Within the environmental approach for the study of fluctuations in fish population abundance, factors that may regulate the overlap in time and space (phasing) of fishes, food supply, and predators, are sought. This trophic phasing analysis is based on the recognition that production of food is a process at least partially independent of the production of consumers. Trophic phasing analysis was applied in investigating production of chum salmon in the Fraser River estuary. Juvenile chum salmon were captured near a tidal flat; the abundance of salmon near the flat was highest in late May in 1985 and in early June in 1986. These salmon relied heavily on harpacticoid copepods as a food source. Individual taxa as well as the assemblage of main prey harpacticoids also had periods of highest abundance in the water column. The blooming period of the prey harpacticoid assemblage coincided with the appearance in the sediment of warming episodes. These warming episodes result from interactions between the daily heat cycle and specific tide patterns. Variations in the degree of overlap of the periods of highest abundance of salmon and harpacticoids could affect the survival of the fishes. The degree of overlap of those periods was hindcasted using indices for the temporal patterns of abundance of salmon and harpacticoids on the flat. The median date of downstream migration at a counting station upstream was used for the salmon; the timing of the second annual occurrence of tide conditions giving rise to a warming event in the sediment was used for harpacticoids. Difference in time between the two events was taken as a phasing index accounting for two degrees of freedom in the process of fish production. There is suggestion of a non-monotonic relationship between the index of survival of even broodyear chum salmon and the hindcasted phasing index. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate

The purpose of this study is to investigate optimal exploitation of a Pacific salmon fishery under the assumption that exclusive property rights in a fishery have been vested in a single or sole owner. Based on a review of the existing fisheries economics literature which focuses largely (but not entirely) on long-term steady state analytics, it is argued that the associated modeling technique does not apply readily to Pacific salmon fisheries. This line of reasoning is supported by the development, along the lines of the existing literature, of both a within-season and a long-term model of a salmon fishery. The within-season model, which finds limited precedent in the literature, provides the opportunity to introduce two relationships important in anadromous salmon fisheries, i.e., a production function with a catch coefficient variable at the vessel level and a stock distribution function, or time-of-entry curve. An analytical general solution is obtained to the model incorporating these features. The intertemporal model incorporates a purely compensatory Ricker-type spawner-recruit curve to define the interseasonal relationship between spawning escapement and future recruits. This model is formulated as an optimal control problem and is solved by using the general form solution to problems of this type which has recently been developed in the literature. A numerical solution to optimal escapement from the Skeena River fishery is obtained for parameters and coefficients estimated from this fishery. Both models have signficiant shortcomings which motivate the development of a more complete model of the fishery. Though it retains the basic features of the within-season and intertemporal models, this larger model allows concurrent within-season and interseason analysis, contains two species in a joint harvesting technology, contains an age structure and a stochastic element, all of which are absent in the two earlier models. This model is simulated on a computer in two formulations -- one dealing with weekly fleet hiring by the sole owner and the other with annual fleet hiring. The alternative fleet hiring assumptions are introduced so as to assess the added efficiency which is provided by more flexible fleet hiring rules which would be an important feature of coast-wide attempts at rationalizing the British Columbia salmon fishery via establishment of property rights. The major findings of the study are several. The determination of an optimal escapement policy via simulation experimentation demonstrates that a computer model of this type can successfully be used in this fashion. The specified minimum annual escapement which maximizes the present value of net profits was 300,000 sockeye and 400,000 pink for annual fleet hiring while the weekly fleet hiring model required the additional application of a weekly minimum escapement of 30% of the available total sockeye and pink stock. Comparing the results of the two fleet hiring assumptions it was concluded that the weekly fleet hiring regime resulted in a larger present value of net profits considering the Skeena River fishery alone. In .a comparison of the optimal fishing effort indicated by the simultion model (as measured in vessel-days) with the effort expended in the actual fishery it was concluded that a minimum estimate of excess effort is approximately .15% for annual fleet hiring and 50% for weekly fleet hiring. Successful development and application of this computer-based model is a significant step towards development of the larger coast-wide model which can be used to estimate optimal capacity for the entire fleet. / Arts, Faculty of / Vancouver School of Economics / Unknown

A computational procedure for optimization of large multidimensional models is presented. The procedure is applied to a model of the Georgia Strait sport and commercial fisheries of Chinook C Oncorhynchus tshawytscha ) and coho ( O. kisutch ) salmon. Optimal seasons for these fisheries are calculated and compared to current regulations. Differences, in form and performance, between the optimal seasons and present seasons are minimal and insignifigant. However, in order to match present age structure, population levels and harvests a value of near zero must be placed on fish left in the water at the end of the season. The computational requirements of the optimization are proportional to those of the model. In the case study in this thesis the optimization required approximately eight to ten times the computer time of the model. / Science, Faculty of / Zoology, Department of / Graduate

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Sequencing and phylogenetic analysis was used to characterise a number of Scottish IPNV isolates. The majority of isolates from Scotland were genetically closely related to the Sp strain of IPNV. There appears to be a link between the IPN status of a farm and the presence of IPNV in the environment but this is short lived as IPNV does not typically persist in natural reservoirs at sufficiently high levels to allow re-infection to occur. Real-time PCR was used to study the expression of a subset of immune relevant genes following IPNV challenges by a natural (co-habitation) and unnatural (i.p.) route. Differences were observed between the two challenge routes which may reflect orientation towards a Th1 or Th2/regulatory response in i.p. and cohabiting infected fish respectively. These results may give us a better understanding of immune regulation in Atlantic salmon, and may lead to improved vaccine development. Real-time PCR was used to analyse the expression of the two Atlantic salmon IRF-1 isoforms, the results show that the IRF-1 gene is induced in response to IPNV infection in kidney tissue and in ASK cells but in macrophages no significant difference in expression was observed. SSH identified several candidate genes that may be part of a protection mechanism in Atlantic salmon important for controlling viral replication and the pathogenic effects of IPNV. Genes that were found to be significantly up-regulated belong functionally to the following groups of processes: proteolysis immune and stress response, transcription/replication, translation, protein transport/protein interactions and the metabolism. This is the first report identifying Vig-2 as being upregulated by IPNV.

Graduation date: 1991

Thesis (M.S.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 96-101). Also available on the World Wide Web.

Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 143-149).

Thesis (Ph. D.)--Oregon State University, 2011. / Printout. Includes bibliographical references (leaves 126-139). Also available on the World Wide Web.

Thesis (M.S.)--Oregon State University, 1980. / Includes bibliographical references (leaves 180-192). Also available online.