Cannibalism is a seemingly aberrant interaction, appearing counter to the fitness of individuals. Yet cannibalism is not overly uncommon, and naturally occurs among aquatic organisms, including larval amphibians. In temporary wetlands larval amphibians are in a race to complete metamorphosis before their aquatic habitat disappears. When intraspecific competition intensifies, eating conspecifics may represent a beneficial if not necessary strategy. The research presented within this thesis aims to characterize factors that influence cannibalism within populations of larval amphibians. Wood frog tadpoles (Lithobates sylvaticus) were used to test potential benefits of cannibalism as a diet, determine if dietary quality and nutritional stress influence cannibalism, and investigate the roles of competition and chemical cues in influencing cannibalism. Larval long-toed salamanders (Ambystoma macrodactylum), and ringed salamanders (A. annulatum) were used to investigate a functional link between trophic polymorphism and cannibalism in natural populations. Results suggest that perceived increases in competition may stimulate some individuals to become less risk averse, and more aggressive, which may in turn facilitate cannibalistic behaviour. Cannibalism itself provided only conditional benefits to larval wood frogs, rather than the optimal growth that would be expected from an ideal diet. However, this may have been the result of individual variation in response to the diet and/or conspecific cues as opposed to a nutritional deficit. In conditions where tadpoles could perceive increased competition they altered their behaviour and morphology in ways that may improve their foraging success and potentially promote cannibalism. Finally, a functional link appears to exist between head morphology and cannibalism in natural wetlands. However, the appearance of this morphology appears related to conditions that may facilitate increased population densities through rapid pond drying.

Habitat fragmentation can influence the genetics of a population through the direct loss of genetic diversity, and by the genetic processes that occur as a result of small remnant populations or the geographic isolation of populations. I examined the population genetics of two woodland amphibian species in localities with different land-use histories. The wood frog (Rana sylvatica) and the red-backed salamander (Plethodon cinereus) use the same general habitat but differ with respect to a few key life-history characteristics relating to dispersal. I then compared between species the relative influence each land-use scenario had on the population genetic structure. I found that habitat fragmentation affected the population genetics of the two amphibians and did so differently for each species. The differential population genetic response of these two amphibians to habitat fragmentation reinforces the important role of life-history characteristics in how the genetic structure of a population is shaped over time.

This study devised a method to detect Ribeiroia ondatrae (class Trematoda) in water-bodies using environmental DNA (eDNA) collected from filtered water samples from selected ponds in the USA and Canada. Species-specific PCR primers were designed to target the Internal Transcribed Spacer-2 (ITS-2) region of the parasite’s genome. The qualitative PCR method was 70% (n=10) accurate in detecting R. ondatrae in ponds previously found to contain the parasite, while the qPCR method was 88.9% (n=9). To examine how the retinoic acid (RA) pathway gene expression may be perturbed during R. ondatrae infections, leading to limb development abnormalities in the wood frog (Lithobates sylvaticus). Multiple sequence alignments were used to design degenerate PCR primers to eight RA biosynthesis genes, but only two gene fragments were identified using this approach. Without effective primer sets it was not possible to measure changes in gene expression in infected frogs.

Ce mémoire de thèse porte sur la propagation d'impulsions ultra-courtes à 160-Gb/s dans des lignes de fibres optiques gérées en dispersion. Dans une première partie, nous décrivons la mise en place expérimentale d'un dispositif SHG-FROG pour la caractérisation de trains d'impulsions à très haute cadence. Par la suite, nous démontrons l'efficacité du phénomène de compression d'un battement sinusoïdal par mélange à quatre ondes multiple pour la génération d'impulsions cadencées à 160-GHz. Afin de corréler au maximum les résultats théoriques et expérimentaux, nous décrivons ensuite la mise an place d'un banc de caractérisation de fibres optiques basée sur l'instabilité modulationnelle. La dernière étape de ce travail de thèse consiste finalement en la réalisation de boucles à recirculation monocanales basées d'une part sur la gestion de la dispersion dense en vue d'applications transocéaniques et d'autre part sur la gestion de la dispersion classique pour des applications de type terrestre.

This study devised a method to detect Ribeiroia ondatrae (class Trematoda) in water-bodies using environmental DNA (eDNA) collected from filtered water samples from selected ponds in the USA and Canada. Species-specific PCR primers were designed to target the Internal Transcribed Spacer-2 (ITS-2) region of the parasite’s genome. The qualitative PCR method was 70% (n=10) accurate in detecting R. ondatrae in ponds previously found to contain the parasite, while the qPCR method was 88.9% (n=9). To examine how the retinoic acid (RA) pathway gene expression may be perturbed during R. ondatrae infections, leading to limb development abnormalities in the wood frog (Lithobates sylvaticus). Multiple sequence alignments were used to design degenerate PCR primers to eight RA biosynthesis genes, but only two gene fragments were identified using this approach. Without effective primer sets it was not possible to measure changes in gene expression in infected frogs.

Ce mémoire de thèse s'inscrit dans le contexte du projet FUTUR financé par l'ANR et concernant le développement de Fonctions optiques pour les Transmissions à très haut débit dans le Réseau coeur et porte sur la génération de sources optiques fibrées très hautes cadences et la caractérisation de fibres optiques microstructurées en verre de Chalcogénure. A cet effet, nous étudions les caractéristiques linéaires et non-linéaires au sein de fibres microstructurées en verre de chalcogénures conçue et réaliser via différentes collaborations dans le cadre du projet de l'ANR FUTUR. Pour cela un grand nombre de méthodes de caractérisations ont été mises au point donnant une comparaison entre une fibre SMF standard et ces fibres microstructurées chalcogénures. Par exemple, un montage interférométrique pour la mesure de la dispersion chromatique pour échantillon court, ou encore de nombreux banc expérimentaux permettant la caractérisation des propriétés non-linéaires de ces fibres (diffusion Raman, diffusion Brillouin, Coefficient non linéaire Kerr...). La seconde partie de ce mémoire présente la mise au point de méthode de conversion d'un battement sinusoïdal en un train d'impulsions hautement cadencé. Il est montré dans ce manuscrit que cette technique a été exploitée au plus prêt de ses limites, par l'obtention d'impulsions extrêmement courtes et par des débits très élevés. Les trains d'impulsions à très hautes cadences ont été caractérisés par un dispositif expérimental SHG-FROG. Une démonstration de la multiplication du débit par deux a été démontrée par l'effet Talbot.

Submitted by Maike Costa (maiksebas@gmail.com) on 2017-09-05T12:44:35Z No. of bitstreams: 1 arquivototal.pdf: 1934445 bytes, checksum: df85a8fce8aac05573575236c659735e (MD5) / Made available in DSpace on 2017-09-05T12:44:35Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 1934445 bytes, checksum: df85a8fce8aac05573575236c659735e (MD5) Previous issue date: 2017-02-16 / Bullfrog meat is a delicacy in many countries and its consumption has expanded in the last decades. The back is a byproduct that presents high nutritional value and its use is being exploited through mechanical deboning, obtaining mechanically separated meat, providing raw material for the elaboration of various food products, which add value to the back, among them surimi. The objective of this study was to study the feasibility of using mechanically separated meat from the back of bullfrogs in the elaboration of surimi gel, evaluating the influence of the number of washing cycles and of different concentrations of corn starch on the characteristics of nutritional quality, Physicochemical properties, sensorial acceptance, and to evaluate its lipid and protein oxidative stability during storage under refrigeration (± 4 ° C) for a period of 60 days. The characterization of the surimi gels was performed from the physicochemical properties of partial chemical evaluation, pH, Aw, CRA, color parameters (L *, a* and b *), texture profile, and nutritional quality through composition Of fatty acids and amino acid profile. The evaluation of oxidative stability was measured by the analysis of TBARS, for lipids, and NBVT, carbonyl compounds and free thiols, for proteins. Sensory acceptance (appearance, taste, color, odor and texture) were also determined. The results showed that the studied variables exerted significant effects on the characteristics of the gels. The washing number was the factor that affected the highest number of parameters studied. Increasing the wash cycles was positive when the lipid content decreased, the gel color improved, the whiteness increased, and the gel firmness improved. Gels have good amounts of polyunsaturated fatty acids (linoleic, linolenic and arachidonic), and it has all the essential amino acids. Changes in oxidative stability were observed during storage, especially after the 30th day. The increase in the number of washing cycles of surimi was an effective method to significantly reduce (p <0.05) the formation of oxidation-indicating compounds, since treatments with higher number of washes had the lowest oxidative values. In sensory evaluation, the preference of the consumers was for firmer and white gels, leading to the choice of treatments 4 and 5, but all the treatments presented means of acceptance index above 70%. It was possible to use DMS in the elaboration of surimi gel, since the processing improved the functional and sensorial properties of this byproduct, making possible the use of the same in food of this genus. / A carne de rã-touro é uma iguaria em muitos países e seu consumo tem se expandido nas últimas décadas. O dorso é um subproduto que apresenta alto valor nutricional e sua utilização está sendo explorada através da desossa mecânica, na obtenção de carne mecanicamente separada, disponibilizando matéria prima para elaboração de diversos produtos alimentares, que venham agregar valor ao dorso, dentre eles o surimi. Neste contexto objetivou-se estudar a viabilidade da utilização da carne mecanicamente separada do dorso de rãstouro na elaboração de gel de surimi, avaliando a influência do número de ciclos de lavagem e de diferentes concentrações de amido de milho sobre as características de qualidade nutricional, propriedades físico-químicas, aceitação sensorial, além de avaliar sua estabilidade oxidativa lipídica e proteica durante armazenamento sob refrigeração (±4 °C) por um período de 60 dias. A caracterização dos géis de surimi foi realizada a partir das propriedades físicoquímicas de avaliação química parcial, pH, Aa, CRA, parâmetros de cor (L*, a* e b*), perfil de textura, e a qualidade nutricional através da composição dos ácidos graxos e perfil aminoacídico. A avaliação da estabilidade oxidativa foi medida a partir da análise de TBARS, para lipídeos, e NBVT, compostos carbonílicos e tióis livres, para proteínas. A aceitação sensorial (aparência, sabor, cor, odor e textura) também foram determinados. Os resultados demonstraram que as variáveis estudadas exerceram efeitos significativo nas características dos géis. Sendo o número de lavagem o fator que afetou o maior número de parâmetros estudados. O aumento dos ciclos de lavagens foi positivo quando diminuiu o teor de lipídios, aperfeiçoou a cor do gel, aumentando o valor da brancura, e melhorou a firmeza do gel. Os géis possuem boas quantidades de ácidos graxos poliinsaturados (linoleico, linolênico e araquidônico), e apresenta todos os aminoácidos essenciais. Foi observado alterações na estabilidade oxidativa durante o armazenamento, sobretudo após o 30º dia. O aumento do número de ciclos de lavagem do surimi foi um método eficaz para reduzir significativamente (p <0,05) a formação dos compostos indicadores da oxidação, pois os tratamentos com maior número de lavagens apresentaram os menores valores oxidativos. Na avaliação sensorial, a preferência dos consumidores foi por géis mais firmes e brancos, conduzindo a escolha dos tratamentos 4 e 5, porém todos os tratamentos apresentaram médias do índice de aceitação acima de 70%. Foi viável a utilização do DMS na elaboração de gel de surimi, pois o processamento melhorou as propriedades funcionais e sensoriais desse subproduto, tornando possível a utilização do mesmo em alimentos desse gênero.

Métodos in vitro utilizando epitélio intestinal animal são importantes ferramentas para avaliar a permeabilidade de fármacos, propriedade que é um importante parâmetro de biodiosponibilidade. Considerando que o maior objetivo na indústria farmacêutica é desenvolver novos fármacos com boa biodisponibilidade oral, o projeto teve como objetivo padronizar o modelo de permeação com membrana de intestino de rã (Rana catesbeiana) em células de Franz, comparando seus resultados com ensaios de células Caco-2. Os fármacos modelo utilizados foram os antivirais zidovudina e aciclovir. A quantidade de fármaco permeado foi determinada por método de eletroforese capilar para o método com intestino de rã touro e por HPLC-UV para os ensaios com células Caco-2. O parâmetro de permeação foi o coeficiente de permeabilidade aparente (Papp) dos fármacos para ambos modelos experimentais. Para estabelecimento do protocolo experimental dos estudos de permeabilidade intestinal de rã, foi proposto um projeto fracionado 24-1 com 4 ensaios adicionais usando o software Minitab, e as variáveis foram: secção intestinal, pH da solução de Ringer e temperatura. A análise do planejamento experimental feita pela estimativa dos parâmetros da regressão obtidos através dos resultados do modelo fatorial possibilitou a determinação dos coeficientes da equação matemática que definiu a influência das variáveis sobre o coeficiente de permeabilidade aparente dos fármacos. Os efeitos das variáveis pH e temperatura interpretados conjuntamente apresentaram interferência leve, porém as variáveis fármaco e secção intestinal interpretados juntos tiveram interferência importante, mostrando maior permeação dos fármacos através da secção inicial do intestino da rã. Os resultados de Papp foram: para o metoprolol, pelo método das células Caco-2 foi de 28 x 10-6 cm/s, valor que está de acordo com demais dados de células Caco-2 na literatura e o valor obtido com células de Franz que mais se adequada a estes resultados e demais disponíveis provenientes de outras técnicas na literatura, foi de 28,1 x 10-6 cm/s, em uma das condições do planejamento estatístico utilizando segmento final da membrana epitelial da rã. No caso do aciclovir, o resultado de Papp de 0,48 x 10-6 cm/s também obtido em uma das condições envolvendo segmento intestinal final da rã foi exatamente igual a o valor 0,48 x 10 - 6 cm/s, encontrado com células Caco-2 no presente estudo e estão de acordo com outros valores disponíveis na literatura por Trapani e colaboradores, 2004 e também com células Caco-2. Para zidovudina o valor de Papp obtido em uma das condições utilizando segmento intestinal inicial da rã, de 13 x 10-6 cm/s, foi a que mais se assemelhou ao obtido pela técnica de células Caco-2, 13,6 x 10-6 cm/s, e também está de acordo com demais dados da literatura. / There are lots of different in vitro technics in the literature using animal intestinal epithelium to estimate permeability of drugs, property that is an important parameter of bioavailabity. Considering that the main objective of Pharmaceutical Companies is the development of new drugs with good oral bioavailabity, the aim of this work was to standardize the permeability of antivirals using in vitro/ex vivo method of intestinal epithelium of Rana catesbeiana in Franz cells and compare these results to those obtained from studies using Caco-2 cells. Zidovudine and Acyclovir were selected as model drugs. The amount of drug permeated will be determined by the method of capillary electrophoresis for assays using Rana Catesbeiana and HPLC-UV for studies with Caco-2 cells. The permeation parameter determined was the apparent permeability coefficient (Papp) of drugs for both experimental models. To establish the experimental protocol to studies of intestinal permeability of frog, it was proposed a fractional 24-1 design with 4 additional tests using Minitab software and the variables were: intestinal section, pH of Ringer solution and temperature. The analysis of the experimental design made by the estimate of the regression parameters obtained from the factorial model results allowed the determination of the coefficients of the mathematical equation that defines the influence of the variables on the apparent permeability coefficient of acyclovir and zidovudine. The effects of pH and temperature interpreted jointly presented a slight interference, but the variables drug and intes tinal section interpreted together had major interference, showing greater permeation of drugs through the initial section of the intestine of the frog . The results of Papp were: for metoprolol, with the method of Caco-2 cells was 28 x 10-6 cm/s, a value which is consistent with other data of Caco-2 cells provided in the literature and the condition obtained with Franz cells that are most suitable for these and other results obtained from other techniques available in the literature, was 28.1 x 10-6 cm/s, provided with the final intestinal segment using frog epithelial membrane. In the case of acyclovir, the result of Papp of 0.48 x 10-6 cm/s obtained in one condition with final frog intestinal segment was exactly equal to the value of 0.48 x 10-6 cm/s, found with Caco-2 cells in the present study and are in agreement with other values available in the literature for Trapani and colegues, 2004 and also with Caco-2 cells. The Papp value for zidovudine obtained with the initial gut segment of frog, 13 x 10-6 cm /s was which more resembled that obtained by the technique of Caco-2 cells, 13.6 x 10-6 cm/s and is also consistent with other literature data.

Increasing human population size is increasing the demand for resources like timber, oil, tea, coffee, and other crops. Plantation crops mimic some aspects of native habitats, and there are studies that report the presence of some native anuran biodiversity in plantations. I focused on tea plantations in the Western Ghats-Sri Lanka Biodiversity Hotspot and studied the diversity and health of anurans in different habitats found within a tea cultivation area, near Munnar region in the Western Ghats, India. The landscape includes tea bushes, native evergreen shola forest patches, and eucalyptus forest stands. I reviewed 40 studies comparing amphibian species richness in plantations and primary forests. The age of the plantation, type of plantation, presence in a biodiversity hotspot, number of species in the dominant plantation type, number of species in the paired forest habitat, and latitudinal zone of the study, did not correlate with species richness, but plantations that had periodic harvesting had higher species richness than plantations that practiced clear-cut harvesting. I tested different methods of standard amphibian sampling in the field season 2012 in Munnar, and found that Visual Encounter Surveys (VES) in the shola habitat and Stream Transects (ST) were the most efficient. Using the VES and ST methods, I sampled amphibians in three upland habitats (tea, shola, and eucalyptus) at four different sites, and 150m of stream transects at each site, for two consecutive monsoon seasons. Fourteen species were encountered in both years and the community structure was similar across the years. The community structure at the four sites that was driven by the presence of exclusive species at each site and species composition in streams was similar across the landscape and was driven by the presence of similar species in streams across the four sites. Two hundred and sixteen anurans of 17 species, were tested for the presence of the lethal fungus Batrachochytrium dendrobatidis. The preliminary results from the Polymerase Chain Reactions were negative. My study provides baseline data for anuran diversity, composition, and health in the Munnar region of India and results of this project can be compared with tea plantations around the world.

Amphibians develop in aquatic environments where they are very susceptible to the effects of pesticides and other environmental contaminants. Glyphosate-based herbicides are widely used and have been shown to affect survival and development of tadpoles under laboratory conditions. The goal my thesis is to determine if agriculturally relevant exposure to Roundup WeatherMax®, a herbicide formulation containing the potassium salt of glyphosate and an undisclosed surfactant, influences the survival and development of wood frogs tadpoles (Lithobates sylvaticus) under both laboratory and field conditions. In the field, experimental wetlands were divided in half using an impermeable curtain so that each wetland contained a treatment and control side. Tadpoles were exposed to two pulses of this herbicide at environmentally realistic concentration (ERC, 0.21 mg acid equivalent (a.e.)/L) and predicted environmental concentrations (PEC, 2.89 mg a.e./L), after which survival, growth, development, and expression of genes involved in metamorphosis were measured. Results indicate that exposure to the PEC is extremely toxic to tadpoles under laboratory conditions but not under field conditions. Results from both experimental conditions show sublethal effects on growth and development, and demonstrate that ERC of glyphosate-based herbicides have the potential to alter hormonal responses during metamorphosis. My secondary objectives were to compare the effects of Roundup WeatherMax® to the well-studied Vision® formulation (containing the isopropylamine (IPA) salt of glyphosate and POEA), and to determine which ingredient(s) are responsible for the sublethal effects on development. Survival, growth and gene expression results indicate that Roundup WeatherMax® has greater toxicity than Vision® formulation. Contrary to my prediction, results suggest that, under realistic exposure scenarios, POEA is not the sole ingredient responsible for the observed developmental effects. However, my results demonstrate that chronic exposure to the POEA surfactant at the PEC (1.43 mg/L) is extremely toxic to wood frog tadpoles in laboratory. As part of the Long-term Experimental Wetlands Area (LEWA) project, this research contributes to overall knowledge of the impacts of glyphosate-based herbicides on aquatic communities.