A simulation algorithm based on biological references points proposed by Powell and Klink (2007) is implemented for predicting the total allowable catch of eastern oysters (Crassostrea virginica) from Louisiana’s coast. The model accepts initial per-square-meter shell mass and oyster size distributions as input. Fishing effort is provided as fractions removed of each resource for each month of the season. The model outputs the expected remaining shell mass and harvests of sack and seed oysters after discrete fishing months. Oyster mortality credits the shell budget, while fishing fractions debit oyster and shell resources. Surviving oysters grow larger along a time-dependent von Bertalanffy growth curve. Fishing fractions are chosen heuristically with the goal of minimizing shell loss. Input data is collected by the Louisiana Department of Wildlife and Fisheries in their annual stock assessment. The model is available as a public web resource at www.oystersentinel.org.

A disposição de esgoto em áreas costeiras pode causar impactos para a vida marinha, alterando a biodiversidade e o equilíbrio do ecossistema chegando a causar graves doenças nos seres humanos. Neste estudo, determinou-se a concentração de um conjunto de marcadores orgânicos moleculares de introdução de esgoto no ambiente marinho: alquilbenzeno lineares (LABs) em amostras de sedimento, ostras (Crassostrea brasiliana), mexilhões (Mytella charruana e Mytella guyanensis) e peixes (Mugil curema) (Valenciennes, 1836) nos Estuário de Cananéia - Iguape e Santos - São Vicente, SP, Brasil. As concentrações de LABs (peso seco) encontradas em amostras de sedimento de Cananéia variaram de <1,0 a 80,6 ng g-1 e em Santos variaram de 6,7 a 1234,0 ng g-1. Em moluscos bivalves as concentrações detectadas em Cananéia encontravam-se na faixa de 90 a 1849 ng g-1(peso seco) e em Santos as concentrações variaram de 110 a 50495 ng g-1(peso seco). Os estudos em peixes de Cananéia apresentaram os seguintes valores médios (ng g-1 em peso seco): músculo (64,7 ± 22,6), pele (124,0 ± 60,1), fígado (164,0 ± 79,2) e rim (9,1 ± 9,9). No estuário de Santos, os tecidos de peixes apresentaram os seguintes valores médios (ng g-1 em peso seco): músculo (95,0 ± 90,1), pele (438,0 ± 437,0), fígado (274,0 ±147,0) e rim (60,7 ± 35,6). Houve diferença significativa entre as amostras analisadas nos tecidos de peixes de Cananéia e Santos evidenciando diferenças de acúmulo de LABs de acordo com o nível de antropização. A detecção de LABs nestas matrizes evidenciou a sua capacidade de acúmulo e reflete a exposição ao esgoto e portanto pode ser utilizadas no monitoramento ambiental. / The sewage disposal in coastal areas can cause impacts to marine life, altering the balance of the ecosystem and biodiversity and causing serious diseases in humans. In this study, the concentration of a set of molecular markers for the introduction of organic sewage into the marine environment: linear alkylbenzene (LAB), in samples of sediment, oysters (Crassostrea brasiliana), mussels (Mytella charruana and Mytella guyanensis) and fish (Mugil curema) (Valenciennes, 1836) from Cananéia - Iguape and Santos - São Vicente estuaries, located in Sao Paulo State, Brazil. LABs concentrations (dry weight) found in sediment samples from Cananéia ranged from <1.0 to 80.6 ng g-1 and from Santos ranged from 6.7 to 1234.0 ng g-1. In bivalve molluscs of Cananéia, the concentrations were in the range 90 to 1849 ng g-1 (dry weight) and in Santos, the concentrations ranged from 110 to 50495 ng g-1 (dry weight). Studies in fish from Cananéia showed the following average values (ng g-1 - dry weight): muscle (64.7 ± 22.6), skin (124.0 ± 60.1), liver (164.0 ± 79.2) and kidney (9.1 ± 9.9). In the Santos estuary, the fish tissue showed the following average values (ng g-1 - dry weight): muscle (95,0 ± 90.1), skin (438 ± 437), liver (274 ± 147) and kidney (60.7 ± 35.6). There were significant differences between the samples of tissues of fish from Cananéia and Santos showing differences in accumulation of LABs according to the level of anthropogenic occupation. The LABs detection in these matrices demonstrated their ability to accumulate and reflects the exposure to sewage and therefore can be used in environmental monitoring.

Os resultados da produção comercial de quatro lotes de \'Ostras do Pacífico\', espécie Crassostrea gigas, correspondentes às safras dos anos 2005/06, 2006/07, 2007/08, 2008/09 foram obtidos de uma fazenda marinha localizada no sul da Ilha de Santa Catarina, no Estado que lidera a produção nacional de moluscos bivalves. Como o processo de engorda das ostras nestas áreas é totalmente realizado em águas marinhas, a relação das características do ambiente de cultivo e o sucesso da produção se fazem evidentes. Dados de temperatura superficial in situ, de concentração de clorofila a obtidos por sensoriamento remoto, de eventos de frentes frias e períodos de El Niño e La Niña foram analisados com o objetivo de estudar possíveis influências destas variáveis ambientais sobre o cultivo das ostras. Os resultados indicaram que os primeiros estágios de cultivo parecem ser decisivos para sobrevivência e rendimento final das safras. A temperatura parece ser o fator principal para a sobrevivência das ostras apresentando uma correlação negativa com a mesma, sendo a clorofila fator secundário, podendo, aparentemente, mitigar os efeitos negativos das altas temperaturas quando em concentrações elevadas. Para o desenvolvimento das ostras a clorofila foi o fator principal. Os eventos de frentes frias, associados a períodos de El Niño e La Niña, parecem influenciar na variação da clorofila na Baía Sul da Ilha de Santa Catarina. / Results of four allotments from a commercial culture of the Pacific oyster, Crassostrea gigas, relative to the 2005/06, 2006/07, 2007/08 and 2008/09 crops were obtained from a marine farm located in the South of Santa Catarina Island, in the main national area for bivalve production. As the grow-out phase of those mollusks is completely performed in the marine environment, the relation between environmental characteristics and the culture success is made clear. In situ sea surface temperature data, remote sensing chlorophyll a concentration data, cold fronts events and El Niño and La Niña periods were evaluated in order to study possible influences of the environmental characteristics upon oyster performance. Results indicated the performance in the first stages as critical regarding both final survival and output of the crops. Temperature seems to be the main responsible factor for survival, based on a negative regression, whereas chlorophyll plays a secondary role in survival but apparently can mitigate the negative effects of elevated temperatures when available in elevated concentrations. On the other hand, chlorophyll is apparently the main factor for oyster development. Cold fronts events associated with El Niño and La Niña periods seem to influence chlorophyll variation in the South Bay of Santa Catarina Island.

Les maladies infectieuses sont souvent étudiées à l'aide d'approches réductionnistes alors qu'elles sont fortement influencées par de nombreux facteurs hôtes et environnementaux en interaction. Ainsi, de nombreuses maladies d’étiologie complexe restent difficiles à caractériser. En développant une approche holistique pour aborder la complexité de l'interaction, (i) nous avons déchiffré les interactions complexes sous-jacentes au syndrome de mortalité des huîtres du Pacifique chez les juvéniles d’huîtres Crassostrea gigas, la principale espèce d'huître exploitée dans le monde et (ii) nous avons validé le mécanisme de pathogénèse quel que soit l’environnement infectieux et le génotype de l’huître. En utilisant une expérience d’infection écologiquement réaliste combinée à des analyses moléculaires (métabarcoding, transcriptomique, et suivi des agents pathogènes) et histologiques sur des familles d'huîtres aux susceptibilités contrastées à la maladie, nous avons démontré que la maladie est causée par une infection multiple avec comme première étape nécessaire l’infection des cellules immunocompétentes de l’huître (les hémocytes) par OsHV-1µvar. La réplication du virus induit un état immunodéprimé de l’huître qui conduit à une septicémie par des bactéries pathogènes opportunistes entraînant la mort des huîtres. En identifiant les interactions intra-hôtes entre les microorganismes et l'immunité de l'hôte, cette étude déchiffre le code du syndrome de mortalité des huîtres du Pacifique et fournit d'importantes données pour la conception de mesures prophylactiques et de programmes de sélection d'huîtres résistantes au syndrome de mortalité. Nous pensons qu'une telle approche de la biologie des systèmes pourrait être appliquée pour déchiffrer d'autres maladies multifactorielles qui affectent des espèces d'invertébrés non modèles dans le monde entier. / Infectious diseases are very often explored using reductionist approaches, despite repeated evidence showing them to be strongly influenced by numerous interacting host and environmental factors. Many diseases with complex etiology therefore remain misunderstood. In this thesis, by developing a holistic approach to tackle the complexity of the interaction, (i) we deciphered the complex intra-host interactions underlying the Pacific oyster mortality syndrome affecting juveniles of Crassostrea gigas, the main oyster species exploited worldwide and (ii) we validated this mechanism in different infectious environments and oyster genotypes. Using ecologically realistic experimental infections combined with thorough molecular (metabarcoding, transcriptomics, pathogen monitoring) and histological analyses on oyster families with contrasting susceptibilities, we demonstrated that the disease is caused by a multiple infection whose initial and necessary step is the infection of oyster haemocytes by a herpesvirus. Viral replication leads to an immune-compromised state of the host, evolving toward subsequent bacteremia by opportunistic bacteria. By identifying critical intra-host interactions between microorganisms and host immunity, this study cracks the code of the Pacific oyster mortality syndrome and provides important molecular data for the design of prophylactic measures and breeding programs dedicated to the production of oysters resistant to the mortality syndrome. We believe that such a systems biology approach could be applied to decipher other multi-factorial diseases that affect non-model invertebrate species worldwide.

Os resultados da produção comercial de quatro lotes de \'Ostras do Pacífico\', espécie Crassostrea gigas, correspondentes às safras dos anos 2005/06, 2006/07, 2007/08, 2008/09 foram obtidos de uma fazenda marinha localizada no sul da Ilha de Santa Catarina, no Estado que lidera a produção nacional de moluscos bivalves. Como o processo de engorda das ostras nestas áreas é totalmente realizado em águas marinhas, a relação das características do ambiente de cultivo e o sucesso da produção se fazem evidentes. Dados de temperatura superficial in situ, de concentração de clorofila a obtidos por sensoriamento remoto, de eventos de frentes frias e períodos de El Niño e La Niña foram analisados com o objetivo de estudar possíveis influências destas variáveis ambientais sobre o cultivo das ostras. Os resultados indicaram que os primeiros estágios de cultivo parecem ser decisivos para sobrevivência e rendimento final das safras. A temperatura parece ser o fator principal para a sobrevivência das ostras apresentando uma correlação negativa com a mesma, sendo a clorofila fator secundário, podendo, aparentemente, mitigar os efeitos negativos das altas temperaturas quando em concentrações elevadas. Para o desenvolvimento das ostras a clorofila foi o fator principal. Os eventos de frentes frias, associados a períodos de El Niño e La Niña, parecem influenciar na variação da clorofila na Baía Sul da Ilha de Santa Catarina. / Results of four allotments from a commercial culture of the Pacific oyster, Crassostrea gigas, relative to the 2005/06, 2006/07, 2007/08 and 2008/09 crops were obtained from a marine farm located in the South of Santa Catarina Island, in the main national area for bivalve production. As the grow-out phase of those mollusks is completely performed in the marine environment, the relation between environmental characteristics and the culture success is made clear. In situ sea surface temperature data, remote sensing chlorophyll a concentration data, cold fronts events and El Niño and La Niña periods were evaluated in order to study possible influences of the environmental characteristics upon oyster performance. Results indicated the performance in the first stages as critical regarding both final survival and output of the crops. Temperature seems to be the main responsible factor for survival, based on a negative regression, whereas chlorophyll plays a secondary role in survival but apparently can mitigate the negative effects of elevated temperatures when available in elevated concentrations. On the other hand, chlorophyll is apparently the main factor for oyster development. Cold fronts events associated with El Niño and La Niña periods seem to influence chlorophyll variation in the South Bay of Santa Catarina Island.

A disposição de esgoto em áreas costeiras pode causar impactos para a vida marinha, alterando a biodiversidade e o equilíbrio do ecossistema chegando a causar graves doenças nos seres humanos. Neste estudo, determinou-se a concentração de um conjunto de marcadores orgânicos moleculares de introdução de esgoto no ambiente marinho: alquilbenzeno lineares (LABs) em amostras de sedimento, ostras (Crassostrea brasiliana), mexilhões (Mytella charruana e Mytella guyanensis) e peixes (Mugil curema) (Valenciennes, 1836) nos Estuário de Cananéia - Iguape e Santos - São Vicente, SP, Brasil. As concentrações de LABs (peso seco) encontradas em amostras de sedimento de Cananéia variaram de <1,0 a 80,6 ng g-1 e em Santos variaram de 6,7 a 1234,0 ng g-1. Em moluscos bivalves as concentrações detectadas em Cananéia encontravam-se na faixa de 90 a 1849 ng g-1(peso seco) e em Santos as concentrações variaram de 110 a 50495 ng g-1(peso seco). Os estudos em peixes de Cananéia apresentaram os seguintes valores médios (ng g-1 em peso seco): músculo (64,7 ± 22,6), pele (124,0 ± 60,1), fígado (164,0 ± 79,2) e rim (9,1 ± 9,9). No estuário de Santos, os tecidos de peixes apresentaram os seguintes valores médios (ng g-1 em peso seco): músculo (95,0 ± 90,1), pele (438,0 ± 437,0), fígado (274,0 ±147,0) e rim (60,7 ± 35,6). Houve diferença significativa entre as amostras analisadas nos tecidos de peixes de Cananéia e Santos evidenciando diferenças de acúmulo de LABs de acordo com o nível de antropização. A detecção de LABs nestas matrizes evidenciou a sua capacidade de acúmulo e reflete a exposição ao esgoto e portanto pode ser utilizadas no monitoramento ambiental. / The sewage disposal in coastal areas can cause impacts to marine life, altering the balance of the ecosystem and biodiversity and causing serious diseases in humans. In this study, the concentration of a set of molecular markers for the introduction of organic sewage into the marine environment: linear alkylbenzene (LAB), in samples of sediment, oysters (Crassostrea brasiliana), mussels (Mytella charruana and Mytella guyanensis) and fish (Mugil curema) (Valenciennes, 1836) from Cananéia - Iguape and Santos - São Vicente estuaries, located in Sao Paulo State, Brazil. LABs concentrations (dry weight) found in sediment samples from Cananéia ranged from <1.0 to 80.6 ng g-1 and from Santos ranged from 6.7 to 1234.0 ng g-1. In bivalve molluscs of Cananéia, the concentrations were in the range 90 to 1849 ng g-1 (dry weight) and in Santos, the concentrations ranged from 110 to 50495 ng g-1 (dry weight). Studies in fish from Cananéia showed the following average values (ng g-1 - dry weight): muscle (64.7 ± 22.6), skin (124.0 ± 60.1), liver (164.0 ± 79.2) and kidney (9.1 ± 9.9). In the Santos estuary, the fish tissue showed the following average values (ng g-1 - dry weight): muscle (95,0 ± 90.1), skin (438 ± 437), liver (274 ± 147) and kidney (60.7 ± 35.6). There were significant differences between the samples of tissues of fish from Cananéia and Santos showing differences in accumulation of LABs according to the level of anthropogenic occupation. The LABs detection in these matrices demonstrated their ability to accumulate and reflects the exposure to sewage and therefore can be used in environmental monitoring.

Comparing the protein compositions of three fishes, grass carp exhibited lower band intensity at 47.9 KDa, β-tropomyosin (36.5 KDa), and missed the band at 15.9 KDa myosin light chain. Bigmouth buffalo had a darker tropomodulin (38.8 KDa) band and smaller α-tropomyosin (33-37 KDa) than silver and grass carp. The breaking force (611.8 g) and deformation (11.7 mm) of silver carp cooked gel were significantly higher than the other two fish products. The addition of starches at 2, 4, and 6% to the grass carp paste lowered the breaking force of the cooked gel in a dose-responsive manner compared to the control (P<0.05), but no differences were found in bigmouth buffalo. The bioumulated Murine Norovirus-1 (MNV-1) was found to maintain infectivity during storage of live oysters at 5°C for 15 days while the inoculated MNV-1 kept infectious for 20 days in cooked surimi and salmon fillet. Treatments with 4.0 kGy X-ray achieved the reductions of 3.7 log PFU mL-1 in pure culture or 2.7, 2.2, and 2.0 log PFU g-1 in half-shell oyster, salmon sushi and tuna salad, respectively. X-ray significantly reduced the population of internalized MNV-1 in live oysters from 4.3 ± 0.4 log PFU g-1 to 3.6 ± 0.5, 3.2 ± 0.2, 2.8 ± 0.2, and 2.5 ± 0.1 log PFU g-1, by 1.0, 2.0, 3.0, and 4.0 kGy X-ray, respectively. The population of MNV-1 was reduced to less than 2.0 log PFU g-1 at 5.0 kGy X-ray. The survivability of live oysters was not significantly affected by treatment with 5.0 kGy X-ray, in comparison with the control, for up to 10 days, respectively, during storage at 5°C. Fish sauce was fermented from the by-products of silver carp. The total nitrogen content of fish sauce made in April, and November were 9.86±0.9 and 9.71±4.5 g/l, respectively, which was significantly (p<0.05) higher than the sample of February (8.45±0.25 g/l ), reflecting seasonal effect. The total nitrogen, amino acid nitrogen, pH, and sodium chloride of fish sauce made from silver carp by-products met the international fish sauce standard code of CODEX STAN 302-2011.

No description available.

Crassostrea gigas est la principale espèce d’huître cultivée dans le monde. Depuis 2008, de sévères épisodes de mortalités affectent les huîtres âgées de moins d’un an en Europe et en Océanie et sont associées à l’émergence de l’Ostreid herpèsvirus μVar (OsHV-1 μVar). En Europe, ces mortalités sont saisonnières et surviennent lorsque la température de l’eau de mer est comprise entre 16°C et 24°C. Dans le cadre de ce travail, l’effet des hautes températures (21°C, 26°C et 29°C) est évalué sur la sensibilité des huîtres à OsHV-1 mais aussi sur la persistance et la virulence du virus. La survie des huîtres infectées maintenues à 29°C (86%) est supérieure à la survie des huîtres placées à 21°C (52%) et à 26°C (43%).Les températures élevées (29°C) diminuent la sensibilité des huîtres à OsHV-1 sans altérer l'infectivité du virus et sa virulence. L’exposition des huîtres infectées à 29°C pourrait réduire l’expression des gènes viraux et la synthèse de virions par la réduction de l’expression de gènes hôtes codant pour des protéines impliquées dans la transcription et la traduction, la réduction de l’expression de gènes impliqués dans le catabolisme, le transport des métabolites, et synthèse de macromolécules.Finalement, l’induction conjointe de l’apoptose, des processus d’ubiquitinylation et de la réponse immunitaire, pourrait permettre l’élimination d’OsHV-1. / Crassostrea gigas is the main species of oyster cultivated in the world. Since 2008, mass mortality events have been affecting oysters aged less than one year old in Europe and Oceania and have been associated with the emergence of the Ostreid herpes virus μVar (OsHV-1 μVar). In Europe, these events are seasonal and occur when the seawater temperature is between 16°C and 24°C. In this work, the effect of high temperatures (21°C, 26°C and 29°C) was evaluated on the susceptibility of oysters to OsHV- 1 but also on the virulence of virus.High temperatures (29°C) reduce the susceptibility of oysters to OsHV-1 without altering the infectivity of the virus and its virulence. High temperature could reduce viral infection and virus synthesis by reducing the expression of host genes that encode proteins involved in transcription and translation, catabolism, metabolites transport, and macromolecules biosynthesis. Finally, the induction of apoptosis, ubiquitinylation processes and immune response could lead to the elimination of OsHV-1.

Vírus causadores de gastroenterite, descritos como pequenos vírus de estrutura arredondada (Small Round Structured Viruses-SRSV), foram detectados em extratos de ostras Crassostrea spp., coletadas em regiões distintas do litoral do Estado de São Paulo, utilizando a Reação em Cadeia por Polimerase com transcrição reversa (RT-PCR).Treze lotes de amostras, contendo 10 g de estômagos e divertículos, foram processados para extração e concentração das partículas virais, mediante adsorção-eluição e precipitação por polietilenoglicol (PEG 6000), e purificação com fluorocarbono (Freon, Dupont Co.) para eliminação prévia dos inibidores da reação de RT-PCR. A extração do ácido nucleico viral, foi realizada com uma mistura de isotiocianato de guanidina e fenol (TRIzol ®, Gibco) e clorofórmio, sendo completada com uma purificação em coluna spin, com membrana de polissulfona (Millipore,Corp.). A reação de RT-PCR foi realizada em uma única etapa, utilizando o kit \'\'Super Script ONE-STEP RT-PCR System\'\'® (Gibco). A reação de amplificação enzimática revelou, por eletroforese em gel de agarose (2%), corada com brometo de etídio, produtos de 123 bp, em 3 (23%) dos 13 lotes de amostras coletadas durante o verão de 1998, sendo verificadas em uma delas por imunomicroscopia eletrônica (IME),partículas de SRSV. Os produtos encontrados pertencem ao grupo genômico G2(Snow Mountain e outros vírus). A aplicação deste método possibilitou pela 1ª vez a detecção molecular de SRSVs no Brasil em ostras naturalmente contaminadas. / The Small Round Structured Viruses (SRSVs) have been associated with gastroenteritis in humans, and were detected in extracts of oysters Crassostrea spp., by Reverse Transcriptase Polymerase Chain Reaction (RT - PCR). Thirteen lots of samples, originated from different regions of the State of São Paulo, were processed for viral particles extraction. The samples, containing 10 g of stomach and diverticula, were extracted by adsorption - elution and polyethylene glycol (PEG 6000) precipitation, and fluorocarbon (Freon, Dupont Co.) was used for purification and previous elimination of RT - PCR inhibitors. For the viral nucleic acid extraction, guanidine isothiocyanate - phenol mixture (TrizolÒ, Gibco ) and chloroform were used, followed by a polysulfone spin column (Millipore, Corp.) purification. The RT-PCR was done in one step, using the \'\'Super Script ONE-STEP RT-PCR System\'\'® (Gibco). The enzimatic amplification reaction run in 2% agarose gel electrophoresis stained with ethidium bromide, revealed 123 bp products in 3 (23%) of the 13 lots of samples collected during the summer of 1998. One of these three samples was positive for SRSV particles by Immune Electron Microscopy (IEM). These 3 products were classified in the Genogroup G2 (Snow Mountain and others viruses). The application of this methodology made it possible to detected, in a molecular basis, the first cases of SRSVs in environmentally contaminated oysters in Brazil.