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• 1181. [Article] Distribution of juvenile salmonids and stream habitat relative to 15-year-old debris-flow deposits in the Oregon Coast Range

  Debris flows, common disturbances in many mountainous areas, initially scour or bury stream habitats; however, debris flows deliver vast amounts of wood, boulders, and gravel that may ultimately form complex ...

  Citation × Citation Citation Abstract Copy Title: Distribution of juvenile salmonids and stream habitat relative to 15-year-old debris-flow deposits in the Oregon Coast Range Author: Kirkby, Kristen-Marie S. Debris flows, common disturbances in many mountainous areas, initially scour or bury stream habitats; however, debris flows deliver vast amounts of wood, boulders, and gravel that may ultimately form complex stream habitat to potentially support a diverse salmonid assemblage. The materials deposited by debris flows would otherwise be inaccessible to streams, and thus deposits may play an important role in creating and maintaining complex salmonid habitat over time. Despite the potential of deposits for increasing habitat complexity, most fish studies have focused on the destructive effects of debris flows and short-term recovery and re-colonization in scour zones. Debris-flows that occurred during the record-setting winter storms of 1996 in western Oregon, USA, provide an opportunity to study intermediate-term effects of debris-flow deposits on abundances and habitat for juvenile salmonids. In this setting, I surveyed salmonid abundance and habitat in three Oregon Coast Range streams that contained several debris-flow deposits from the 1996 storms. I explained fish abundance using hierarchical models, accounting for heterogeneous detection probabilities with repeated counts from multiple-pass snorkeling. The "best" hierarchical model of detection probability and abundance was selected (QAIC) from pool and snorkel-pass characteristics separately for juvenile coho salmon (Oncorhynchus kisutch), age 0+ trout, and age 1+ trout (Oncorhynchus spp.) in each stream. Adding distance to the nearest 1996 debris-flow deposit (DDF) produced a significant drop-in-deviance for four of nine "best" models, including at least one in each stream and for each species/age-class. In these four models, salmonid abundance decreased with increasing distance from deposit. As a potential explanation, several pool habitat characteristics were correlated (Spearman's rank) with DDF. Results varied across streams, but generally, percent of substrate as bedrock was lower and boulder density and percent substrate as gravel were higher closer to deposits. Although repeat counts are increasingly used in hierarchical modeling of heterogeneous detection probabilities and abundance for other wildlife species, studies of fish often rely on uncalibrated, single-pass snorkel counts. When exploring the value of repeat counts, I found that juvenile salmonid abundance decreased with increasing distance from debris-flow deposits in more multiple-pass hierarchical models that accounted for heterogeneous detection probabilities than for single-pass models that did not. Thus, modeling heterogeneous detection probabilities with repeated snorkel counts may be beneficial in other situations, addressing limitations of uncalibrated indices without relying on methods such as electrofishing, which may be difficult or impossible for remote study areas, longer surveys, or sensitive species. My findings suggest that debris-flow deposits may influence salmonid abundances after 15 years, and support management of debris flow-prone hillslopes and low-order channels to deliver elements of stream habitat complexity. Title: Distribution of juvenile salmonids and stream habitat relative to 15-year-old debris-flow deposits in the Oregon Coast Range Author: Kirkby, Kristen-Marie S. Debris flows, common disturbances in many mountainous areas, initially scour or bury stream habitats; however, debris flows deliver vast amounts of wood, boulders, and gravel that may ultimately form complex stream habitat to potentially support a diverse salmonid assemblage. The materials deposited by debris flows would otherwise be inaccessible to streams, and thus deposits may play an important role in creating and maintaining complex salmonid habitat over time. Despite the potential of deposits for increasing habitat complexity, most fish studies have focused on the destructive effects of debris flows and short-term recovery and re-colonization in scour zones. Debris-flows that occurred during the record-setting winter storms of 1996 in western Oregon, USA, provide an opportunity to study intermediate-term effects of debris-flow deposits on abundances and habitat for juvenile salmonids. In this setting, I surveyed salmonid abundance and habitat in three Oregon Coast Range streams that contained several debris-flow deposits from the 1996 storms. I explained fish abundance using hierarchical models, accounting for heterogeneous detection probabilities with repeated counts from multiple-pass snorkeling. The "best" hierarchical model of detection probability and abundance was selected (QAIC) from pool and snorkel-pass characteristics separately for juvenile coho salmon (Oncorhynchus kisutch), age 0+ trout, and age 1+ trout (Oncorhynchus spp.) in each stream. Adding distance to the nearest 1996 debris-flow deposit (DDF) produced a significant drop-in-deviance for four of nine "best" models, including at least one in each stream and for each species/age-class. In these four models, salmonid abundance decreased with increasing distance from deposit. As a potential explanation, several pool habitat characteristics were correlated (Spearman's rank) with DDF. Results varied across streams, but generally, percent of substrate as bedrock was lower and boulder density and percent substrate as gravel were higher closer to deposits. Although repeat counts are increasingly used in hierarchical modeling of heterogeneous detection probabilities and abundance for other wildlife species, studies of fish often rely on uncalibrated, single-pass snorkel counts. When exploring the value of repeat counts, I found that juvenile salmonid abundance decreased with increasing distance from debris-flow deposits in more multiple-pass hierarchical models that accounted for heterogeneous detection probabilities than for single-pass models that did not. Thus, modeling heterogeneous detection probabilities with repeated snorkel counts may be beneficial in other situations, addressing limitations of uncalibrated indices without relying on methods such as electrofishing, which may be difficult or impossible for remote study areas, longer surveys, or sensitive species. My findings suggest that debris-flow deposits may influence salmonid abundances after 15 years, and support management of debris flow-prone hillslopes and low-order channels to deliver elements of stream habitat complexity. Close

• 1182. [Article] Irrigated agriculture, energy, and endangered species in the Upper Klamath Basin : evaluating trade-offs and interconnections

  In 2001, an extreme drought tightened water supply in the Upper Klamath Basin (basin) while earlier increases in Endangered Species Act (ESA) water requirements for basin fish species that same year elevated ...

  Citation × Citation Citation Abstract Copy Title: Irrigated agriculture, energy, and endangered species in the Upper Klamath Basin : evaluating trade-offs and interconnections Author: Boehlert, Brent B. In 2001, an extreme drought tightened water supply in the Upper Klamath Basin (basin) while earlier increases in Endangered Species Act (ESA) water requirements for basin fish species that same year elevated demands. The Bureau of Reclamation (Reclamation), which manages irrigation water in parts of the basin located near the Oregon-California border, responded to ESA Section 7 obligations by severely curtailing water allocations to Reclamation Project irrigators for the 2001 growing season, costing irrigators an estimated $35 million in farm income. This event has directed attention to several important factors that may further undermine effective water management in the basin. These include higher ESA flow requirements due to a recent Ninth Circuit Court ruling and a ten-fold energy rate increase to irrigators resulting from a mid-2006 contract expiration with the regional energy provider. The overall objective of this research is to assess the impact of changes in ESA flow requirements and energy prices on the Upper Klamath Basin farm economy given variable levels of water trading flexibility and groundwater availability. A mathematical programming and Geographic Information System (GIS) framework is used in which farm decisions are assumed to maximize net revenue subject to hydrological, institutional, economic, and agronomic constraints. The results suggest that greater development of basin groundwater resources and the institution of a flexible water bank may be sufficient to mitigate the majority of costs related to increased ESA flow requirements in future years. Title: Irrigated agriculture, energy, and endangered species in the Upper Klamath Basin : evaluating trade-offs and interconnections Author: Boehlert, Brent B. In 2001, an extreme drought tightened water supply in the Upper Klamath Basin (basin) while earlier increases in Endangered Species Act (ESA) water requirements for basin fish species that same year elevated demands. The Bureau of Reclamation (Reclamation), which manages irrigation water in parts of the basin located near the Oregon-California border, responded to ESA Section 7 obligations by severely curtailing water allocations to Reclamation Project irrigators for the 2001 growing season, costing irrigators an estimated $35 million in farm income. This event has directed attention to several important factors that may further undermine effective water management in the basin. These include higher ESA flow requirements due to a recent Ninth Circuit Court ruling and a ten-fold energy rate increase to irrigators resulting from a mid-2006 contract expiration with the regional energy provider. The overall objective of this research is to assess the impact of changes in ESA flow requirements and energy prices on the Upper Klamath Basin farm economy given variable levels of water trading flexibility and groundwater availability. A mathematical programming and Geographic Information System (GIS) framework is used in which farm decisions are assumed to maximize net revenue subject to hydrological, institutional, economic, and agronomic constraints. The results suggest that greater development of basin groundwater resources and the institution of a flexible water bank may be sufficient to mitigate the majority of costs related to increased ESA flow requirements in future years. Close

• 1183. [Article] Persistent infection of salmonid cell lines with infectious pancreatic necrosis virus : a model for the carrier state in trout

  Persistent infections with infectious pancreatic necrosis virus (IPNV) were established in two salmonid cell lines and in live brook trout. Virus inocula containing high concentrations of defective interfering ...

  Citation × Citation Citation Abstract Copy Title: Persistent infection of salmonid cell lines with infectious pancreatic necrosis virus : a model for the carrier state in trout Author: Hedrick, Ronald Paul Persistent infections with infectious pancreatic necrosis virus (IPNV) were established in two salmonid cell lines and in live brook trout. Virus inocula containing high concentrations of defective interfering IPNV enhanced but were not a requirement for the establishment of persistent infections in cell lines derived from steelhead trout (STE-137) and chinook salmon (CHSE-214) embryos. Persistent infections were initiated in live brook trout by feeding a ration containing IPNV. Viral persistence was demonstrated by the detection of infectious virus in cell culture fluids and carrier trout feces. A fluctuating release of low levels of virus was characteristic of viral persistence both in vitro and in vivo. Infectious virus was produced by 0.06 to 1.0% of the cells in carrier brook trout tissues and cell lines persistently infected with IPNV. Viral persistence in these cell lines was further characterized by the presence of viral antigens in 1% or less of the cell population. These cells were often in advanced stages of infection indicating that death results from viral replication. The remainder of the cells in the population is protected from superinfection with homologous but not heterologous viruses. Protection is disrupted by passages of these cells in growth medium containing anti-IPNV antibody. Extended propagations with high levels of antibody cures persistent infection. Low levels of infectious virus released during IPNV persistence results from limiting the number of cells as well as the amount of infectious virus produced by persistently infected cells. Interferon, temperature sensitive and defective interfering viruses are known to control infectious virus production in certain persistently infected cell lines. Interferon and temperature sensitive virus were not detected during IPNV persistence in STE-137 and CHSE-214 cell lines in this study. Interferon was also not detected in carrier brook trout sera tested on rainbow trout (RTG -2) cells but this did not preclude its presence. The amount of infectious virus produced during viral persistence seems instead to be controlled by the production of defective interfering virus. Defective interfering virus was isolated from STE-137 cell culture persistently infected with IPNV by isopycnic centrifugation in CsC1. This virus had a density of 1.29 g/cc. Infectious virus (1.33 g/cc) was also produced by these cells. Defective interfering virus effectively suppressed the yields of infectious virus from control STE-137 cells infected with both viruses. The production of defective virus was also supported by electron microscopic examinations of persistently infected STE-137 cells. These results indicated that the production of defective interfering IPNV by persistently infected cell lines may control infectious virus replication and prevent the cytocidal effect that usually is accompanied by IPNV infection. The similarities between viral persistence in these cell lines and carrier brook trout suggest that the same virus-host cell interactions may be involved both in vitro and in vivo. These cell lines can therefore serve as invaluable models for understanding persistent IPNV infections. Title: Persistent infection of salmonid cell lines with infectious pancreatic necrosis virus : a model for the carrier state in trout Author: Hedrick, Ronald Paul Persistent infections with infectious pancreatic necrosis virus (IPNV) were established in two salmonid cell lines and in live brook trout. Virus inocula containing high concentrations of defective interfering IPNV enhanced but were not a requirement for the establishment of persistent infections in cell lines derived from steelhead trout (STE-137) and chinook salmon (CHSE-214) embryos. Persistent infections were initiated in live brook trout by feeding a ration containing IPNV. Viral persistence was demonstrated by the detection of infectious virus in cell culture fluids and carrier trout feces. A fluctuating release of low levels of virus was characteristic of viral persistence both in vitro and in vivo. Infectious virus was produced by 0.06 to 1.0% of the cells in carrier brook trout tissues and cell lines persistently infected with IPNV. Viral persistence in these cell lines was further characterized by the presence of viral antigens in 1% or less of the cell population. These cells were often in advanced stages of infection indicating that death results from viral replication. The remainder of the cells in the population is protected from superinfection with homologous but not heterologous viruses. Protection is disrupted by passages of these cells in growth medium containing anti-IPNV antibody. Extended propagations with high levels of antibody cures persistent infection. Low levels of infectious virus released during IPNV persistence results from limiting the number of cells as well as the amount of infectious virus produced by persistently infected cells. Interferon, temperature sensitive and defective interfering viruses are known to control infectious virus production in certain persistently infected cell lines. Interferon and temperature sensitive virus were not detected during IPNV persistence in STE-137 and CHSE-214 cell lines in this study. Interferon was also not detected in carrier brook trout sera tested on rainbow trout (RTG -2) cells but this did not preclude its presence. The amount of infectious virus produced during viral persistence seems instead to be controlled by the production of defective interfering virus. Defective interfering virus was isolated from STE-137 cell culture persistently infected with IPNV by isopycnic centrifugation in CsC1. This virus had a density of 1.29 g/cc. Infectious virus (1.33 g/cc) was also produced by these cells. Defective interfering virus effectively suppressed the yields of infectious virus from control STE-137 cells infected with both viruses. The production of defective virus was also supported by electron microscopic examinations of persistently infected STE-137 cells. These results indicated that the production of defective interfering IPNV by persistently infected cell lines may control infectious virus replication and prevent the cytocidal effect that usually is accompanied by IPNV infection. The similarities between viral persistence in these cell lines and carrier brook trout suggest that the same virus-host cell interactions may be involved both in vitro and in vivo. These cell lines can therefore serve as invaluable models for understanding persistent IPNV infections. Close

• 1184. [Article] BOD and toxicity of log leachates

  A series of log storage experiments were conducted to determine whether leachates derived from water storage of logs are acutely toxic to fish. Log segments approximately 18 inches long and 16 inches in ...

  Citation × Citation Citation Abstract Copy Title: BOD and toxicity of log leachates Author: Atkinson, Sheridan William A series of log storage experiments were conducted to determine whether leachates derived from water storage of logs are acutely toxic to fish. Log segments approximately 18 inches long and 16 inches in diameter were stored in tanks and held submerged for a period of 7 days. The holding water containing leached materials was made toxic with mercury to retard biological decomposition of the leached substances. Mercury was selectively removed from leachate samples by chelation prior to biochemical oxygen demand (BOD) and bioassay testing. Trout and salmon fry were subjected to the leachate water in short term acute bioassay tests. Results are reported as a median tolerance limit, (TLm), i. e., the concentration of leachate at which 50 percent of the test fish died for any given exposure time. Leachates were also tested for BOD₅, BOD k-rate, chemical oxygen demand (COD), wood sugar and Pearl Benson Index (PBI). Test results show that leachates from Douglas fir stored in fresh water exert a slight acute toxicity to fish. A TLm₉₆ of 20 percent leachate by volume, for a 50 year old Douglas fir log, was the most toxic leachate observed. Leachates from ponderosa pine, hemlock and an older fir log stored under identical conditions produced no measurable acute toxicity. Leachates contained a significant quantity of BOD and PBI exerting substances. The highest BOD₅, (1.36 g/ft² of submerged surface area) was exerted by leachate from a ponderosa pine log segment stored with bark removed. The highest PBI valve (12.5 g/ft²), was observed for leachate from a young Douglas fir log segment. BOD:COD ratios and BOD k-rate ranged widely for the various leachates, but were relatively low which indicated a significant fraction of non-biodegradable substances. Hoffbuhr (9) also observed a high non-biodegradable fraction in samples taken from log storage ponds. Wood sugars were found to account for a large part of the degradable portion of leachates. Leachate from ponderosa pine log with bark intact exerted a high BOD and also contained the highest concentration of wood sugar observed, 0.84 g/ft². Title: BOD and toxicity of log leachates Author: Atkinson, Sheridan William A series of log storage experiments were conducted to determine whether leachates derived from water storage of logs are acutely toxic to fish. Log segments approximately 18 inches long and 16 inches in diameter were stored in tanks and held submerged for a period of 7 days. The holding water containing leached materials was made toxic with mercury to retard biological decomposition of the leached substances. Mercury was selectively removed from leachate samples by chelation prior to biochemical oxygen demand (BOD) and bioassay testing. Trout and salmon fry were subjected to the leachate water in short term acute bioassay tests. Results are reported as a median tolerance limit, (TLm), i. e., the concentration of leachate at which 50 percent of the test fish died for any given exposure time. Leachates were also tested for BOD₅, BOD k-rate, chemical oxygen demand (COD), wood sugar and Pearl Benson Index (PBI). Test results show that leachates from Douglas fir stored in fresh water exert a slight acute toxicity to fish. A TLm₉₆ of 20 percent leachate by volume, for a 50 year old Douglas fir log, was the most toxic leachate observed. Leachates from ponderosa pine, hemlock and an older fir log stored under identical conditions produced no measurable acute toxicity. Leachates contained a significant quantity of BOD and PBI exerting substances. The highest BOD₅, (1.36 g/ft² of submerged surface area) was exerted by leachate from a ponderosa pine log segment stored with bark removed. The highest PBI valve (12.5 g/ft²), was observed for leachate from a young Douglas fir log segment. BOD:COD ratios and BOD k-rate ranged widely for the various leachates, but were relatively low which indicated a significant fraction of non-biodegradable substances. Hoffbuhr (9) also observed a high non-biodegradable fraction in samples taken from log storage ponds. Wood sugars were found to account for a large part of the degradable portion of leachates. Leachate from ponderosa pine log with bark intact exerted a high BOD and also contained the highest concentration of wood sugar observed, 0.84 g/ft². Close

• 1185. [Article] A partial economic analysis of hatchery propagation and commercial harvest of salmonid resources in Oregon

  The general purpose of this study was to formulate and conduct an economic analysis of some issues associated with managing commercial salmonid resources in Oregon. Since the Fish Commission of Oregon ...

  Citation × Citation Citation Abstract Copy Title: A partial economic analysis of hatchery propagation and commercial harvest of salmonid resources in Oregon Author: Mattox, Bruce Wade, 1941- The general purpose of this study was to formulate and conduct an economic analysis of some issues associated with managing commercial salmonid resources in Oregon. Since the Fish Commission of Oregon has the responsibility for managing these resources, it provides the institutional framework for this study. Within this framework, the following specific objectives were established: 1. To identify, in a predictive sense, an aggregate production function for the hatchery operations of the Commission. 2. To identify implications of the statistically determined function. 3. To theoretically relate hatchery production of salmonids to the allocation of harvesting resources in salmonid fisheries. 4. To offer theoretical explanations for any escapement of salmonids from the fishery in excess of the amount which is needed to maintain salmonid populations at selected levels over time. Data on hatchery operations were obtained for 15 major hatcheries operated by the Fish Commission during the time period from the beginning of October in 1968 through April of 1970. Least-squares multiple regression techniques were used to estimate linear and log-linear hatchery production functions. The equations which were estimated included a food variable which was reasoned to be a proxy variable for the operating expenses other than food expenditures and fixed facilities. The estimated equations also contained a variable which represented water temperatures for May through October and a similar variable representing water temperatures for November through April. Estimation of the equations resulted in tentative acceptance of hypotheses that the Commission combines inputs in fixed proportions and realizes constant returns to size from its hatchery operations. Results of estimation also indicated that water temperatures can adversely affect hatchery output when they enter the upper and lower portions of the observed temperature range, and that possibilities exist for substituting water temperature control for the food variable. Theoretical constructs used to examine effects of hatchery production on allocations of harvesting resources to salmonid fisheries indicated that, given open-access, excessive harvesting resources can enter the fisheries as a result of hatchery production. Theoretical constructs also indicated that some regulatory policies which are applied in salmonid fisheries can cause escapement of salmonids from the commercial fisheries to be in excess of the amount needed to maintain salmonid populations at selected levels. Title: A partial economic analysis of hatchery propagation and commercial harvest of salmonid resources in Oregon Author: Mattox, Bruce Wade, 1941- The general purpose of this study was to formulate and conduct an economic analysis of some issues associated with managing commercial salmonid resources in Oregon. Since the Fish Commission of Oregon has the responsibility for managing these resources, it provides the institutional framework for this study. Within this framework, the following specific objectives were established: 1. To identify, in a predictive sense, an aggregate production function for the hatchery operations of the Commission. 2. To identify implications of the statistically determined function. 3. To theoretically relate hatchery production of salmonids to the allocation of harvesting resources in salmonid fisheries. 4. To offer theoretical explanations for any escapement of salmonids from the fishery in excess of the amount which is needed to maintain salmonid populations at selected levels over time. Data on hatchery operations were obtained for 15 major hatcheries operated by the Fish Commission during the time period from the beginning of October in 1968 through April of 1970. Least-squares multiple regression techniques were used to estimate linear and log-linear hatchery production functions. The equations which were estimated included a food variable which was reasoned to be a proxy variable for the operating expenses other than food expenditures and fixed facilities. The estimated equations also contained a variable which represented water temperatures for May through October and a similar variable representing water temperatures for November through April. Estimation of the equations resulted in tentative acceptance of hypotheses that the Commission combines inputs in fixed proportions and realizes constant returns to size from its hatchery operations. Results of estimation also indicated that water temperatures can adversely affect hatchery output when they enter the upper and lower portions of the observed temperature range, and that possibilities exist for substituting water temperature control for the food variable. Theoretical constructs used to examine effects of hatchery production on allocations of harvesting resources to salmonid fisheries indicated that, given open-access, excessive harvesting resources can enter the fisheries as a result of hatchery production. Theoretical constructs also indicated that some regulatory policies which are applied in salmonid fisheries can cause escapement of salmonids from the commercial fisheries to be in excess of the amount needed to maintain salmonid populations at selected levels. Close

• 1186. [Article] Heterogeneous thermal habitat for northeast Oregon stream fishes

  Discrete coldwater patches within warm streams provide potential thermal refuge for coldwater fishes during periods of heat stress. This analysis focused on heterogeneity in stream water temperatures as ...

  Citation × Citation Citation Abstract Copy Title: Heterogeneous thermal habitat for northeast Oregon stream fishes Author: Ebersole, Joseph L. Discrete coldwater patches within warm streams provide potential thermal refuge for coldwater fishes during periods of heat stress. This analysis focused on heterogeneity in stream water temperatures as influenced by local influx of cooler subsurface waters. Using field thermal probes and recording thermistors, we identified and characterized coldwater patches potentially serving as thermal refugia for coldwater fishes. Coldwater patches within the surface waters of summer-warm streams generally occurred along the stream channel margin and were classified into four morphological types. Isolation, measured as distance of the coldwater patch from the main channel, was related to the composition of fish assemblages occurring within coldwater patches. Assemblages dominated by catostomids used coldwater patches furthest from the main channel, while salmonids utilized coldwater patches closer to the main channel. Increased isolation of coldwater patches from the main channel was hypothesized to incur greater risks of predation and greater energetic demands on fishes moving between coldwater patches and the main channel. Coldwater patch isolation distance increased in stream channels that were wider and shallower, and riparian canopy density over coldwater patches decreased with increasing channel width:depth. Strong vertical gradients in temperature associated with heating of surface layers of coldwater patches exposed to solar radiation superimposed upon vertical gradients in dissolved oxygen may restrict suitable refuge volumes for stream salmonids within coldwater patches. These relationships suggest that stream channel and riparian characteristics may influence connectivity and suitability of coldwater patches for stream fishes. Coldwater patch availability (measured as frequency and relative area) was positively associated with higher abundances of rainbow trout within stream reaches, after accounting for other habitat characteristics influencing abundance. Chinook salmon abundance was positively associated with coldwater patch frequency, but was not associated with coldwater patch area within streams. These results suggest that the physiognomy, distribution and connectivity of coldwater patches, important attributes determining the effectiveness of these habitats as thermal refugia for stream fishes, are associated with reach-level channel bedform and riparian features. We propose that patterns of thermal heterogeneity associated with channel morphology may provide an important aspect of habitat structure for stream fishes. Title: Heterogeneous thermal habitat for northeast Oregon stream fishes Author: Ebersole, Joseph L. Discrete coldwater patches within warm streams provide potential thermal refuge for coldwater fishes during periods of heat stress. This analysis focused on heterogeneity in stream water temperatures as influenced by local influx of cooler subsurface waters. Using field thermal probes and recording thermistors, we identified and characterized coldwater patches potentially serving as thermal refugia for coldwater fishes. Coldwater patches within the surface waters of summer-warm streams generally occurred along the stream channel margin and were classified into four morphological types. Isolation, measured as distance of the coldwater patch from the main channel, was related to the composition of fish assemblages occurring within coldwater patches. Assemblages dominated by catostomids used coldwater patches furthest from the main channel, while salmonids utilized coldwater patches closer to the main channel. Increased isolation of coldwater patches from the main channel was hypothesized to incur greater risks of predation and greater energetic demands on fishes moving between coldwater patches and the main channel. Coldwater patch isolation distance increased in stream channels that were wider and shallower, and riparian canopy density over coldwater patches decreased with increasing channel width:depth. Strong vertical gradients in temperature associated with heating of surface layers of coldwater patches exposed to solar radiation superimposed upon vertical gradients in dissolved oxygen may restrict suitable refuge volumes for stream salmonids within coldwater patches. These relationships suggest that stream channel and riparian characteristics may influence connectivity and suitability of coldwater patches for stream fishes. Coldwater patch availability (measured as frequency and relative area) was positively associated with higher abundances of rainbow trout within stream reaches, after accounting for other habitat characteristics influencing abundance. Chinook salmon abundance was positively associated with coldwater patch frequency, but was not associated with coldwater patch area within streams. These results suggest that the physiognomy, distribution and connectivity of coldwater patches, important attributes determining the effectiveness of these habitats as thermal refugia for stream fishes, are associated with reach-level channel bedform and riparian features. We propose that patterns of thermal heterogeneity associated with channel morphology may provide an important aspect of habitat structure for stream fishes. Close

• 1187. [Article] Direct injection gas chromatography of volatiles from fishery products

  The use of gas chromatography for the separation, comparison, and subsequent identification of flavor volatiles from food products has proven highly successful in recent years. The development of various ...

  Citation × Citation Citation Abstract Copy Title: Direct injection gas chromatography of volatiles from fishery products Author: Hilderbrand, Kenneth S. The use of gas chromatography for the separation, comparison, and subsequent identification of flavor volatiles from food products has proven highly successful in recent years. The development of various techniques for the concentration of the volatiles before gas chromatographic analysis has greatly extended the use of this important analytical tool. The injection of vapors directly into the chromatograph without prior concentration is the simplest method and has been used successfully on many food products. However, the use of this technique on the volatiles of fishery products has met with limited success. The complexity and nature of the flavor compounds found in fishery products have required the use of highly sensitive instruments and columns with very efficient separation power. The purpose of this investigation was to develop a method for the separation and comparison of volatiles from fishery products by this direct vapor injection technique. Preliminary investigations showed that a nine foot column of diisodecyl phthalate on 80/100 mesh, methanoic KOH treated, celite 545, operated isothermally at 35°C, would give satisfactory separation of one to three ml samples of volatiles from heated fishery products. The technique was not, however, sensitive enough to allow direct sampling of cold products unless they were highly spoiled or autoxidized. This investigation showed that direct vapor injection, using the column and conditions described, will show differences between size and number of peaks in heated fresh, oxidized, and spoiled fishery products. Several peaks in autoxidizing menhaden oil were shown to increase with hours of oxidation and a peak with the same retention time as trimethylamine was observed in the chromatograms of spoiled fish. The direct injection technique did not show large differences between fresh dover sole, rockfish, oysters, or beef. Tentative identification of various peaks from the chromatograms of oxidized salmon oil was attempted by comparison of retention data to known compounds and by functional group analysis by the method of Hoff and Feit (34). In this manner the possible existance of C₁ to C₇ alkanals, 2-hexen-1-al, methane, heptane, ethanol, butanol, and acetone was shown. The methods of tentative identification used were preliminary in nature and confirming tests would be necessary before positive identifications could be made. A comparison of chromatograms from fish, oysters, beef, and fish oils showed that several similar peaks appear in every case. These peaks were found at retention times of 0.71, 0.87, 1.42, 2.21, 2.83, 3.62, 5.20, and 5.51 minutes. Title: Direct injection gas chromatography of volatiles from fishery products Author: Hilderbrand, Kenneth S. The use of gas chromatography for the separation, comparison, and subsequent identification of flavor volatiles from food products has proven highly successful in recent years. The development of various techniques for the concentration of the volatiles before gas chromatographic analysis has greatly extended the use of this important analytical tool. The injection of vapors directly into the chromatograph without prior concentration is the simplest method and has been used successfully on many food products. However, the use of this technique on the volatiles of fishery products has met with limited success. The complexity and nature of the flavor compounds found in fishery products have required the use of highly sensitive instruments and columns with very efficient separation power. The purpose of this investigation was to develop a method for the separation and comparison of volatiles from fishery products by this direct vapor injection technique. Preliminary investigations showed that a nine foot column of diisodecyl phthalate on 80/100 mesh, methanoic KOH treated, celite 545, operated isothermally at 35°C, would give satisfactory separation of one to three ml samples of volatiles from heated fishery products. The technique was not, however, sensitive enough to allow direct sampling of cold products unless they were highly spoiled or autoxidized. This investigation showed that direct vapor injection, using the column and conditions described, will show differences between size and number of peaks in heated fresh, oxidized, and spoiled fishery products. Several peaks in autoxidizing menhaden oil were shown to increase with hours of oxidation and a peak with the same retention time as trimethylamine was observed in the chromatograms of spoiled fish. The direct injection technique did not show large differences between fresh dover sole, rockfish, oysters, or beef. Tentative identification of various peaks from the chromatograms of oxidized salmon oil was attempted by comparison of retention data to known compounds and by functional group analysis by the method of Hoff and Feit (34). In this manner the possible existance of C₁ to C₇ alkanals, 2-hexen-1-al, methane, heptane, ethanol, butanol, and acetone was shown. The methods of tentative identification used were preliminary in nature and confirming tests would be necessary before positive identifications could be made. A comparison of chromatograms from fish, oysters, beef, and fish oils showed that several similar peaks appear in every case. These peaks were found at retention times of 0.71, 0.87, 1.42, 2.21, 2.83, 3.62, 5.20, and 5.51 minutes. Close

• 1188. [Article] Temperature-modulated 7,12-dimethylbenz(a)antheracene carcinogenicity in rainbow trout

  Temperature influences the incidence of chemically induced cancer in fish, with warmer temperatures being associated with higher cancer incidence. The mechanisms of temperature-modulated chemical carcinogenesis ...

  Citation × Citation Citation Abstract Copy Title: Temperature-modulated 7,12-dimethylbenz(a)antheracene carcinogenicity in rainbow trout Author: Zahr, Camille Reda Temperature influences the incidence of chemically induced cancer in fish, with warmer temperatures being associated with higher cancer incidence. The mechanisms of temperature-modulated chemical carcinogenesis in fish, however, have not been described in detail. Therefore, one primary objective of this study was increased understanding of how temperature-modulated genotoxicity of 7,12- dimethylbenz(a)anthracene (DMBA) corresponded with tumor response. The second entails the potential of temperature to modulate cancer promotion. Rainbow trout (Oncorhyncus mykiss) (2 g) were acclimated at 10, 14 or 18°C for one month and then exposed to 1.0 ppm DMBA in their water for 20 hr. Exposures were at respective acclimation temperatures or 10 and 18°C acclimated fish were shifted to 14°C for DMBA exposures. Adduction of [³H]DMBA to hepatic DNA 21 days after exposure was higher in 10°C than 18°C fish exposed at their respective acclimation temperatures. However, in fish shifted to 14°C, the concentration of hepatic [³H]DMBA DNA adducts was similar in 10°C and 18°C acclimated fish at that time. Temperature effects on tumor incidence were assessed 9 months after DMBA waterborne exposures. Incidence of stomach, liver and swim-bladder cancer increased with rearing temperature. Differences in tumor incidence were less marked in fish reared at the same temperature (14°C). Retrospective analyses of livers from a tumor study initiated with aflatoxin B1 (AFB1) was conducted with antibodies to endogenous proliferating nuclear antigen (PCNA). Proliferating cells were scored by counting labeled nuclei in 5 random 10x fields using an image analysis program (BIOQUANT SYSTEM IV). There was no significant increase in numbers of PCNA labeled hepatocytes with temperature. The influence of acclimation temperature on plasma mitogens that stimulate cell division was assessed in cultured Chinook salmon embryo cells (CHSE-214). Plasma from rainbow trout (120-150 g) acclimated to either 10 or 18°C for at least four weeks stimulated in vitro proliferation of CHSE-214 cells to the same extent. This study demonstrated that chemically induced tumors in fish were modulated by temperature not only through genotoxin disposition and formation but also through persistence of DNA adducts. It also discounted the role of mitogenesis in temperature-modulated chemical carcinogenesis. Title: Temperature-modulated 7,12-dimethylbenz(a)antheracene carcinogenicity in rainbow trout Author: Zahr, Camille Reda Temperature influences the incidence of chemically induced cancer in fish, with warmer temperatures being associated with higher cancer incidence. The mechanisms of temperature-modulated chemical carcinogenesis in fish, however, have not been described in detail. Therefore, one primary objective of this study was increased understanding of how temperature-modulated genotoxicity of 7,12- dimethylbenz(a)anthracene (DMBA) corresponded with tumor response. The second entails the potential of temperature to modulate cancer promotion. Rainbow trout (Oncorhyncus mykiss) (2 g) were acclimated at 10, 14 or 18°C for one month and then exposed to 1.0 ppm DMBA in their water for 20 hr. Exposures were at respective acclimation temperatures or 10 and 18°C acclimated fish were shifted to 14°C for DMBA exposures. Adduction of [³H]DMBA to hepatic DNA 21 days after exposure was higher in 10°C than 18°C fish exposed at their respective acclimation temperatures. However, in fish shifted to 14°C, the concentration of hepatic [³H]DMBA DNA adducts was similar in 10°C and 18°C acclimated fish at that time. Temperature effects on tumor incidence were assessed 9 months after DMBA waterborne exposures. Incidence of stomach, liver and swim-bladder cancer increased with rearing temperature. Differences in tumor incidence were less marked in fish reared at the same temperature (14°C). Retrospective analyses of livers from a tumor study initiated with aflatoxin B1 (AFB1) was conducted with antibodies to endogenous proliferating nuclear antigen (PCNA). Proliferating cells were scored by counting labeled nuclei in 5 random 10x fields using an image analysis program (BIOQUANT SYSTEM IV). There was no significant increase in numbers of PCNA labeled hepatocytes with temperature. The influence of acclimation temperature on plasma mitogens that stimulate cell division was assessed in cultured Chinook salmon embryo cells (CHSE-214). Plasma from rainbow trout (120-150 g) acclimated to either 10 or 18°C for at least four weeks stimulated in vitro proliferation of CHSE-214 cells to the same extent. This study demonstrated that chemically induced tumors in fish were modulated by temperature not only through genotoxin disposition and formation but also through persistence of DNA adducts. It also discounted the role of mitogenesis in temperature-modulated chemical carcinogenesis. Close

• 1189. [Article] On Intermediate Models for Barotropic Continental Shelf and Slope Flow Fields. Part I: Formulation and Comparison of Exact Solutions

  Motivated by the general objective of pursuing oceanographic process and data assimilation studies of the complex, nonlinear eddy and jet current fields observed over the continental shelf and slope off ...

  Citation × Citation Citation Abstract Copy Title: On Intermediate Models for Barotropic Continental Shelf and Slope Flow Fields. Part I: Formulation and Comparison of Exact Solutions Author: Barth, J. A., Allen, J. S., Newberger, P. A. Motivated by the general objective of pursuing oceanographic process and data assimilation studies of the complex, nonlinear eddy and jet current fields observed over the continental shelf and slope off the west coast of the United States, we investigate the use of intermediate models for that purpose. Intermediate models contain physics between that in the primitive equations and that in the quasigeostrophic equations and are capable of representing subinertial frequency motion over the O(1) topographic variations typical of the continental slope, while filtering out high-frequency gravity-inertial waves. As an initial step, we compare and evaluate several intermediate models applied to the f-plane shallow-water equations for flows over topography. The accuracy and utility of the intermediate models are assessed by a comparison of exact analytical and numerical solutions with those of the primitive shallow-water equations (SWE) and with those of the quasi-geostrophic equations (QG). The intermediate models that we consider are based on the geostrophic momentum (GM) approximation, the derivation of Salmon (1983) utilizing Hamilton's principle (HP), a geostrophic vorticity (GV) approximation, the quasi-geostrophic momentum and full continuity equations (IM), the linear balance equations (LBE), the balance equations (BE), the related balance-type (HBE, BEM, NBE) and modified linear balance equations (LQBE), the slow equations (SE) of Lynch (1989), and the modified slow equations (MSE). In Part I, we discuss the intermediate models and develop formulations that are suitable for numerical solution in physical coordinates for use in Parts II and III. We investigate the capability of the intermediate models to represent linear ageostrophic coastally trapped waves, i.e., Kelvin and continental shelf waves, and demonstrate that they do so with accuracy consistent with standard linear low-frequency approximations. We also assess the accuracy of the models by a comparison of exact nonlinear analytical solutions to the SWE for steady flow in an elliptic paraboloid and for unsteady motion of elliptical vortices in a circular paraboloid with corresponding analytical solutions to the intermediate models and to QG. General results from the exact solution comparisons include the following. Many of the intermediate models are capable of producing more accurate solutions than QG over a range of Rossby numbers 0 < ϵ < 1. In some cases, the intermediate models provide accurate approximate solutions where QG is not applicable and fails to give a relevant solution. Considerable parameter-dependent variation in quality exists, however, among the different intermediate models. For the particular problems considered here, BE, HBE, BEM, NBE, and MSE reproduce the exact results of the SWE while LBE and LQBE give the same approximation as QG. The accuracy of the models is typically in the order GV, GM, IM, HP, and QG, with GV most accurate and IM and HP sometimes less accurate than QG. Title: On Intermediate Models for Barotropic Continental Shelf and Slope Flow Fields. Part I: Formulation and Comparison of Exact Solutions Author: Barth, J. A., Allen, J. S., Newberger, P. A. Motivated by the general objective of pursuing oceanographic process and data assimilation studies of the complex, nonlinear eddy and jet current fields observed over the continental shelf and slope off the west coast of the United States, we investigate the use of intermediate models for that purpose. Intermediate models contain physics between that in the primitive equations and that in the quasigeostrophic equations and are capable of representing subinertial frequency motion over the O(1) topographic variations typical of the continental slope, while filtering out high-frequency gravity-inertial waves. As an initial step, we compare and evaluate several intermediate models applied to the f-plane shallow-water equations for flows over topography. The accuracy and utility of the intermediate models are assessed by a comparison of exact analytical and numerical solutions with those of the primitive shallow-water equations (SWE) and with those of the quasi-geostrophic equations (QG). The intermediate models that we consider are based on the geostrophic momentum (GM) approximation, the derivation of Salmon (1983) utilizing Hamilton's principle (HP), a geostrophic vorticity (GV) approximation, the quasi-geostrophic momentum and full continuity equations (IM), the linear balance equations (LBE), the balance equations (BE), the related balance-type (HBE, BEM, NBE) and modified linear balance equations (LQBE), the slow equations (SE) of Lynch (1989), and the modified slow equations (MSE). In Part I, we discuss the intermediate models and develop formulations that are suitable for numerical solution in physical coordinates for use in Parts II and III. We investigate the capability of the intermediate models to represent linear ageostrophic coastally trapped waves, i.e., Kelvin and continental shelf waves, and demonstrate that they do so with accuracy consistent with standard linear low-frequency approximations. We also assess the accuracy of the models by a comparison of exact nonlinear analytical solutions to the SWE for steady flow in an elliptic paraboloid and for unsteady motion of elliptical vortices in a circular paraboloid with corresponding analytical solutions to the intermediate models and to QG. General results from the exact solution comparisons include the following. Many of the intermediate models are capable of producing more accurate solutions than QG over a range of Rossby numbers 0 < ϵ < 1. In some cases, the intermediate models provide accurate approximate solutions where QG is not applicable and fails to give a relevant solution. Considerable parameter-dependent variation in quality exists, however, among the different intermediate models. For the particular problems considered here, BE, HBE, BEM, NBE, and MSE reproduce the exact results of the SWE while LBE and LQBE give the same approximation as QG. The accuracy of the models is typically in the order GV, GM, IM, HP, and QG, with GV most accurate and IM and HP sometimes less accurate than QG. Close

• 1190. [Article] On Intermediate Models for Barotropic Continental Shelf and Slope Flow Fields. Part II: Comparison of Numerical Model Solutions in Doubly Periodic Domains

  As part of a program to improve understanding of the dynamics of the complicated, vigorous eddy and jet flow fields recently observed over the continental shelf and slope, we investigate the potential ...

  Citation × Citation Citation Abstract Copy Title: On Intermediate Models for Barotropic Continental Shelf and Slope Flow Fields. Part II: Comparison of Numerical Model Solutions in Doubly Periodic Domains Author: Newberger, P. A., Allen, J. S., Barth, J. A. As part of a program to improve understanding of the dynamics of the complicated, vigorous eddy and jet flow fields recently observed over the continental shelf and slope, we investigate the potential of intermediate models for use in both process and data assimilation studies of these flows. Intermediate models incorporate physics simpler than that contained in the full primitive equations yet more complete than in the quasi-geostrophic equations, and are capable of representing subinertial flows over O(1) bottom topographic variations and/or with O(1) isopycnal slopes. In addition, intermediate models dynamically filter out high-frequency gravity- inertial motions leading, potentially, to higher computational efficiency and well-posed limited area forecast/hindcast models. Initial studies focus on single layer flows on an f-plane with a free surface, governed by the shallow-water equations. In Part I, various intermediate models are formulated and their accuracy assessed by comparing some exact nonlinear analytical solutions that exist for the shallow-water equations with corresponding analytical solutions of the intermediate models. Here in Part II, an extensive set of numerical finite-difference solutions to initial-value problems in doubly periodic domains (to isolate model differences from the influence of boundary condition implementation on solid walls) is used to determine the accuracy of various intermediate models by comparing their predictions with those of a shallow-water equation model that uses a potential enstrophy and energy conserving numerical scheme (SWE). Intermediate model results are also contrasted with those from a quasi-geostrophic (QG) model. The intermediate models considered are based on the geostrophic momentum (GM) approximation, the derivation of Salmon utilizing Hamilton's principle (HP), a geostrophic vorticity (GV) approximation, a combination of the quasi-geostrophic momentum and full continuity equations (IM), the linear balance equations (LBE), the balance equations (BE), the related balance-type (HBE, BEM, NBE) and modified linear balance equations (LQBE), and on Lynch's slow equations in their original form (SE) and in a modified form (MSE). In addition, a semi-implicit version (SEMI) of the shallow-water equations, which numerically filters high-frequency motions, is included in the study. The basic initial-value problem used to test the various intermediate models involves sinusoidal flow over a symmetric Gaussian-shaped bottom topographic feature. Comparisons are made for a range of the relevant dimensionless model parameters including the strength of the flow (as measured by the Rossby number), the square of the ratio of a characteristic horizontal length scale to the Rossby radius of deformation, and the height of the topographic feature. A second initial-value problem involves the evolution of a rotating elliptical vortex over both flat and variable bottom topography. Results show that in cases with low local Rossby number flow, but with large topographic height, most of the intermediate models are substantially more accurate than QG. Even for flows with O(1) local Rossby numbers, some of the intermediate models continue to give excellent results. Specifically, BE, BEM and SEMI consistently do the best in the comparisons. Although the relative ordering of the remaining models is somewhat parameter-dependent, in general the next most accurate models are MSE and LQBE followed by HP and NBE. These are followed in quality by GV and GM while the remaining models, HBE, IM and LBE, perform least accurately for the range of parameters studied. Generally, intermediate models that have an integral invariant corresponding to conservation of potential enstrophy do better than those without, with the best results coming from models which have this property and a nonlinear balance equation. Title: On Intermediate Models for Barotropic Continental Shelf and Slope Flow Fields. Part II: Comparison of Numerical Model Solutions in Doubly Periodic Domains Author: Newberger, P. A., Allen, J. S., Barth, J. A. As part of a program to improve understanding of the dynamics of the complicated, vigorous eddy and jet flow fields recently observed over the continental shelf and slope, we investigate the potential of intermediate models for use in both process and data assimilation studies of these flows. Intermediate models incorporate physics simpler than that contained in the full primitive equations yet more complete than in the quasi-geostrophic equations, and are capable of representing subinertial flows over O(1) bottom topographic variations and/or with O(1) isopycnal slopes. In addition, intermediate models dynamically filter out high-frequency gravity- inertial motions leading, potentially, to higher computational efficiency and well-posed limited area forecast/hindcast models. Initial studies focus on single layer flows on an f-plane with a free surface, governed by the shallow-water equations. In Part I, various intermediate models are formulated and their accuracy assessed by comparing some exact nonlinear analytical solutions that exist for the shallow-water equations with corresponding analytical solutions of the intermediate models. Here in Part II, an extensive set of numerical finite-difference solutions to initial-value problems in doubly periodic domains (to isolate model differences from the influence of boundary condition implementation on solid walls) is used to determine the accuracy of various intermediate models by comparing their predictions with those of a shallow-water equation model that uses a potential enstrophy and energy conserving numerical scheme (SWE). Intermediate model results are also contrasted with those from a quasi-geostrophic (QG) model. The intermediate models considered are based on the geostrophic momentum (GM) approximation, the derivation of Salmon utilizing Hamilton's principle (HP), a geostrophic vorticity (GV) approximation, a combination of the quasi-geostrophic momentum and full continuity equations (IM), the linear balance equations (LBE), the balance equations (BE), the related balance-type (HBE, BEM, NBE) and modified linear balance equations (LQBE), and on Lynch's slow equations in their original form (SE) and in a modified form (MSE). In addition, a semi-implicit version (SEMI) of the shallow-water equations, which numerically filters high-frequency motions, is included in the study. The basic initial-value problem used to test the various intermediate models involves sinusoidal flow over a symmetric Gaussian-shaped bottom topographic feature. Comparisons are made for a range of the relevant dimensionless model parameters including the strength of the flow (as measured by the Rossby number), the square of the ratio of a characteristic horizontal length scale to the Rossby radius of deformation, and the height of the topographic feature. A second initial-value problem involves the evolution of a rotating elliptical vortex over both flat and variable bottom topography. Results show that in cases with low local Rossby number flow, but with large topographic height, most of the intermediate models are substantially more accurate than QG. Even for flows with O(1) local Rossby numbers, some of the intermediate models continue to give excellent results. Specifically, BE, BEM and SEMI consistently do the best in the comparisons. Although the relative ordering of the remaining models is somewhat parameter-dependent, in general the next most accurate models are MSE and LQBE followed by HP and NBE. These are followed in quality by GV and GM while the remaining models, HBE, IM and LBE, perform least accurately for the range of parameters studied. Generally, intermediate models that have an integral invariant corresponding to conservation of potential enstrophy do better than those without, with the best results coming from models which have this property and a nonlinear balance equation. Close