Thesis (Ph. D.)--University of Washington, 1991. / Vita. Includes bibliographical references (leaves [47]-56).

Thesis (Ph. D.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 174-191). Also available on the World Wide Web.

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 152-163).

Thesis (Ph. D.)--University of Washington, 1996. / Vita. Includes bibliographical references.

Thesis (Ph. D., Natural Resources)--University of Idaho, December 2007. / Major professor: Kenneth D. Cain. Includes bibliographical references. Also available online (PDF file) by subscription or by purchasing the individual file.

Thesis (M.Sc.)--Aberdeen University, 2009. / Title from web page (viewed on Dec. 1, 2009). Includes bibliographical references.

Diss. (sammanfattning) Göteborg : Göteborgs universitet, 2010. / Härtill 5 uppsatser.

Animals in general, but fish in particular, inhabit environments characterized by dynamic photic conditions that are influenced by cyclical events such as the night-day cycle, or by spatial heterogeneity in the distribution of light. Effects of these dynamic properties on the visual system are compounded in salmonid fishes by migrations that expose individuals to various types of habitats, at various stages of their ontogeny. This dissertation examines some of the adaptations that enable the retina of salmonid fishes to cope with their changes of “visual environment” caused by migration and by the night-day cycle. In the first part of this dissertation, I used a combination of optic nerve response (ONR) recordings and conventional histology of the retina to investigate the ontogeny of sensitivity to ultraviolet (UV) light in salmonid fishes. I found that the UV cone mechanism contributed mostly to the ON response of retinal ganglion cells in rainbow trout (Oncorhpichus mykiss). Furthermore, the presence of UV sensitivity in rainbow trout was associated with the presence of accessory corner cones in the retinal cone mosaic, as both UV sensitivity and these cones were absent in larger (59.5-83 5g) juveniles. These results suggest that corner cones in the salmonid retina are sensitive to UV light, and that their ontogenetic disappearance leads to the loss of UV sensitivity. The changes in the photic environment that occur when mature salmonid fishes return to their natal stream to reproduce mirror those undergone during the first migration. To determine if the accessory comer cones, lost during this first migration, reappear at the time of the return migration, I studied the structure of the photoreceptor layer in sexually mature Pacific salmonids from four species: chinook (O. tschawytscha), chum (O. keta) and coho (O. kisutch) salmon, and rainbow trout. I found accessory comer cones over a large area of the dorso-temporal retina in all four species examined, which provides support for the contention that these cones are the product of late cellular addition. I investigated possible pathways for visual information to various brain centers in rainbow trout by labelling retinal projections and torus semicircularis connections in the same individuals. Double-labelling of neuronal tracts revealed two possible indirect pathways between the retina and the torus semicircularis, through the accessory optic center of the diencephalon and the optic tectum respectively. In the second part of this dissertation, I qualitatively and quantitatively examined the effects of various levels and spectral types of ambient lighting conditions on the sensitivity and time course of multi-unit responses recorded from the optic nerve of juvenile rainbow trout. Change in threshold from the dark-adapted state to progressively brighter ambient light conditions was examined at four wavelengths (380, 430, 540 and 620 nm) and found to be linear over most of the scotopic range, with a slope around 0.8. The results also suggested that, under mesopic conditions, rods and the long-wavelength cone mechanism were active simultaneously, in their respective parts of the spectrum. Implicit time, or time-to-peak of the scotopic responses decreased with stimulus intensity following a logarithmic relationship with a slope of -0.10, suggesting that the scotopic system of trout acts as an 11-stage low-pass filter, a number similar to that inferred in cat and rat, but different from other non-mammalian vertebrates. Similarly, implicit time at threshold decreased logarithmically with background intensity for the scotopic system, with a slope of -0.09 Varying the spectral content of ambient light led to differences in sensitivity and time course of ONRs across the spectrum, suggesting physiological differences between cone mechanisms. Possible implications for the coding of visual information are briefly discussed. In conclusion I provide a qualitative model of light adaptation in the trout visual system. / Graduate

Growth and immunity are essential physiological functions that are each energetically costly. Thus, energetic allocation into these systems must be appropriately balanced throughout life. Such 'tradeoffs' require molecular-level cross talk between growth and immunity. Limited data suggests that the growth hormone (GH) – insulin-like growth factor (IGF) axis, a key pathway regulating vertebrate growth, also has a role in immune function. Here I exploit salmonid fishes to characterise the regulation of GH-IGF axis genes under multiple experimental contexts where growth and immunity were being traded-off. Specifically, I examined the transcriptional response of the GH-IGF axis to in vivo immune-stimulation at different stages of ontogeny, considering several tissue contexts (i.e. whole fish, immune tissues, and skeletal muscle) and animals with distinct growth rates driven by GH-overexpression. To better contextualise the data, I established the regulation of key gene markers for muscle growth and immune status. Further, I considered gene duplicates retained from whole-genome duplication events in salmonid evolutionary history, exploiting new genomic resources for gene characterisation (e.g. novel IGF-IR paralogues). Four major conclusions arose from my studies. First, up-regulation of IGFBP-1A1 and IGFBP-6A2 (known IGF inhibitors), following disease challenge, suggests that IGF signalling is repressed during infection, promoting energetic reallocation towards immunity. Second, the combined regulation of multiple IGF system genes in immune tissues suggests that while IGF signalling is repressed during infection, IGFBP-6A2 may directly stimulate immune tissues, likely via IGF-independent mechanisms. Third, coregulation of IGFBP-1A1 and IGFBP-6A2 with immune markers indicates direct regulation of the IGF system by conserved cytokine pathways. Finally, an altered skeletal muscle response to immune-stimulation suggests that modulation of GH-IGF axis regulation by GH-overexpression results in compromised fish health. Overall, these findings have broad implications for aquaculture, where fast growth and immunocompetence are traded-off, while improving our basic understanding of fish growth and immunity.

Aeromonas salmonicida is a Gram negative pathogenic fish bacterium. To facilitate the construction of the chromosomal map of A.salmonicida A449, several previously uncharacterized genes, including recA and four fla genes were identified. While the location of all the genes identified as a result of this study were mapped on the chromosome, the recA and fla genes were further characterized at the molecular level. The A.salmonicida A449 recA was cloned, sequenced and expressed in vitro. The 1059 bp recA open reading frame encoded a 353 amino acid protein with predicted molecular weight (Mᵣ) of 37,900. Southern blot analysis was performed to demonstrate the high degree of conservation between the A449 recA and those of the other typical and atypical strains of A.salmonicida examined. The predicted amino acid sequence of A.salmonicida A449 RecA was found to possess a number of domains identical to those characterized in Escherichia coli RecA.These included domains for adenosine triphosphate binding, DNA binding and protein-protein interactions. The A.salmonicida A449 recA was mobilized into an E.coli recA strain and was shown to allow increased survival in the presence of the chemical mutagen methyl methane sulfonate and ultra violet (uv) irradiation. The rate of the A.salmonicida A449 recA-mediated recombination in E. coli was increased by exposure to uv light, which suggested that SOS induction in A.salmonicida paralleled that of E.coli. The A.salmonicida A449 recA also possessed a potential regulatory SOS-box in the DNA 5' of the gene. A novel flagellin operon was identified in A.salmonicida A449, characterization of which revealed the presence of two tandemly linked flagellin structural genes flaA and flaB. The flaA and flaB genes were in turn tandemly linked to flaG encoding a protein of unknown function, and flaH encoding a protein homologous to the Hook Associated Protein II of other bacteria. The flaA and flaB genes with 79% nucleotide sequence identity, were conserved in typical and atypical strains of A.salmonicida, and displayed significant divergence at the nucleotide level from the fla genes of the motile species Aeromonas hydrophila and Aeromonas veronii biotype sobria. flaA, flaB and flaG encode unprocessed proteins with predicted Ms of 32,351, 32,056 and 15,965 respectively. When cloned under the control of the Ptac promoter, flaB was highly expressed when induced in E. coli DH5α, and FlaB protein was detectable even in the uninduced state. In flaA clones containing intact upstream sequence, FlaA was barely detectable when uninduced and poorly expressed on induction. The A.salmonicida flagellins are antigenically cross-reactive with A. hydrophila TF7 flagellin(s), and evolutionally closely related to the flagellins of Pseudomonas aeruginosa and Vibrio anguillarum.Electron microscopy showed that A. salmonicida A449 expresses unsheathed polar flagella at extremely low frequency. Finally, the physical and genetic map of the chromosome of A. salmonicida A449 was constructed using pulsed-field gel electrophoresis and Southern blot analysis. The three restriction enzymes used in the map construction were CeuI, Pmel and PacI. The chromosome of A. salmonicida A449, with an estimated size of 4,658 ± 29.75 kb, was determined to be circular in structure. Several genes of A. salmonicida, including those which encoded proteins implicated in virulence, were localized on the chromosome map. The chromosomal locations of the recA and fla genes were also identified. The global genomic relationship between the typical and atypical strains of A. salmonicida was investigated by comparing the CeuI cleavage fingerprint of the respective genomes.The results showed that the typical strains were indeed very homogenous as had been previously reported. The atypical strains expressed extensive variation both in the number of DNA fragments obtained with CeuI and also in the digestion fingerprint. The comparison of the CeuI digestion fingerprint of atypical strains revealed a clustering of some strains which suggested that this could be a powerful taxonomic tool for better classification of the atypical group. The two A. sobria strains analyzed with CeuI were also homogenous and showed significant similarities to the A. salmonicida typical strains CeuI genomic fingerprints. In contrast, four A. hydrophila strains yielded CeuI-derived fragments which like the atypical strain varied both in number and patterns. There was also minimal observed similarities between the genome of A. hydrophila strains and the A. salmonicida strains. / Graduate