simple case, then on an industrial case.

The common concept in this thesis was to adapt and develop quantitative mass spectrometric assays focusing on reagents originating from the Human Protein Atlas project to quantify proteins in human cell lines, tissues and blood. The work is based around stable isotope labeled protein fragment standards that each represent a small part of a human protein-coding gene. This thesis shows how they can be used in various formats to describe the protein landscape and be used to standardize mass spectrometry experiments. The first part of the thesis describes the use of antibodies in combination with heavy stable isotope labeled antigens to establish a semi-automated protocol for protein quantification of complex samples with fast analysis time  (Paper~I). Paper II introduces a semi-automated cloning protocol that can be used to selectively clone variants of recombinant proteins, and highlights the automation process that is necessary for large-scale proteomics endeavors. This paper also describes the technology that was used to clone all protein standards that are used in all of the included papers.                       The second part of the thesis includes papers that focus on the generation and application of antibody-free targeted mass spectrometry methods. Here, absolute protein copy numbers were determined across human cell lines and tissues (Paper III) and the protein data was correlated against transcriptomics data. Proteins were quantified to validate antibodies in a novel method that evaluates antibodies based on differential protein expression across multiple cell lines (Paper IV). Finally, a large-scale study was performed to generate targeted proteomics assays (Paper V) based on protein fragments. Here, assay coordinates were mapped for more than 10,000 human protein-coding genes and a subset of peptides was thereafter used to determine absolute protein levels of 49 proteins in human serum.                       In conclusion, this thesis describes the development of methods for protein quantification by targeted mass spectrometry and the use of recombinant protein fragment standards as the common denominator. / <p>QC 20161013</p>