Le nord du système du Courant de Humboldt (NHCS), le long des côtes péruviennes, est l'une des régions océanique les plus productives au monde. Il représente moins de 0.1% de la surface des océans mondiaux mais contribue actuellement à plus de 10% des captures mondiales en poissons, avec l’anchois Engraulis ringens comme espèce emblématique. Comparé aux autres systèmes d’upwelling de bord Est, la forte productivité en poissons ne peut être expliquée par une productivité primaire plus élevée. Par contre, le NCHS est la région où El Niño, et la variabilité climatique en général est la plus notable. D’autre part, les eaux de surface oxygénées recouvrent une zone de minimum d’oxygène extrêmement intense et superficielle. L’objectif principal de ce travail est de mieux comprendre les relations trophiques au sein du NHCS en combinant l'analyse de contenus stomacaux et d'isotopes stables. Cette étude se focalise sur une variété d’organismes allant des bas niveaux trophiques comme le zooplancton aux prédateurs supérieurs (oiseaux et les otaries à fourrure). Elle combine des études de contenus stomacaux ponctuelles et sur le long terme d’espèces clés telles que l’anchois et la sardine Sardinops sagax et une analyse plus globale, basée sur l'utilisation d'isotopes stables et considérant l’ensemble du réseau trophique dans les années récentes (2008 – 2012). Les analyses des contenus stomacaux d'anchois et de sardine ont permis de revisiter l'écologie de ces espèces. En effet, bien que le phytoplancton domine largement les contenus stomacaux en termes d’abondance numérique, le zooplancton est de loin la composante alimentaire la plus importante pour ces deux espèces en termes de carbone. Dans le cas de l’anchois, les euphausiacés contribuent à plus de 67.5% du carbone ingéré, suivis par les copépodes (26.3%). Sélectionner les proies les plus grandes telles que les euphausiacés procure un avantage énergétique pour l’anchois dans cet écosystème où les carences en oxygène imposent de fortes contraintes métaboliques aux poissons pélagiques. La sardine se nourrit de zooplancton plus petit que l’anchois (copépodes plus petits et moins d’euphausiacés). Ainsi, la compétition trophique entre les sardines et les anchois est minimisée dans le NSCH par le partage de la ressource zooplancton selon sa taille, comme cela a déjà été montré dans d’autres écosystèmes. Ces résultats remettent en question la compréhension première de la position des petits poissons pélagiques (zooplanctonophage et non phytoplanctonophage) dans la chaine trophique ce qui implique de reconsidérer le fonctionnement et les modèles trophiques du NCHS. Afin d’obtenir une compréhension plus globale de la position trophique relative des principaux composants du NHCS une approche basée sur des analyses d’isotopes stables (δ13C et δ15N) a été utilisée. Pour ce faire, la signature isotopique d'échantillons de 13 groupes taxonomiques (zooplancton, poissons, calmars et prédateurs supérieurs) prélevés entre 2008 et 2011 a été déterminée. Les valeurs de δ15N obtenues sont fortement impactées par l’espèce, la taille et la latitude. Le long de la cote péruvienne, la zone de minimum d’oxygène devient en effet plus intense et plus superficielle au sud de ~7.5ºS impactant fortement la valeur de δ15N de la ligne de base. Nous avons donc utilisé un modèle linéaire à effet mixte prenant en compte les effets latitude et taille afin de prédire la position trophique relative des composants clés de l’écosystème. Ces analyses isotopiques confirment les résultats issus des contenus stomacaux sur le régime alimentaire de l’anchois et mettent en évidence l’importance potentielle d’une composante souvent négligée de l’écosystème, la galathée pélagique Pleuroncodes monodon. En effet, nos résultats supportent l’hypothèse selon laquelle cette espèce s’alimenterait en partie sur les oeufs et larves d’anchois, menaçant ainsi les premiers stades de vie des espèces exploitées. [...] / The northern Humboldt Current system (NHCS) off Peru is one of the most productive world marine regions. It represents less than 0.1% of the world ocean surface but presently sustains about 10% of the world fish catch, with the Peruvian anchovy or anchoveta Engraulis ringens as emblematic fish resource. Compared with other eastern boundary upwelling systems, the higher fish productivity of the NHCS cannot be explained by a corresponding higher primary productivity. On another hand, the NHCS is the region where El Niño, and climate variability in general, is most notable. Also, surface oxygenated waters overlie an intense and extremely shallow Oxygen Minimum Zone (OMZ). In this context, the main objective of this study is to better understand the trophic flows in the NHCS using both stomach content and stable isotope analyses. The study focuses on a variety of organisms from low trophic levels such as zooplankton to top predators (seabirds and fur seals). The approach combines both long-term and specific studies on emblematic species such as anchoveta, and sardine Sardinops sagax and a more inclusive analysis considering the 'global' food web in the recent years (2008 –2012) using stable isotope analysis.Revisiting anchovy and sardine we show that whereas phytoplankton largely dominated anchoveta and sardine diets in terms of numerical abundance, the carbon content of prey items indicated that zooplankton was by far the most important dietary component. Indeed for anchovy euphausiids contributed 67.5% of dietary carbon, followed by copepods (26.3%).Selecting the largest prey, the euphausiids, provide an energetic advantage for anchoveta in its ecosystem where oxygen depletion imposes strong metabolic constrain to pelagic fish. Sardine feed on smaller zooplankton than do anchoveta, with sardine diet consisting of smaller copepods and fewer euphausiids than anchoveta diet. Hence, trophic competition between sardine and anchovy in the northern Humboldt Current system is minimized by their partitioning of the zooplankton food resource based on prey size, as has been reported in other systems.These results suggest an ecological role for pelagic fish that challenges previous understanding of their position in the foodweb (zooplanktophagous instead of phytophagous), the functioning and the trophic models of the NHCS.Finally to obtain a more comprehensive vision of the relative trophic position of NHCS main components we used stable isotope analyses. For that purpose we analyzed the δ13C and δ15N stable isotope values of thirteen taxonomic categories collected off Peru from 2008 - 2011, i.e., zooplankton, fish, squids and air-breathing top predators. The δ15N isotope signature was strongly impacted by the species, the body length and the latitude. Along the Peruvian coast, the OMZ get more intense and shallow south of ~7.5ºS impacting the baseline nitrogen stable isotopes. Employing a linear mixed-effects modelling approach taking into account the latitudinal and body length effects, we provide a new vision of the relative trophic position of key ecosystem components. Also we confirm stomach content-based results on anchoveta Engraulis ringens and highlight the potential remarkable importance of an often neglected ecosystem component, the squat lobster Pleuroncodes monodon. Indeed, our results support the hypothesis according to which this species forage to some extent on fish eggs and larvae and can thus predate on the first life stages of exploited species. However, the δ13C values of these two species suggest that anchoveta and squat lobster do not exactly share the same habitat. This would potentially reduce some direct competition and/or predation.

The spider mite occurrence, on soybean (Glycine max (L.) Merril), is sporadic and associated whit dry periods. Recently, in continuous years, was reported mite outbreaks in soybean, in some sites of Rio Grande do Sul State. In this context two research was conducted, one in summer crop 2004/05 and other in 2005/06. The first was carried for study the mite occurrence and geographic distribution, on soybean, from some place of Rio Grande do Sul State. The second was conducted for study the effect of the two soybean cultivars and of some weed management systems on mite density and study their population dynamic on soybean. In summer crop 2004/05 was carried some mite samplings in soybean field at State. The mite species found, all beloung to the Tetranychidae family, are Mononychellus planki (McGregor), Tetranychus desertorum Banks, T. gigas Pritchard & Baker, T. ludeni Zacher and T. urticae Koch. Most of this species are well distributed in the diferents sampling regions of this study. From the results was made a species distribution map and a taxonomic key. In summer crop 2005/06, in Santa Maria, RS, 11 treatments was study. Its was constitute in two soybean cultivars, one transgenic glyphosato-tolerant and other non-transgenic, every one whit five weed management systems: (1) without management; (2) hand management; (3) herbicide bentazone + sethoxydim; (4) bentazone only; (5) sethoxydim only. The 11th treatment was the herbicide glyphosate sprayed on the transgenic soybean. The mite species found in this study are M. planki and T. gigas. The weed management systems is more determinant, on the spider mite population on soybean, than the soybean cultivar. The mite population presenteded inverse correlation whit weed infestation and weed density. The climatic fators determined the mite population flutuation and the population peak occured in the initial period of soybean pods development. / A ocorrência de ácaros-praga em soja (Glycine max (L.) Merril) é esporádica e está, comumente, associada à períodos de estiagem. Recentemente, em safras seguidas, foram observados ataques severos de ácaros à soja em algumas regiões do estado do Rio Grande do Sul. Neste contexto foram realizados dois experimentos, um na safra agrícola 2004/05 e outro em 2005/06. O primeiro teve objetivo de estudar a ocorrência e a distribuição geográfica de ácaros fitófagos, associados à soja, em municípios de seis regiões produtoras do estado do Rio Grande do Sul. O segundo objetivou avaliar o efeito de duas cultivares de soja e de diferentes sistemas de manejo de plantas daninhas sobre a densidade populacional de ácaros em soja e estudar a dinâmica populacional destes ácaros na cultura. Em 2004/05 foram realizadas amostragens de ácaros em lavouras de soja no Estado. As espécies de ácaros encontradas são Mononychellus planki (McGregor), Tetranychus desertorum Banks, T. gigas Pritchard & Baker, T. ludeni Zacher e T. urticae Koch, todos são tetraniquídeos. A maior parte destas espécies estiveram bem distribuídas nas diferentes regiões amostradas neste levantamento. Com base nestes resultados foi elaborado um mapa com a distribuição das espécies e uma chave de identificação. Em 2005/06 foram estudados, em Santa Maria, RS, 11 tratamentos. Estes consistiram em duas cultivares de soja, uma transgênica glifosato-tolerante e a outra não-transgênica, cada uma sob cinco sistemas de manejo de plantas daninhas: (1) sem controle; (2) arranquio manual; (3) manejo tradicional com os herbicidas bentazona e setoxidim; (4) apenas com bentazona; (5) apenas com setoxidim. E adicionalmente um tratamento com o herbicida glifosato sobre a cultivar de soja transgênica. Os ácaros-praga ocorrentes foram M. planki e T. gigas. A densidade populacional destes ácaros em soja foi mais afetada pelos sistemas de manejo de plantas daninhas do que pela cultivar, e esteve inversamente correlacionada com a quantidade e diversidade de plantas daninhas. A flutuação populacional destes ácaros foi influenciada por fatores climáticos e o pico populacional ocorreu na fase de início da formação de legumes da soja.

L’huître creuse, Crassostrea gigas, est une espèce dont la production aquacole représente un intérêt économique tant au niveau mondial qu’aux niveaux européen et français. Cependant, cette espèce subit des mortalités estivales enregistrées dès le début du 20ème siècle et, depuis 2008, ce phénomène s’est amplifié et menace essentiellement les huîtres juvéniles. La production aquacole d’huître creuse subit les conséquences de ces mortalités massives ; c’est pourquoi ce phénomène est étudié depuis de nombreuses années. En France, la bactérie Vibrio splendidus et le virus Ostreid Herpes Virus 1 (OsHV-1) sont le plus souvent associés aux épisodes de mortalités massives d’huîtres creuses juvéniles et il a été démontré que les individus sélectionnés pour leur résistance aux mortalités estivales étaient capables de ralentir l’augmentation de la charge virale en OsHV-1 dans leurs tissus puis de la faire régresser. Ces mêmes individus présenteraient également un effort reproducteur plus modeste que des individus sélectionnés pour leur sensibilité aux mortalités estivales. Ce travail de thèse s’inscrit dans ce contexte et a donc eu pour principal objectif d’améliorer la connaissance de l’architecture génétique de la reproduction de C. gigas en identifiant des régions du génome ou QTLs (Quantitative Trait Loci) impliquées dans l’effort reproducteur et de mettre en évidence d’éventuelles relations génétiques entre survie et reproduction, des QTLs impliqués dans la survie ayant déjà été détectés. Afin de caractériser l’effort reproducteur, il a été nécessaire de développer un ensemble de nouveaux outils. D’un point de vue biologique, 21 familles F2 ont été produites à partir des lignées sélectionnées pour leur réponse contrastée aux mortalités estivales. D’un point de vue moléculaire, de nouveaux marqueurs SNP (Single Nucleotide Polymorphism) ont été développés afin d’augmenter la densité de la carte génétique déjà disponible pour C. gigas. D’un point de vue technique, l’Imagerie par Résonance Magnétique (IRM) a permis d’observer la gamétogenèse de 300 individus d’une même famille F2 au cours de huit sessions réparties sur deux années alors que les études précédentes étaient limitées à une observation ponctuelle; les méthodes classiques d’observation de la gamétogenèse entrainant nécessairement la mort des animaux. Une forte corrélation a été mise en évidence entre les observations par IRM et par la méthode classique de l’histologie. En plus de l’estimation du rapport gonado-somatique (indice traditionnellement utilisé pour caractériser l’effort reproducteur), l’IRM a également permis d’observer des variations individuelles de la cinétique de la gamétogenèse ainsi que des différences entre les mâles et les femelles; le sexe étant identifiable sur les images obtenues par IRM. Parallèlement, 300 individus de deux autres familles F2 ont été sacrifiés pour estimer le rapport gonado-somatique par histologie. Cette approche a ainsi permis de détecter des QTLs impliqués dans de nombreux traits concernant la gamétogenèse. Des individus provenant des trois familles F2 caractérisés pour l’effort reproducteur ont été caractérisés pour la survie à un épisode de mortalités estivales. Cette étude a permis de détecter des QTLs impliqués dans le caractère « survie ». Ces QTLs correspondent, pour certains, à ceux détectés au cours d’une étude précédente. De plus, ces QTLs sont parfois colocalisés avec des QTLs impliqués dans l’effort reproducteur. Bien que la reproduction de l’huître creuse soit un caractère complexe à suivre, les nouveaux outils utilisés au cours de ce travail de thèse ont permis d’acquérir de nouvelles connaissances. Le séquençage du génome complet de Crassostrea gigas ainsi que les nouvelles méthodes de séquençage pourront peut-être permettre d’affiner les régions QTLs détectées. / The Pacific oyster, Crassostrea gigas, is a major aquacultured species whose production represents an economic interest at worldwide, european and french levels. However, this species undergoes summer mortalities recorded from the beginning of the 20th century and, since 2008, this phenomenon increased and threatens mainly juvenile oysters. Aquaculture production of oysters suffers consequences of mass mortalities, that’s why this phenomenon has been studied for many years. In France, the bacterium Vibrio splendidus and the Ostreid virus Herpes Virus 1 (OsHV-1) are often associated with mass mortality outbreaks of juveniles oysters and it was demonstrated that selected individuals for resistance to summer mortality were able to slow the increasing in viral load OsHV-1 in their tissues and then to decline it. These same individuals also present a lighter reproductive effort than individuals selected for their sensitivity to summer mortality. In this context, this study aimed to improve the knowledge of genetic architecture of reproduction of C. gigas by identifying some regions of the genome called QTLs (Quantitative Trait Loci) involved in reproductive effort and highlighting possible genetic relationships between reproduction and survival; QTLs involved in survival being already detected. To characterize the reproductive effort, it was necessary to develop a set of new tools. From a biological point of view, 21 F2 families were produced from lines selected for their contrasting response to summer mortality. From a molecular point of view, new SNPs (Single NucleotidePolymorphism) were developed to increase density of the genetic map already available for C. gigas. On a technical point of view, Magnetic Resonance Imaging (MRI) allowed to observe the gametogenesis of 300 individuals of the same family F2 during eight sessions over two years while previous studies were limited to a one-time observation because of the conventional methods of observation of gametogenesis leading necessarily to the death of the animals. A strong correlation was found between observations by MRI and observations by the conventional method of histology. In addition to the estimation of gonadic index (index traditionally used to characterize there productive effort), MRI also revealed individual variations in kinetics of gametogenesis and differences between males and females, the sex being identifiable on MRI images. In parallel, 300 individuals from two F2 families were sacrificed to estimate the gonadic index by histology. This approach enabled the detection of QTLs involved in many gametogenesis traits. Individuals from the three families characterized for F2 reproductive effort were characterized for survival during a summer mortality outbreak. This study was able to detect QTLs involved in the trait "survival". These QTLs correspond to some of those detected in a previous study. In addition, these QTLs are often collocated with QTLs involved in reproductive effort. Although there production of the Pacific oyster is a complex trait to follow, the new tools used in this thesis allowed acquiring new knowledges. The sequencing of genome of Crassostrea gigas and Next-Generation Sequencing technologies may be able to help to refine the detected QTL regions.

Interannual variability of Humboldt squid (Dosidicus gigas) occurrence in the northern California Current System is largely unknown. In Oregon, the distribution of this versatile predator and what is influencing their range expansion from Mexico is poorly understood due to the recent nature of their "invasion" and a lack of monitoring. Humboldt squid are large predators that have the potential to affect ecosystem structure and fisheries because of their high-energy demands and ability to exploit a variety of oceanographic conditions and prey sources. Developing baseline distribution information is a critical first step to assess their potential ecological, social, and economic impacts, and to develop models to predict future range expansion. This study has two main objectives: (1) to document where and when Humboldt squid have been present in Oregon through cooperative fisheries research, and (2) to correlate the sightings with oceanographic conditions using a geographic information system (GIS) and species distribution modeling (SDM). I conducted 54 interviews with local fishermen and aggregated their squid sightings with available fishery-independent survey and fishery-dependent observer data from the National Marine Fisheries Service. I compiled a total of 339 Humboldt squid sightings, reported for the years 2002-2011 from the Oregon coast to 131�� west longitude. Correlation analyses were performed for Humboldt squid sightings and sea surface temperature (SST), chlorophyll a content (chla), sea surface height anomalies (SSH), dissolved oxygen at 30 m depth (30 m DO), and sea surface salinity (SSS) using a GIS, nonparametric multiplicative regression (NPMR) habitat modeling, and maximum entropy modeling (Maxent). Results indicate that oceanographic conditions have the potential to influence Humboldt squid occurrence, and in Oregon, sightings vary temporally and spatially. Combining the sightings from fishermen and scientific surveys greatly enhanced the spatial extent of the data. Humboldt squid were most frequently observed between 124.4��W and 125��W in proximity to the shelf-break at the 200 m isobath, with peak sightings (116) recorded in 2009 and the fewest (6) reported in 2003 and 2011. The highest occurrence of Humboldt squid were observed at a SST of 10.5-13.0��C, 0.26-3.0 mg m����� chla content, -4.0-1.0 m SSH anomalies, 32.2-32.8 psu SSS, and at 3-4.5 ml L����� and 6-7 ml L����� 30 m depth DO. Maps of estimated likelihood of occurrence generated by NPMR were consistent with overlayed observations from fishermen, which were not used in the model because they were limited to presence-only information. An interdisciplinary approach that incorporates cooperative fisheries research and ecosystem-based management is necessary for monitoring Humboldt squid in Oregon. Traditional methods are insufficient because Humboldt squid are data-poor, highly migratory, and are main predators of many commercially important fisheries in Oregon. Based on my findings, sightings recorded by fishermen covered a much larger area over a longer time frame than the scientific survey and observer data, and excluding their knowledge would have led to a different interpretation of Humboldt squid distribution and environmental tolerances. Although there is uncertainty in the data from potential map bias or misidentification of smaller Humboldt squid, incorporating sightings from fishermen with traditional fisheries research increases the quantity and quality of information. Cooperative monitoring for Humboldt squid could include training in species identification and sea condition reporting in logbooks. Future "invasions" are likely, and more eyes on the water will improve our understanding of the behavior and impacts of Humboldt squid on coastal resources. / Graduation date: 2013

Norovirus (NoV) is a significant cause of gastroenteritis globally, and the consumption of oysters is frequently linked to outbreaks. Depuration is the principle means employed to reduce levels of potentially harmful agents or toxins in shellfish. The aim of this thesis is to construct mathematical models which can describe the depuration dynamics of water-borne pathogens, and specifically examine the dynamics of NoV during depuration for a population shellfish. Legislation is currently under consideration within the EU by the Directorate-General for Health and Consumers (DG SANCO) to limit the maximum level of NoV that consumers are exposed to via this route. Therefore it is important to the utility of the thesis that any models constructed should incorporate control measures which could be used to implement minimum NoV levels. Doing so allowed calculation of minimum depuration times that would be required to adhere to the control measures incorporated into the models. In addition to modelling the impact on pathogens during the depuration, we wished to gain some insight into how the variability, and not just the mean levels, of water-borne pathogens can be as important with respect to the length of depuration required to minimise any food safety risks to the consumer. This proved difficult in the absence of any data sets that can be used to calculate variability measures, as little data is currently available to inform these values for NoV. However, our modelling techniques were able to calculate an upper limit on the variability of water-borne pathogens that can be well approximated by lognormal distributions. Finally we construct a model which provided linkage between the depuration process and the accretion of pathogens by shellfish while still within farming waters. This model proposed that the pulses of untreated waste waters released by sewage treatment works due to high levels of rainfall would be transmitted into shellfish whilst filter-feeding.

Orientador: Maeli Dal Pai Silva / Tese ( doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-18T12:24:51Z (GMT). No. of bitstreams: 1 Carani_FernandaRegina_D.pdf: 24872848 bytes, checksum: e4b7c794fa866be614e932ec5a33eaf6 (MD5) Previous issue date: 2011 / Resumo: O pirarucu (Arapaima gigas) caracteriza-se como uma espécie promissora para a Aqüicultura, devido principalmente às suas características de rápido crescimento e rusticidade. Sua criação em regime intensivo tem obtido enorme sucesso, podendo alcançar até 10 quilos de peso corporal em apenas um ano de criação. O pirarucu é considerado hoje uma das mais importantes espécies de peixes da bacia Amazônica e, por esta razão, é primordial que se investigue os mecanismos celulares e moleculares que controlam o rápido crescimento muscular, contribuindo com novas estratégias de criação e com a manutenção da espécie. O crescimento do músculo estriado esquelético nos peixes pode ocorrer por dois mecanismos: hipertrofia e/ou hiperplasia das fibras, a partir de células satélites ou mioblastos. Esse processo é controlado por Fatores Reguladores Miogênicos (MRFs) e pelo fator de crescimento Miostatina. O objetivo do presente estudo foi avaliar as características morfológicas e o crescimento muscular hipertrófico e hiperplásico, bem como analisar a expressão gênica e protéica da MyoD, da Miogenina e da Miostatina na musculatura esquelética do pirarucu (A. gigas), em diferentes fases de crescimento. Os animais utilizados no presente estudo foram provenientes de duas pisciculturas: na primeira, foram obtidos os "alevinos" (pós-larvas; 48 g); na segunda, os animais em diferentes estágios de crescimento, divididos em quatro grupos de acordo com o peso corporal. Grupo A (50 gramas, n=7), grupo B (420 gramas, n=7), grupo C (5,5 quilogramas, n=7) e grupo D (9,1 quilogramas, n=7). As amostras musculares foram coletadas, congeladas e submetidas à coloração HE, para avaliação do padrão morfológico das fibras, e à reação para a enzima NADH-TR, para avaliar o metabolismo oxidativo das fibras. Para avaliar o padrão de crescimento hiperplásico e hipertrófico da musculatura branca, foi calculado o menor diâmetro de uma população de fibras por animal, e estas foram distribuídas em classes, na dependência do seu diâmetro. A análise da expressão gênica de MyoD, miogenina e miostatina foi feita por Reação em Cadeia da Polimerase após Transcrição Reversa (RTqPCR); para análise da expressão protéica, foi utilizado o Western Blot. A distribuição das fibras em classes de diâmetro exibiu o seguinte padrão: o grupo A mostrou a maior parte das fibras na classe 20, o grupo B, na classe 50, o grupo C, nas classes 50 e 80, e o grupo D, na classe 80. Isso indica uma alta taxa de hiperplasia das fibras nos grupos menores (A e B) e alta hipertrofia das fibras nos grupos maiores (C e D). Para a análise da expressão gênica de MyoD e miogenina no músculo vermelho e branco dos "alevinos", não houve diferença estatística; para a miostatina, houve expressão diferencial, com os maiores níveis encontrados no músculo branco em comparação com o músculo vermelho. Na avaliação da expressão de MyoD e miogenina, tanto a expressão gênica como a expressão protéica não mostraram diferença significativa. Por outro lado, a expressão gênica da miostatina foi menor no grupo A e maior nos demais, e a expressão da proteína miostatina foi maior no grupo A, diminuindo nos demais grupos. Estes resultados refletem as características de crescimento muscular da espécie e sugerem que a expressão dos MRFs e da miostatina são responsáveis pelo balanço entre a hiperplasia e a hipertrofia das fibras, contribuindo para o rápido crescimento da espécie e a manutenção das características do filé / Abstract: Pirarucu (Arapaima gigas) is a promising fish species for Aquaculture programs mainly by the fast growing feature and rusticity. Their rearing under intensive conditions generated much successful results, as they reach up to 10 kilograms in just one year. Considered one of the most important fish species from Amazon basin, it is of primary interest to investigate the cellular and molecular mechanisms that control the fast muscle growth in pirarucu, providing information for new rearing strategies and species conservation. In most fish, skeletal muscle growth occurs by two mechanisms: hypertrophy and hyperplasia, from satellite cells or myoblasts. These process are under control by Myogenic Regulatory Factors (MRFs) and by the growth factor Myostatin. The animals were obtained from two pisciculture, where we got the alevin pirarucu (n=7; 48 grams weight), and the specimens at different growth stages, divided into groups according body weight. Group A (50 grams, n=7), group B (420 grams, n=7), group C (5,5 kilograms, n=7) and group D (9,1 kilograms, n=7). Muscle samples were collected, frozen and stained with HE for morphological analysis, and submitted to NADH-TR enzyme reaction for oxidative methabolism analysis. To evaluate hyperplasic and hypertrophic muscle growth, it was measured the smallest diameter from a set of fibers, which were grouped into diameter classes. Gene expression analysis of MyoD, Myogenin and Myostatin were performed by Quantitative Polimerase Chain Reaction after Reverse Transcription (RT-qPCR); protein content analysis was by Western Blot technique. Muscle fibers distribution in classes showed the following pattern: group A showed most fibers in class 20, group B, in class 50, group C, in classes 50 and 80, and group D, in class 80. This is an indicative of high fiber hiperplasia rate in groups A and B, and high hypertrophy in groups C and D. There was no statistical difference in MyoD and Myogenin genes expression in red and white muscles of pirarucu; however, Myostatin expression showed high levels in white muscle compared to red muscle. Evaluating MyoD and Myogenin expression in white muscle of pirarucu at different growth stages, both gene and protein levels were similar. Myostatin gene expression was low in group A and high in the other groups; on the other hand, Myostatin protein was high in group A and low in the other groups. These results reflect the muscle growth characteristics in pirarucu and suggest that the MRFs and Myostatin expression are controlling the balance between hyperplasic and hypertrophic mechanisms, promoting the fast rate feature of pirarucu and their fillet quality / Doutorado / Biologia Celular / Doutor em Biologia Celular e Estrutural

The United States Pacific Northwest is well known for its shellfish farming. Historically, commercial harvests were dominated by the native Olympia oyster, Ostrea lurida, but over-exploitation, habitat degradation, and competition and predation by non-native species has drastically depleted their densities and extirpated many local populations. As a result, shellfish aquaculture production has shifted to the introduced Pacific oyster, Crassostrea gigas. An underlying objective of this dissertation is the use of molecular genetics to improve our ability to accurately identifying optimal oyster broodstock for either restoration of Olympia oysters or farming of Pacific oysters. The ecological benefits provided by oysters as well as the Olympia oyster's historical significance, has motivated numerous restoration/supplementation efforts but these efforts are proceeding without a clear understanding of the genetic structure among extant populations, which could be substantial as a consequence of limited dispersal, local adaptation and/or anthropogenic impacts. To facilitate this understanding, we isolated and characterized 19 polymorphic microsatellites and used 8 of these to study the genetic structure of 2,712 individuals collected from 25 remnant Olympia oyster populations between the northern tip of Vancouver Island BC and Elkhorn Slough CA. Gene flow among geographically separated extant Olympia oyster populations is surprisingly limited for a marine invertebrate species whose free-swimming larvae are capable of planktonic dispersal as long as favorable water conditions exist. We found a significant correlation between geographic and genetic distances supporting the premise that coastal populations are isolated by distance. Genetic structure among remnant populations was not limited to broad geographic regions but was also present at sub-regional scales in both Puget Sound WA and San Francisco Bay CA. Until it can be determined whether genetically differentiated O. lurida populations are locally adapted, restoration projects and resource managers should be cautious of random mixing or transplantation of stocks where gene flow is restricted. As we transition from our Olympia oyster population analysis to our Pacific oyster quantitative analysis, we recognize that traditional quantitative trait locus (QTL) mapping strategies use crosses among inbred lines to create segregating populations. Unfortunately, even low levels of inbreeding in the Pacific oyster (Crassostrea gigas) can substantially depress economically important quantitative traits such as yield and survival, potentially complicating subsequent QTL analyses. To circumvent this problem, we constructed an integrated linkage map for Pacific oysters, consisting of 65 microsatellite (18 of which were previously unmapped) and 212 AFLP markers using a full-sib cross between phenotypically differentiated outbred families. We identified 10 linkage groups (LG1-LG10) spanning 710.48 cM, with an average genomic coverage of 91.39% and an average distance between markers of 2.62 cM. Average marker saturation was 27.7 per linkage group, ranging between 19 (LG9) and 36 markers (LG3). Using this map we identified 12 quantitative trait loci (QTLs) and 5 potential QTLs in the F1 outcross population of 236 full-sib Pacific oysters for four growth-related morphometric measures, including individual wet live weight, shell length, shell width and shell depth measured at four post-fertilization time points: plant-out (average age of 140 days), first year interim (average age of 358 days), second year interim (average age of 644 days) and harvest (average age of 950 days). Mapped QTLs and potential QTLs accounted for an average of 11.2% of the total phenotypic variation and ranged between 2.1 and 33.1%. Although QTL or potential QTL were mapped to all Pacific oyster linkage groups with the exception of LG2, LG8 and LG9, three groups (LG4, LG10 and LG5) were associated with three or more QTL or potential QTL. We conclude that alleles accounting for a significant proportion of the total phenotypic variation for morphometric measures that influence harvest yield remain segregating within the broodstock of West Coast Pacific oyster selective breeding programs. / Graduation date: 2012