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Many rivers are affected by man-induced regulations of stream-flow. The effects of these on the instream biota have been studied widely and it is generally accepted that assessment tools for the management of regulated rivers are of vital importance. In particular predictive instream habitat models like the Physical Habitat Simulation Model (PHABSIM) have become popular for this purpose with users world-wide. These models predict discharge-related changes in instream habitat availability for target species by modelling the hydraulic geometry of the river reach on the one and the microhabitat preferences of the species on the other side. Despite their popularity, validation studies for this approach have met many difficulties which are mostly related to the biological part of the model, the habitat preference curves. A review of these studies undertaken here reveals that very little information has been published on two main assumptions of the models: 1. The habitat preference of a species is independent of stream discharge 2. The habitat preference of a species is independent of the species population density Most validation studies are undertaken in field situations. As such they frequently have had problems relating to sampling the microhabitat use consistently, a lack of experimental control and variations in other secondary variables. It was thus decided to conduct controlled experiments in a large indoor flume. Young-of-year Atlantic salmon (Salmo salar) caught in a nearby stream were stocked into pool-riffle sequences, landscaped within a natural substrate, in observation areas of 3.6 metres length and 1 metre width. Microhabitat use of fish was recorded at three different discharges within a 15-fold discharge variation. It was found that the mean column velocity preference of the juvenile salmon, calculated by the standard method, varied largely, mainly due to a shift of preference for low water velocities. "Weighted usable area" (WUA) calculations, the final output of instream habitat models, varied up to two-fold due to these differences in preference. Habitat preference also varied with population density. Fish preferred the riffle habitat at low population density and the pool habitat during high population density. Fish used higher mean column velocities during low population density. There are hence fundamental problems related to the approach of using density functions as preference indices as is commonly done for building habitat preference curves, because of a bias for habitat availability. A new approach using Geographic Information Systems (GIS) is taken by comparing the microhabitat conditions fish experience at their chosen positions with the conditions fish would have experienced had they maintained the positions used at the other discharges. It was found that fish adjusted their positions towards significantly different microhabitats between low flow positions and the positions at the other two flows. This research demonstrates how microhabitat use and preference of wild-caught juvenile salmon varied with discharge and population density in a large near-natural flume. The error introduced by these variations to instream habitat model predictions was large. It confirms that habitat preference curves built as density functions on empirical fish observation data are bound to misrepresent the overall habitat requirements of a species life stage which in the case of juvenile salmon appeared wide and flexible over the range of discharge.

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Salmonid alphaviruses (SAV) are a group of viruses that have recently emerged as a serious threat to the salmonid aquaculture industry in Europe. Over recent years, diseases caused by SAV have severely hampered the Scottish, Irish and Norwegian Atlantic salmon industry, and are considered to be among the major economically important viral diseases affecting the industry at present. Amongst the six subtypes characterised so far, Salmonid alphavirus 1 (SAV1) causes severe pathology in the heart, pancreas and the skeletal muscle of Atlantic salmon leading to death and growth retardation in the affected fish. The biochemical characteristics of the virus and the sequential pathology of the diseases caused by SAV have been described; however the mechanisms responsible for causing the disease and the host defence mechanisms against the virus are poorly defined. This thesis therefore examined the pathogenesis of SAV infection at the cellular and molecular level in vivo in salmon and in vitro in salmonid cells, with a special emphasis on host immune defence mechanisms against the virus. SAV was first isolated from Chinook salmon embryo-214 (CHSE-214) cells in 1995 in Ireland. Several cell lines have since been used to grow the virus. In the present study, three established salmonid cell lines, Chum salmon heart -1 (CHH-1), CHSE-214 and Salmon head kidney -1 (SHK-1) were evaluated for their ability to support the isolation of SAV-1 from infected fish tissue, with CHH-1 cells giving the fastest cytopathic effect (CPE) during primary isolation. The CPE appeared as localised cell-rounding on CHH-1 and CHSE-214 cells, although in SHK-1 cells, the cells were seen to slough off the monolayer relatively later than with the other two cell lines during the infection. The host response to SAV infection was evaluated by experimentally infecting Atlantic salmon parr using a cell culture-adapted virus isolate. A quantitative reverse transcription polymerase chain reaction (qRT-PCR) was developed to examine the virus load in the fish, from which it was found that the highest viral RNA copy number was detected at 5 day post infection (d.p.i), of the 90 day experimental infection period. Characteristic pathological lesions were only seen in the pancreas and the heart but not in the skeletal muscles of the infected fish. A gene expression study using qRT-PCR revealed the rapid induction of interferon (INF) and INF-associated genes in the head kidney of the infected fish compared to the control fish. The Mx protein was found to be highly expressed in the heart and the mucous membranes of infected fish by immunohistochemistry. Interestingly, the pathological changes that were seen occurred some time after the peak expression of genes associated with the INF-1-pathway. When the host-virus interaction of Atlantic salmon infected with SAV was examined using a microarray, a potent first line defence response was observed, together with the signatures of early activation of the adaptive immune response during the initial stages of the infection. Genes associated with transcription, translation and lipid metabolism were significantly differentially expressed in virus infected fish compared to control fish. A large array of antiviral genes was significantly expressed, amongst which were some of the genes also described in mammalian alphavirus infections. Genes associated with apoptosis and anti-apoptosis were also seen to be differentially regulated showing the complexity of the host-virus interaction. Collectively, all of these findings suggest that a non-specific antiviral immune response takes place providing rapid immune protection during the early stages of SAV infection in salmon. In the study on morphogenesis of SAV in salmonid cells using electron microscopy (EM), a rapid internalization of virus into the cells and generation of replication complexes using the secretory pathway of the cell, similar to mammalian alphavirus replication was observed. The mature viruses were released through surface projections, acquiring envelopes from the host cell membrane. From the ultrastructural studies of the salmonid cells infected with SAV, a progressive chromatin marginalisation and condensation could be seen, leading to cellular fragmentation, forming membrane bound apoptotic bodies, characteristic of progressive apoptosis. The activation of caspase-3 in the cytoplasm and genomic DNA damage were also seen in the infected fish cells, indicating that apoptosis is the main cause of cell death during SAV infection. The results of this study have increased our knowledge and understanding of the cellular and molecular mechanisms involved in the pathogenesis of SAV infection, emphasising the importance of the first line defence mechanisms against SAV infection in salmon. This has given an interesting insight into the host mechanisms used to combat the virus during infection, and will undoubtedly be useful for designing new vaccines and management strategies for prevention and control of this important disease

Thesis (doctoral)--Swedish University of Agricultural Sciences, 2005. / Thesis documentation sheet inserted. Appendix includes six papers and manuscripts co-authored with others. Also issued electronically via World Wide Web in PDF format; online version lacks appendix of papers.

Lateral instability exerts considerable influence on the sedimentology, planform, and hydraulic characteristics of gravel-bed rivers. Because Atlantic salmon (Salmo salar) tolerate a narrow range of depths, velocities and substrate sizes, the quality and quantity of habitat available to salmon should vary with level of river instability. In the Riviere Nouvelle, a Gaspe river destabilized by deforestation and past channelization projects, the effect of lateral instability on habitat was variable. Fines content in riffle substrates did not show a significant relationship to local bank erosion rates, even where the rate was as high as 10 myr$ sp{-1}$ and the proportion of fines entering the channel was much higher than that found in riffles substrates (an excess of fines in potential spawning riffles reduces spawning success among salmonids). For juveniles, availability of hydraulically suitable habitat was largest where lateral instability resulted in aggradation of the river bed and development of a braided pattern. Hydraulic habitat availability was lowest where erosion patterns led to high planform curvature levels and to scouring of bed materials. In general, because of the relatively high power of the Riviere Nouvelle, structures or processes leading to diminishment of depths or velocities (e.g. aggradation) resulted in an increase in the amount of juvenile habitat available.

Although the watersheds of the Petite Cascapedia and Bonaventure Rivers, Gaspe Peninsula, have broadly similar geology and land use, their segment-scale river geomorphology is contrasted by subtle differences in valley characteristics that are a legacy of their individual geomorphic histories. These differences have consequences on the distribution of Atlantic salmon habitat such as boulder abundance (for parr rearing and overwintering habitats) and spawning substrate quality. Parr preference for boulder-rich river segments (1--5 km) was observed in the Bonaventure River. In the study systems redd distribution was sensitive to relatively small changes in the fines content of riffle substrate. River segments flowing through moderately narrow semi-alluvial valleys present better overall parr habitat (high boulder abundance) and better spawning substrate quality (percentage of sand) than wider valley sections. These differences are due to additional sources of coarse sediment, higher shear stresses, and lower bank erosion rates in such valleys.

Thesis (Ph.D.)--Memorial University of Newfoundland, 1999. / Bibliography: leaves 212-224.

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