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Abstract The long-term monitoring programme for the River Teno Atlantic salmon (Salmo salar L.) stocks has covered the juvenile densities (25 yr) and the abundance and characteristics of the returning adults (31 yr). The feasibility of the programme was examined by studying the interrelationships between the yearly catches and juvenile salmon densities, performance and reliability of the electrofishing method, and the effects of fishing regulations on the salmon stocks. Finally, juvenile salmon abundances were related to the available fluvial habitat and reference levels were defined by using habitat models. Extensive seasonal variation in juvenile salmon density was apparent. The densities of fry and parr showed an increase from early summer towards late August and a subsequent decline towards the autumn. Long-term electrofishing monitoring is recommended to be carried out in as standardized a form as possible in order to reduce variations in catchability. Over the 25-year monitoring period, the abundance of parr (1+) increased in one sampling site cluster out of nine clusters and declined in one cluster. Fry densities increased in seven clusters. Juvenile densities exhibited considerable temporal and spatial variation. Similarly, the salmon catches varied extensively, and the numbers of 1-2SW salmon and previous spawners increased. The numbers of 1–2SW female salmon in the catches and the subsequent juvenile densities were significantly related, as regression models explained 19–44% of the variation in juvenile abundance. The juvenile monitoring allows evaluation of the relative spawner abundance in preceding years, confirming the information provided by catch statistics. Juvenile salmon densities explained 23–41% of the variation in subsequent 1–2SW salmon catches. Significant correlations were detected with a lag of one year between the subsequent sea-age groups of salmon in the catches. Thus, these relationships can be used for forecasting future salmon abundances. Large areas of high habitat quality in the River Teno system fail to meet their expected juvenile densities, and factors others than physical habitat characteristics, such as a lack of spawners, restrict the juvenile abundance. More than 50% of the permanent sampling sites where habitat would predict high densities (≥ 50 parr per 100 m2) had observed densities in the mid (10–49) or low density category (< 10). It was expected that the densities should increase after regulatory measures implemented in 1989–1990, but results indicate that the reference levels of parr densities have not been attained and the densities have not increased, whereas a general increase in salmon fry densities was detected. Nonetheless, the management measures have succeeded in maintaining the River Teno salmon stocks, which still today enable and support diversified fisheries.

Atlantic salmon (Salmo salar L.) has been domesticated since the 1960s and has undergone over 10 generations of artificial selection for economically important traits. As a result, domesticated salmon have diverged with respect to a number of phenotypic, genotypic and behavioural traits from their wild counterparts. Since the selection pressures that are present in the wild differ greatly from the ones that shape salmon under culture conditions, domesticated salmon stocks are considered to be maladapted to natural conditions. Despite strict regulations, insoluble issues pertaining to large-scale cage rearing of farmed fish mean that there is a continuous presence of farm escapees in the wild. Gene flow from escapees has been perceived as a factor in the decline of wild populations, suggested to occur through disruption of local adaptation. This study aims to improve understanding of the genetic differences between wild and domesticated stocks by comparing the transcriptomes of Figgjo (wild) and Mowi (domesticated) strains. A series of common garden experiments have been performed, utilizing pure and reciprocal hybrid crosses of the wild and domesticated stocks, reared under two different conditions and sampled at four time points and three distinct life stages (embryo, sac-fry and feeding fry). Microarray interrogations were performed employing a 44K custom microarray design to identify genes and gene pathways that are differentially expressed between the stocks. KEGG-based functional analyses have been implemented using different gene set enrichment packages, and dominance and additive parameters were calculated from normalized expression values to predict the mode of heritability of the genes identified as differentially expressed between stocks. Most biological functions represented in wild and domesticated crosses were consistent across life stages and environments. The transcriptomic differences detected between stocks in multiple developmental stages likely reflected adaptations to selection pressures differing between natural and aquaculture environments. Down-regulated environmental information processing and immune and nervous system functions in domesticated vs. wild fish may be due to local adaptation to captivity. These included reduced information acquisition and processing systems, altered stress responsiveness and changes in feeding behaviour. In line with the resource allocation theory of production trait animals, reduced immune function was coupled with increased expression of growth and development related pathways in domesticated salmon, compared to wild counterparts. Although there is support for this trade-off in all life-stages, resource allocation showed a shift over time; possibly reflecting variation in the utilization of energy sources during the transition from endogenous to exogenous feeding. Differences in cell communication and signalling pathways between wild and domesticated stocks, associated with organogenesis during the embryo stage, reflect sampling time and are indicative of altered organ development in response to domestication. Stress responses common across stocks included the down-regulation of cellular processes, including cell cycle and meiosis, and genetic information processing, such as replication and repair, transcription and translation pathways, probably reflecting the reallocation of energy resources away from growth and towards the restoration of homeostasis. Moreover, the mobilization of energy to cover the increased demands of maintaining homeostasis was indicated by the up-regulation of some metabolic pathways, mostly involved in energy, lipid and carbohydrate metabolism in response to stress. The analysis also revealed cross-specific stress responses, including indicators of a non-additive stress response in hybrid crosses. Most differentially expressed transcripts exhibited additive (31-59%) or maternal dominant (19-33%) inheritance patterns, although maternal over-dominance (23-26%) was also significant in the embryo stage. The mode of heritability of some immune transcripts was suggestive of maternal environmental influence having been affected by aquaculture. This study has demonstrated that biological functions affected by domestication include those associated with allocation of resources, involve reduction of information acquisition and processing systems and may lead to loss of local adaptation to wild conditions. Since such changes may affect key systems, such as immunity and responsiveness to stress, they can potentially have serious negative consequences under natural conditions. Transcriptomic differences observed between wild and domesticated stocks primarily exhibited additive and maternal dominant inheritance modes. Since gene-flow from farmed fish can be frequent and primarily concerns farmed females, this suggests that introgression due to repeated large scale escape events has the capacity to significantly erode local adaptation.

Memoria para optar al Título Profesional de Ingeniero Agrónomo / El afrecho de soya (AS) ha sido utilizado como sustituto de la harina de pescado (HP) debido a su bajo precio, disponibilidad y propiedades nutricionales, pero su nivel de inclusión ha estado limitado debido a la presencia de factores anti-nutricionales. Varias alternativas han sido planteadas para reducir los niveles de estos compuestos (Polisacáridos no derivados del almidón (NSP), alfa-Galactosidos (GOS), saponinas, lectinas, etc.) una de ellas es el pre-tratamiento de la soya mediante Fermentación en Estado Sólido (SSF), sin embargo hay poca información disponible sobre los efectos del afrecho de soya fermentada (ASF) en alimentos para salmónidos, aun mas hay pocos estudios que hagan referencia al efecto que causan las fuentes proteicas vegetales en el intestino proximal.

La gestion durable des ressources naturelles vivantes est un problème majeur dans un contexte de raréfaction, dû à l'impact de l'homme et à une incertitude omniprésente. Améliorer les outils existant et en développer de nouveaux pour conseiller les gestionnaires sur l'évolution potentielle des ressources naturelles vivantes, selon divers scénarios environnementaux et de gestion, est nécessaire. Cette thèse a pour but de contribuer au développement d'une méthodologie pour l'aide à la décision pour la gestion des ressources naturelles vivantes, tout en prenant en compte les sources d'incertitude majeures. Ce travail est appliqué au cas de la population de saumon atlantique (Salmo salar L.) de la Nivelle (France). Cette population fait l'objet d'un programme de suivi à long terme et cette espèce a été largement étudiée. Cette dernière est menacée mais elle est toujours ciblée par la pêche commerciale et récréative. Elle illustre la dualité entre conservation et exploitation, qui est au coeur de la gestion des ressources naturelles vivantes. Pour gérer une population, il est nécessaire de comprendre sa dynamique et de prédire son évolution sous divers scénarios environnementaux et de gestion. L'approche Bayésienne fournit un cadre cohérent pour quantifier l'incertitude sous ses différentes formes. Les modèles hiérarchiques permettent l'assimilation de sources de données multiples et de faire des inférences et des prédictions sur des grandeurs spatio-temporelles inconnues. Un modèle stochastique d'état Bayésien, i.e. un modèle hiérarchique Bayésien dynamique, est construit pour étudier la dynamique de la population d'intérêt et pour prédire son évolution. La théorie de la décision en univers incertain fournit un cadre pour aider un individu dans ses choix, mais son application reste difficile. En théorie, une fonction d'utilité qui dépend des conséquences des alternatives de gestion reflète les préférences d'un individu unique impliqué dans un problème décisionnel. En pratique, sa construction est malaisée. Premièrement, il estdifficile de définir une valeur pour chaque conséquence. Deuxièmement, il y a généralement plus d'un individu impliqué dans le problème décisionnel. Par conséquent, on obtient une classe de fonctions d'utilité. De par les différents intérêts, souvent conflictuels, que les gestionnaires ont à prendre en compte, la fonction d'utilité est multi variée. Dans cette thèse, une classe de fonctions d'utilité bi-variées est construite. Elle prend en compte l'incertitude concernant la fonction, les variations de préférence entre les acteurs et la dualité d'intérêts exploitation vs conservation. Ensuite, une analyse de la robustesse est réalisée pour étudier si la décision optimale, i.e. l'utilité espérée maximale, varie lorsque la fonction d'utilité varie.La méthodologie développée dans cette thèse s'est avérée possible et fructueuse. Elle fournit un cadre cohérent pour organiser les interactions entre scientifiques, acteurs et gestionnaires pour atteindre une compréhension commune des problèmes de décision dans la gestion des ressources naturelles vivantes. En reconnaissant explicitement la diversité des acteurs, elle permet d'identifier des conflits potentiels et de guider les gestionnaires vers des compromis acceptables. Cependant, elle demande un haut niveau de formation et d'expertise en modélisation et en calcul. Elle implique également un temps d'analyse important. Comment rendre ces exigences compatibles avec le niveau actuel d'expertise et les agendas à court terme des structures de gestion est un challenge principal pour le futur. / The sustainable management of natural living resources is a major issue in a context of increasing scarcity due to human impact and of pervasive uncertainty. Improving existing tools and developing new ones to advise decision makers on the potential evolution of natural living resources, according to various management and environmental scenarios, is requested. This PhD aims at contributing to the development of a methodology for decision making for natural living resources management, while taking into account major sources of uncertainty. This is achieved through the study case of the Atlantic salmon (Salmo salar L.) population ofthe Nivelle River (France). This population is subjected to a long term monitoring program and the species has been extensively studied. Atlantic salmon is a threatened species but still targeted by commercial and recreational fisheries. It illustrates the duality between conservation and exploitation which is at the heart of natural living resource management. To manage a population, it is necessary to understand its dynamics and to predict its evolution under various management and environmental scenarios. The Bayesian approach provides a coherent framework to quantify uncertainty in its different forms. Hierarchical models allow the assimilation of multiple sources of data and to make spatio-temporal inferences and predictions. A Bayesian state space model, i.e. a Bayesian dynamic hierarchical model, is constructed to study the dynamics of the population of interest and topredict its evolution. The decision theory under uncertainty provides a framework to help an individual in its choices, but its application still raises difficulties. In theory, a utility function depending on the consequences of alternative actions reflects the preferences of a single individual involved in a decision problem. In practice, its construction is challenging. Firstly, it is difficult to assign a value for each consequence. Secondly, there is usually more than one individual involved in the decision problem. Consequently, we obtain a set of utility functions. Due to the various and often conflicting interests the decision maker has to take into account, the utility function is multivariate. In this PhD, a set of bivariate utility functions is constructed. It accounts for the uncertainty about the function, the variation of preferences among stakeholders and the dual interests of exploitation vs conservation. Next, a robustness analysis is performed to study if the optimal decision, i.e. associated to the maximum expected utility, varies when the utility function varies. The methodology developed in this PhD proved practicable and fruitful. It provides a coherent framework for organizing the interactions between scientists, stakeholders and decision makers for reaching a common understanding of decision problems in the management of natural living resources. By acknowledging explicitly the diversity among stakeholders, it allows to identify potential conflict and it helps guiding decision makers towards acceptable trade-off actions. However, it requires a high level of training and expertise in modelling and computation. It involves also thoughtful and time consuming analyses. How to render these requirements compatible with the current level of expertise and the short term agendas of management bodies is a main challenge for the near future.

There are five endemic populations of migratory Atlantic salmon (Salmo salar, Salmonidae) and brown trout (Salmo trutta, Salmonidae) remaining in Lake Vänern, whereof two are salmon and three are trout. There is one population of each species in Klarälven, also one of each in Gullspångsälven and there is a population of trout still remaining in Tidan River. Since the beginning of the 20th century endemic populations of salmon and trout have either vanished or declined dramatically due to the construction of hydropower in the rivers around the lake, and still today the future of the remaining populations remains uncertain. To manage salmonid fishes effectively more knowledge of their ecology throughout their different life-stages is needed. A large part of the Lake Vänern salmonoids lives are spent in the lake, where a mayor mortality factor is recreational fishing, especially angling. Estimation of fishing effort and catch is important in order to remain a sustainable fishery. In Lake Vänern commercial fishers are bound to report their catch, but anglers are not, -even though they are now thought to be responsible for the largest proportion of the catch. Angler interviews and access point surveys are the best ways to get accurate information in order to assess sport fish effort and catch. There are drawbacks of this method though that includes large costs, logistical problems and biased results due to the higher chance of interviewing the most avid anglers. To hand out mail-surveys is a kind of off-site survey that is less costly compare to interviews, but the drawbacks are bigger in getting correct information due to biased results from non-respondence. A study was conducted to compare an interview-survey with a mail-in survey, in which the interviews were conducted in Lillängshamnen, a port on the northern coast of Lake Vänern, and the mail-in surveys were distributed in different ports around the lake, though not in Lillängshamnen. This study shows a significant difference in catch per boat day between the interviews and mail-in survey. To find out more about how to develop the interview-survey there was also an analysis done on the correlation between weather and the number of interviews that were collected. One could find a negative correlation between numbers of interviews collected and the wind ratio, where very few interviews were collected once the wind speed measured more than 5-8 meters per second. There are improvements to be made both for the conduction of interviews and mail-in surveys, including more staff for conducting interviews at different ports and follow-ups on the non-respondents for the mail-in survey. / Av atlantlax (Salmo salar, Salmonidae) och öring (Salmo trutta, Salmonidae) finns idag fem endemiska populationer kvar i Vänern varav två är av lax och tre av öring. Det finns en klarälvsvariant av båda arterna, likaså finns det en gullspångsvariant av varje och sen finns även en öringpopulation kvar i Tidan. Sen början av 1900-talet har populationer av lax och öring utrotats eller minskat kraftigt till följd av vattenkraftens utbyggnad i vattendragen runt Vänern, och än idag är de resterande populationernas framtid oviss. För att kunna förvalta laxfiskarna på ett bra sätt krävs kunskaper om deras ekologi i dess olika livsstadier. En stor del av laxfiskarna runt Vänerns liv tillbringas i Vänern, där en mortalitetsfaktor består av fritidsfisket, då främst trolling. Uppskattning av ansträngning och fångst är viktigt för att hålla fisket i sjön på en hållbar nivå. Yrkesfisket måste rapportera all sin fångst men detta krävs inte av trollingfisket som idag tros stå för den största proportionen lax- och öringsfångst i Vänern. Genomförandet av intervjuer är en typ av plats- och åtkomstpunktsundersökning och är den bästa metoden att samla in korrekt information för att uppskatta sportfiskets ansträngning och fångst. Det finns dock nackdelar i form av stora kostnader, svår logistik och vinklade resultat då de mest entusiastiska fiskarna löper större chans att bli intervjuade. Att dela ut enkäter är en form av distansundersökning och även brevundersökning som kostar betydligt mindre än att genomföra intervjuer men brister vad gäller svarsfrekvens som i sin tur leder till vinklade resultat. En studie gjordes för att jämföra intervjuer med enkäter, där intervjuer genomfördes i Lillängshamnen på Vänerns norra kust och enkäter delades ut i olika hamnar runt hela Vänern, dock ej i Lillängshamnen. Denna undersökning visade att enkäter har en signifikant större fångst per båt än intervjuer. För att ta reda på mer om hur genomförandet av intervjuer skulle kunna förbättras undersöktes hur vädret påverkade antalet intervjuer som genomfördes. Man fick en negativ korrelation mellan antalet genomförda intervjuer och vindhastighet där ytterst få intervjuer genomfördes i vindhastigheter över 5-8 meter per sekund. Det finns förbättringspotential vad gäller både genomförandet av intervjuer och enkätundersökningar, bland annat mer personal till att kunna intervjua fler folk i olika hamnar och uppföljning på de enkäter som inte svarats på.

Fiskars passager genom vattenkraftverk är förenat med hög dödlighet. För att minska vattenkraftens påverkan på fiskbestånd har olika fiskledare utvecklats. I denna laboratoriestudie utvärderades tre typer av icke-fysiska fiskledare och deras effektivitet i att leda odlade smolt av Atlantlax (Salmo salar L.) till en önskad passage. Målet med denna studie var att undersöka om det var möjligt att leda odlade laxsmolt till en önskad passage med hjälp av bubblor, strobeljus eller en kombination av bubblor och strobeljus. Med relativt enkla medel och låg kostnad konstruerades fiskledare som bestod av en perforerad slang driven av en luftkompressor samt en ljusramp med fyra LED-lampor vilka blinkade simultant med 480 bpm. Fem replikat genomfördes för vardera behandling, bubblor, strobeljus och bubblor/strobeljus, samt sex replikat i kontrollen. Under en timmes behandling fick tio laxsmolt, märkta med PIT-tag, passera en av två antenner, varav den ena var utrustad med en fiskledare, under vandring i nedströms riktning i ett strömakvarium. Denna studie visade att fiskledare av samtliga tre metoder ledde smolt till en önskad passage under behandlingens första femton minuter. Vidare visade fiskledaren bestående av bubblor en fortsatt ledande förmåga över hela behandlingsperioden (60 minuter), medan fiskledarna av strobeljus- och bubbel/strobeljus inte visade en sådan effekt. / Passages by fish through hydropower plants are associated with high mortality. In order to reduce the impact of hydropower plants on fish stocks, a variety of fish guiding systems have evolved. In this laboratory study, three types of non-physical fish guiding systems were evaluated by their efficiency in leading cultivated smolt of Atlantic salmon (Salmo salar L.) to a desired passage. This study aimed to answer if it is possible to guide salmon smolt to a desired safe passage by using bubbles, strobe light or a combination of bubbles and strobe light. With relatively simple means and low cost, fish-guides were constructed consisting of a perforated tube driven by an air compressor and a light ramp with four LED lights, which simultaneously flashed at 480 bpm. Five replicates were performed for each treatment; bubbles, strobe light and bubbles / strobe light, as well as six replicates for the controls. During one hour of treatment, ten salmon smolt, marked with PIT tag, could pass one of two antennas, where one had a fish-guide in front of the antenna, while migrating downstream in a stream aquarium. This study showed that fish-guides of all three methods led smolt to a desired passage during the first fifteen minutes of treatment. Furthermore, the bubble method showed a continuous guiding capacity throughout the treatment period (60 minutes), while the strobe light and bubble/strobe light did not show such an effect.

Global warming, a consequence of the ongoing climate change, is expected to increase the mean global temperature by up to 5°C this century. This is predicted to have various impacts on the earth's ecosystems and especially on ectotherms which cannot regulate body temperature by endogenous heat production. There is an intensified interest in investigating the outcomes of climate change and the role of developmental phenotypic plasticity in relation to environmental conditions experienced early in life. Here I compare the body shape and fin size of juvenile Atlantic salmon that had been incubated at two different temperature regimes during embryogenesis. Morphometric methods were used to compare body size through a box-truss network of Euclidean distances and the data were then analyzed using discriminant analysis. Fin size was analyzed by comparing fin area using analysis of covariance with body size as the covariate. The fish incubated in ambient (cold) temperatures differed from the fish incubated in ca. 4°C warmer temperatures by having a deeper body shape and bigger pectoral fin area. There was no significant difference for dorsal fin area. My findings support the notion that Atlantic salmon are morphologically plastic when exposed to different temperature regimes during embryogenesis, but additional studies are needed to determine the ecological consequences of these changes. / Global uppvärmning, en konsekvens av pågående klimatförändringar, förväntas öka den globala medeltemperaturen med upp till 5°C det här århundradet. Det här förväntas ha stor påverkan på jordens ekosystem och speciellt ektotermer som inte kan reglera sin kroppstemperatur genom endogen värmeproduktion. Intresset har intensifierats för att undersöka klimatförändringarnas utfall och rollen som fenotypisk plasticitet har som svar på tidiga miljöförhållanden. Kroppsform och fenstorlek jämfördes hos juvenil atlantlax som inkuberats i två olika temperaturbehandlingar under embryogenesen. Morfometri användes för att undersöka kroppsformen genom ett box-truss nätverk av euklidiska avstånd som sedan analyserades med en diskriminant funktionsanalys. Fenstorleken analyserades genom att mäta fenornas area som sedan användes i en kovariansanalys med kroppsstorlek som kovariat. Fiskarna som inkuberades i normal (kall) temperatur skiljde sig från fiskarna som inkuberats i ca 4°C varmare temperatur genom att ha en djupare kroppsform och större area på bröstfenorna. Det fanns ingen signifikant skillnad mellan ryggfenornas area. Mina resultat stödjer idén att atlantlaxen är morfologiskt plastisk när den utsätts för olika temperaturbehandlingar under embryogenesen, men ytterligare studier behövs för att identifiera de ekologiska konsekvenserna av dessa förändringar.

The intestinal tract of salmonids provides a dynamic interface that not only mediates nutrient uptake but also functions as the first line of defence against ingested pathogens. Exposure of the immune system to beneficial microorganisms and different dietary immunostimulants via the intestine has been shown to prime the immune system and help in the development of immune competence. Furthermore, the morphology and function of teleostean intestines are known to respond to feed components and to ingested and resident bacterial communities. Histological appraisal is still generally considered to be the gold standard for sensitive assessment of the effects of such dietary modulation. The aim of the present study was to improve understanding of salmonid intestinal function, structure and dynamics and to use the knowledge gained to develop a model for analysis, which would allow intestinal health to be assessed with respect to different intestinal communities and feed components. Virtual histology, the process of assessing digital images of histological slides, is gaining momentum as an approach to supplement traditional histological evaluation methodologies and at the same time, image analysis of digitised histological sections provides a practical means for quantifiable assessment of structural and functional changes in tissues, being both objective and reproducible. This project focused on the development of a rapid, practical analytical methodology based on advanced image analysis, that was able to measure and characterise a range of features of the intestinal histology of Atlantic salmon in a quantitative manner. In the first research chapter, the development of a novel histological assessment system based upon advanced image analysis was described, this being developed with the help of a soybean feed model known to induce enteropathy in Atlantic salmon. This tool targeted the evaluation of the extent of morphological changes occurring in the distal intestine of Atlantic salmon following dietary modulation. The final analytical methodology arrived at, could be conducted with minimal user-interaction, allowing rapid and objective assessment of 12 continuous variables per histological frame analysed. The processing time required for each histological frame was roughly 20-25 min, which greatly improved the efficiency of conducting such a quantitative assessment with respect to the time taken for a subjective semi-quantitative alternative approach. Significant agreement between the fully automated and the manual morphometric image segmentation was achieved, however, the strength of this quantitative approach was enhanced by the employment of interactive procedures, which enabled the operator / observer to rectify preceding automated segmentation steps, and account for the specimen’s variations. Results indicated that image analysis provided a viable alternative to a pathologist’s manual scoring, being more practical and time-efficient. In the second research chapter, feeding Atlantic salmon a high inclusion level of unrefined SBM (25 %) produced an inflammatory response in the distal intestine as previously described by other authors. The model feed trial successfully generated differentiable states, although these were not, for the most part, systemically differentiable through the majority of standard immunological procedures used, being only detectable morphologically. Quantitation of morphometric parameters associated with histological sections using the newly developed image analysis tool successfully allowed identification of major morphological changes. Image analysis was thus shown to provide a powerful tool for describing the histomorphological structure of Atlantic salmon distal intestine. In turn, the semi-automated image analysis methods were able to distinguish normal intestinal mucosa from those affected by enteritis. While individual parameters were less discriminatory, use of multivariate techniques allowed better discrimination of states and is likely to prove the most productive approach in further studies. Work described in the third research chapter sought to validate the semi-automated image analysis system to establish that it was measuring the parameters it was purported to be measuring, and to provide reassurance that it could reliably measure pre-determined features. This study, using the same sections for semi-quantitative and quantitative analyses, demonstrated that the quantitative indices performed well when compared to analogous semi-quantitative descriptive parameters of assessment for enteritis prognosis. The excellent reproducibility and accuracy performance levels indicated that the image analysis system was a useful and reliable morphometric method for the quantification of SB-induced enteritis in salmon. Other characteristics such as rapidity, simplicity and adaptability favour this method for image analysis, and are particularly useful where less experienced interpreters are performing the analysis. The work described in the fourth research chapter characterised changes in the morphology of the intestinal epithelial cells occurring as a result of dietary modulation and aspects of inflammatory infiltration, using a selected panel of enzyme and IHC markers. To accomplish this, image analysis techniques were used to evaluate and systematically optimise a quantitative immunolabelling assessment protocol. Digital computer-assisted quantification of labelling for cell proliferation and regeneration; programmed cell death or apoptosis; EGCs and t-cell like infiltrates; mobilisation of stress-related protein regenerative processes and facilitation of nutrient uptake and ion transport provided encouraging results. Through the description of the intestinal cellular responses at a molecular level, such IHC expression profiling further characterised the inflammatory reaction generated by the enteropathic diet. In addition, a number of potential diagnostic parameters were described for fish intestinal health e.g. the relative levels of antigenicity and the spatial distribution of antigens in tissues. Work described in the final research chapter focused on detailed characterisation of intestinal MCs / EGCs in order to try to elucidate their functional role in the intestinal immune responses. Through an understanding of their distribution, composition and ultrastructure, the intention was to better characterise these cells and their functional properties. The general morphology, histochemical characteristics and tissue distribution of these cells were explored in detail using histochemical, IHC and immunogold staining / labelling, visualised using light, confocal and TEM microscopy. Despite these extensive investigations, their physiological function and the content of their granules still remain somewhat obscure, although a role as immunodulatory cells reacting to various exogeneous signals through a finely regulated process and comparable to that causing the degranulation of mammalian MCs is suggested. The histochemical staining properties demonstrated for salmonid MCs / EGCs seem to resemble those of mammalian mucosal mast cells, with both acidophilic and basophilic components in their granules, and a granule content containing neuromodulator / neurotransmitter-peptides such as serotonin, met-enkephalin and substance-p. Consequently, distinguishable bio-chromogenic markers have been identified that are of utility in generating a discriminatory profile for image analysis of such cells.

Ce projet a été conduit dans le contexte général du renforcement de la population naturelle de Saumon atlantique de l'Allier et s'est focalisé sur les modalités de croissance des juvéniles et tacons en grand cours d'eau. Nous nous sommes intéréssés au développement des juvéniles relâchés dans le milieu naturel, avant de considérer ensuite la chaîne trophique dans son ensemble. Notre travail avait plusieurs objectifs : 1-Effectuer une analyse de l'alimentation, de la croissance et du statut nutritionnel des tacons issus d'une salmoniculture, relâchés et recapturés le long du continuum fluvial de l'Allier ; 2-Evaluer si, en raison de compositions en acides gras différentes, les macroinvertébrés pouvaient affecter la croissance des tacons, ainsi que leur survie hivernale ; 3-Déterminer, grâce à une approche par les AG biomarqueurs, l'origine des composés lipidiques retrouvés dans les macroinvertébrés et identifier les sources de C assimilées par ces derniers le long du continuum fluvial.