This thesis tests the hypothesis that innate immunity may be enhanced immediately following a stressful event. The experiments characterize the acute effects of the fight or flight response on some immunological and endocrine parameters in rainbow trout (Oncorhynchus mykiss). Plasma cortisol and catecholamines were elevated within seconds of the initiation of an acute handling stressor consisting of 30 seconds in the air and five, 10 or 20 minutes in a shallow bucket of water. Plasma lysozyme activity increased after stress, however, the increases were not statistically significant unless variation was reduced by serial bleeding of the same individual trout before and after stress. A more "resting" fish was achieved by use of the anesthetic 2-phenoxy-ethanol which was surreptitiously introduced into the tanks before the initial bleed. Individual fish were then revived in freshwater and stressed as before. Enhancement of lysozyme activity was evident although levels of plasma stress hormones in fish that were anesthetized, revived and stressed were less than when fish were similarly stressed without anesthetic. Levels of cortisol and catecholamines increased within seconds of capture and aerial exposure, returned to near pre-stress levels after the fish had been placed in a shallow bucket of water for 30 seconds, then increased again. Evaluation of the influence of acute stress on survival following challenge with the pathogen Vibrio anguillarum yielded equivocal data. Results presented here suggest that enhancement of innate defenses as part of the fight or flight response merits further evaluation. / Graduation date: 1997

Redband trout density was examined in three forested streams in central Oregon at two scales, pool channel unit and microhabitat. Two streams were in roadless areas and one was in a "highly managed" watershed. At the larger spatial scale, trout displayed a seasonal shift in habitat use from early to late summer. There was a positive correlation between trout density and pool structural complexity during summer base flow. The association was intensified throughout the summer as stream flow continued to drop. The structural complexity of each pool was quantified using an index integrating structural variability and depth. Twenty-two pools were divided into microhabitats, or pool subunits with similar characteristics using a qualitative classification scheme describing different structural elements comprising the pool habitat. Microhabitat was partitioned between fry and older trout throughout the summer: Fry generally used stream margins, backwaters, and shallow areas; whereas, trout one year and older used deep areas (depth greater that 0.5 m) and cover associated with substrate and wood. The use of cover by trout one year and older doubled from June to August. This change in use was coupled with the increased association with structural complexity at the channel unit scale. The large substrate and wood that provided cover also increased the structural complexity of the pool. As trout increased their use of cover, their densities increased in more complex pools. Man-made log weir pools in a simplified stream were evaluated for their structural complexity and compared to the shallow natural pools in the same reach. Log weir pools had greater average depth, but were less complex than natural pools, and could maintain a similar density of trout. The structural complexity in natural pools appears to compensate for their shallow depth. Log weir pools enhanced with placement of a rootwad supported higher densities of trout. Addition of a rootwad provided microhabitats associated with cover that were lacking in weir pools without other structures added. When using instream construction to create pool habitat, complex structure that provides microhabitats associated with cover is more effective at holding higher densities of fish under late summer low flow conditions. / Graduation date: 1996

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.

Graduation date: 1992

Rainbow trout were exposed to aluminum at pH 7.25 and 8.25 and four hardnesses (10, 30, 80, and 120 ppm CaCO₃) for 96 hours in a continuous-flow system and mortality and aluminum accumulation in the gills were determined. Temperature, pH, and dissolved oxygen were measured daily for each treatment. Dissolved and total aluminum concentrations and hardness were determined following exposure periods of 48 and 96 hours. Aluminum was most toxic at pH 8.25, and was more toxic at lower than at higher hardnesses. Water hardness provided a significant protective effect against aluminum-induced mortality (p < 0.05), and there were no significant effects for water hardness on gill accumulation at either of pH. At pH 7.25 no mortalities occurred under any conditions. At pH 8.25, the accumulation of aluminum in gill tissues was higher than for pH 7.25 following exposure for 96 hours. In addition, aluminum concentration and exposure time had a significantly cumulative effect on fish mortality (p < 0.05). Possible mechanisms for aluminum toxicity and the accumulation of aluminum in the gills of rainbow trout were attributed to the forms and solubilities of aluminum species at different pH values. Competition between Ca²⁺ and aluminum for binding sites on the gills likely influenced aluminum toxic action. / Graduation date: 1992

The peripheral-type benzodiazepine receptor (PTBR) of trout brain was pharmacologically characterized and pyrethroid interaction with this site investigated. High-affinity binding sites for [³H]PK 11195 were detected in brain membranes of rainbow trout; these shared some of the characteristics of the PTBR of rodent brain (i.e., high affinity for PK 11195 and an endogenous ligand protoporphyrin IX) but were unique in the low affinity for Ro5-4864. Permethrin displaced [³H]PK 11195 binding with micromolar affinity while deltamethrin had less than 50% efficacy at displacement. Thus the PTBR appeared not to be relevant to pyrethroid toxicity in rainbow trout. Pyrethroid interaction with the GABA, receptor was investigated using [³⁵S]TBPS as a radioligand probe and by measurement of GABA-stimulated ³⁶c1- influx in vesicle preparations. At micromolar concentrations, deltamethrin, cypermethrin isomers and other pyrethroids inhibited [³⁵S]TBPS binding by 55- 95% with limited stereoselectivity. Pyrethroids were found to effect a GABAdependent inhibition of [³⁵S]TBPS binding. Ro5-4864, which showed micromolar affinity for the trout PTBR, produced a GABA-modulated interaction with [³⁵S]TBPS binding. These results delineate the reciprocal allosteric interactions between a pyrethroid binding site, a Ro5-4864 binding site, the GABA recognition moiety and the TBPS binding site in trout brain. However, pyrethroids exhibited a modest affinity for this binding site on the GABAA receptor. Pyrethroids indirectly inhibited the GABA-dependent influx of ³⁶Cl⁻into trout brain synaptoneurosomes by increasing the basal uptake of chloride, thereby compromising the ability of the vesicles to respond to applications of GABA. This pyrethroid effect was of nanomolar potency, stereospecific, tetrodotoxinsensitive and mimicked by veratridine. These results suggest that the primary effect of pyrethroids in trout brain, as measured by this assay, was due to an interaction with voltage-dependent sodium channels, increasing sodium conductance and thereby increasing the basal uptake of ³⁶Cl⁻ through a voltagesensitive channel. The convulsant activity of deltamethrin was tested in rainbow trout. The EC₅₀ for convulsant severity was 32 μg /kg body weight. By comparison, pyrethroids at these concentrations in rodents produce no overt toxicity but act as potent proconvulsants. / Graduation date: 1990

Coral trout, Plectropomus Ieopardus, is a high-volume, high-priced species in the international live reef food fish trade. Each year more than 8,000 tonnes of fish, worth over a billion Hong Kong dollars, are exported from the Philippines, Indonesia, Malaysia and Australia for consumption in Hong Kong and Mainland China. Its wild populations are believed to be declining in all major source countries with the exception of Australia which manages its fisheries. Concerns over the sustainability of coral trout fisheries, which are major livelihood for some coastal communities, have been raised. To assess whether the fisheries are biologically sustainable, this study developed two different stock assessments synthesizing the best available scientific knowledge and fisheries data of coral trout or grouper stocks for two major sources of production. For the coral trout fishery in the Municipality of Taytay in the Province of Palawan, Philippines, only stock life-history was available in literature, while for Indonesia only catch and effort data were provided for 11 major fishing grounds for groupers including coral trout, by a major live fish trader. Given the nature of the data available, two types of fisheries models were developed for the assessments. For Taytay, a per-recruit model was constructed to simulate catch and stock response to a range of fishing levels based on life-history processes. With the current fishing level estimated from sampled catch, the model indicated that the fishery was unsustainable in Taytay because the spawning stock was overexploited. Right-based catch control, export quota, minimum size, spawning season and aggregation closures were proposed for the recovery of spawning and the spawning stock. Studying stock abundance, sex change and uses of the fish other than export, for example domestic use and mortality levels, will improve the assessment rigour. For Indonesia, a mult-grouper species per-area-based Fox model was fitted to recent catch and effort data. The assessment determined catch and trade quotas for management and highlighted the need for rights-based adaptive management. The assessment found on fishing ground where the groupers including coral trout were fished much beyond sustainable levels and suggested immediate reduction of catch and number of fishers. Monitoring catch, effort and stock abundance and understanding larval dispersal and recruitment can help verify model assumptions and improve their accuracy. For the great many data-poor, unassessed grouper fisheries, similar assessments can be carried out gather data and evaluate fisheries sustainability, while management measures derived from the two assessments here could be used to inform management until more data and assessments become available. Data gaps for improvement of models were identified in the study. Both assessments in this study viewed community-based management as essential to resolve the weak enforcement capacity of Southeast Asian states in fisheries management. For management in and by communities lacking expertise and resource, a greater synergy between various parties is critical, which includes institutional legitimacy of community’s property rights, outreach and capacity building by NGOs, compliance of traders with regulations, sustainable trade practices as well as financial support from consumer’s choices and philanthropy. / published_or_final_version / Biological Sciences / Master / Master of Philosophy

Red mark syndrome (RMS) is a non-lethal skin condition, of unknown aetiology, affecting rainbow trout (Oncorhynchus mykiss) in the United Kingdom since 2003. It has now spread to 50% of the rainbow trout farms, resulting in great economic losses due to the downgrading of the product. There are also similar skin conditions in rainbow trout, for instance strawberry disease (SD) in the USA. As with RMS, the aetiological agent of this disease is also unknown. Several potential aetiological agents have been proposed, including a Rickettsia-like organism (RLO) in SD in the USA and Flavobacterium psychrophilum in RMS in the UK. The aim of the research presented here was to investigate the causative agent of RMS and to establish if there is a relationship between RMS and SD. An RLO was found to be associated with both RMS and SD-affected fish using immunohistochemistry (IHC) and polymerase chain reaction (PCR). The results of the IHC, together with the similarities in the pathology between the two conditions, suggest that RMS and SD are most likely the same disease (Chapter 2). In an attempt to isolate the RLO, F. psychrophilum or other suspected causative agents of RMS, several artificial bacteriological media, cell culture methods and novel techniques such as MagnaBind™ IgG beads (magnetic beads) were utilized. Although initial results appeared promising, no specific bacterial or viral agent was isolated using these methods. Transmission electron microscopy was used to analyse samples in an attempt to visualise any viruses and/or the RLO suspected of causing RMS (Chapter 3), but none were seen. Investigation into the involvement of both the RLO and F. psychrophilum in RMS using primary culture and IHC, together with the more advanced techniques of MALDI-TOF–MS and 16s rRNA gene sequencing, showed no association between F. psychrophilum and RMS. A quantitative PCR (qPCR), together with IHC, showed a positive correlation between the RLO and RMS-affected tissue, but this did not v distinguish between primary or secondary involvement of the organism. Results following analysis of samples using other assays, including ELISA and IHC, both using serum from naturally infected individuals, 16s rRNA gene PCR and bacterial isolation, were inconclusive, with methods requiring further optimisation for future use. The qPCR used in the study also needs to be fully optimised, as the results of a ring trial between three laboratories were considerably different (Chapter 4). Cohabitation challenges were conducted in the USA to investigate the involvement of the RLO in the early stages of SD. Clinical signs of SD were clearly evident in a small percentage of the cohabitated naïve fish. In most of these cases the DNA of the RLO could be detected, but again primary or secondary involvement could not be determined due to the small sample size (Chapter 5). In conclusion, the results from the analysis of samples by PCR, IHC with anti-F. psychrophilum PAbs, MALDI-TOF-MS and 16s rRNA gene sequencing indicate that F. psychrophilum is unlikely to be the causative aetiological agent of RMS. Although Koch’s postulates were not fulfilled, a strong correlation was obtained between the RLO and RMS-affected fish in the IHC, PCR and qPCR using RLO specific primers. It is unclear however, if the involvement of the RLO is as a primary or secondary pathogen. The RLO associated with RMS appears to have antigens in common with Piscirickettsia salmonis (from the results of the IHC), the causative agent of Salmon Rickettsial Syndrome, for which commercial vaccines are available, and should therefore be investigated as a form of mitigation for RMS, since the RLO has not yet been isolated and a traditional inactivated whole cell vaccine is not possible at this time. Efforts to isolate the RLO should continue and the involvement of other pathogens in RMS should be investigated further with new cutting edge techniques such as next generation sequencing or random multiplex (RT)-PCR to rule out viral involvement in the disease.

This thesis addresses the issue of hybridization between native westslope cutthroat trout (Oncorhynchus clarkii lewisi) and introduced rainbow trout (O. mykiss), giving strong consideration to their differing glacial refugia during the Wisconsin Glaciation. We hypothesize that having more recently derived from an anadromous form O. mykiss will possess life history characteristics more typical of a highly anadromous species. This hypothesis would also predict hybrids to be intermediate in these characteristics. In a comparison of growth rates and survivorship (Chapter 2) O. clarkii lewisi were found to employ a slower growing, longer lived strategy than O. mykiss, with hybrids typically being intermediate. Additionally, O. mykiss were also found to have aerobic and anaerobic metabolic capacities superior to O. clarkii lewisi in a first time comparison of these species (Chapter 3). These results support the glacial refuge hypothesis, but furthermore provide a potential explanation of the establishment of the elevational gradient commonly observed in hybridization studies. It would seem likely that O. mykiss would require more productive reaches being a faster growing, shorter lived species with higher metabolic costs. This study confirmed the gradient of O. mykiss persisting at lower elevations, trending through a hybrid zone to pure O. clarkii lewisi in headwater reaches and above migratory barriers (Chapter 2). A similar gradient was also reported when considering only the hybrid population, supporting the notion that habitat preference is under some genotypic control. The importance of migratory barriers was found to decrease with elevation suggesting potential additional limiting factors. Hybrid individuals were also found to be intermediate in morphological characteristics (Chapter 4). The confidence in differentiating between pure and non-pure O. clarkii lewisi was found to increase with the number of O. mykiss alleles (degree of hybridization) an individual possessed. Morphological-based identification was found to be an efficient, cost-friendly, preliminary assessment tool that could be useful in limiting the number of sites needing detailed genetic assessment. / 152 leaves : ill. (some col.) ; 29 cm.

Bull trout are a species of fish native to the coldwater mountain streams of Alberta. Because this species is of special conservation concern and displays finely dissected population structure, it is well suited as a model species to test the utility of versatile conservation genetics tools. One such tool, a genetic clustering method, was used to discern the hierarchical population structure of bull trout in the core of their range in South-West Alberta. The method also revealed patterns of gene flow by way of assignment tests. Populations defined by this method were then used as reference populations for mixed-migrant assignment tests, revealing that clustering method-defined populations may be more suitable for such tests rather than traditional approaches that define reference populations by sampling location. Combined with spatial data a posteriori, assignment tests had additional utility of discerning spatial scale of movement for juvenile and adult salmonids. This technique provided further evidence that assignment tests may be powerful indirect tools for evaluating migration, and that longrange inter-stream dispersal in juvenile salmonid fish may be more common than previously assumed. / xi, 174 leaves : ill. ; 29 cm. --