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• 1801. [Article] Time budget and habitat use patterns of marbled godwits (Limosa fedoa beringiae) breeding on the Alaska Peninsula

  Diurnal time budgets and habitat use patterns of breeding Ugashik marbled godwits (Limosa fedoa beringiae) were studied on the north-central portion of the Alaska Peninsula during spring and summer 1995-1996. ...

  Citation × Citation Citation Abstract Copy Title: Time budget and habitat use patterns of marbled godwits (Limosa fedoa beringiae) breeding on the Alaska Peninsula Author: Mehall-Niswander, Angela C. Diurnal time budgets and habitat use patterns of breeding Ugashik marbled godwits (Limosa fedoa beringiae) were studied on the north-central portion of the Alaska Peninsula during spring and summer 1995-1996. Marbled godwits were observed from blinds and behaviors were described for the four phases of the breeding season: pair-formation, egg-laying, incubation and post-hatching. During pair-formation, males spent the majority of time performing flight displays (40.2%), most notably the ceremonial flight (30.7%). Males spent 34.3% of the egg-laying period guarding their mates probably to reduce the threat of cuckoldry. Females incubated during the daytime and males incubated at night. Off-duty males were engaged in maintenance activities (49.4%) or were alert/erect (22.7%). Four marbled godwit nests and the first newly hatched, downy marbled godwit chicks ever recorded in Alaska were found within the study site. One parent guarded the chicks which allowed the other to forage in nearby wetlands. Males performed male-exit flight as they prepared to depart for coastal staging lagoons approximately three weeks after their chicks hatched. Interspecific and intraspecific hostility peaked during the post-hatching period although aggressiveness towards neighboring shorebirds decreased. Godwits may benefit from the aggressive nature of some neighboring shorebirds and more timid species may receive a similar benefit from nesting close to godwit semi-colonies. The scattering of nests in loose semi-colonies may reduce predation by offering both nest concealment and group defense. Cover types and microhabitat characteristics were compared between sites used by marbled godwits ("present") and paired sites where no godwits were observed throughout the breeding season ("absent"), and among sites used for broodrearing, foraging, ground display and nesting. Logistic regression models predicted the probability of godwit occurrence or the probability of a godwit broodrearing, foraging, displaying or nesting based upon significant site features. Results indicate that different cover types were used for broodrearing, foraging, ground display and nesting, and cover types differed between present and absent sites. Microhabitat characteristics were different between present and absent sites, and they varied among the different use sites. The odds of finding a godwit at a site or the odds of finding a godwit broodrearing, foraging, displaying or nesting changed with changes in the significant microhabitat characteristics. As the percent shrub cover increased the odds of finding a brood or a nest increased 2.65-fold and 1.95-fold, respectively. The vegetation at broodrearing sites was taller (1.6 dm) than the vegetation at the other use sites, while the vegetation at nest sites was considerably shorter (1.3 dm) and denser. The probability of finding a godwit foraging increased with increasing forb cover and water depth, and decreasing shrub and moss cover and site roughness. Godwits used the periphery of wetlands for ground display. These grassy areas were typically transition zones between the wetland itself and the drier shrub communities. Title: Time budget and habitat use patterns of marbled godwits (Limosa fedoa beringiae) breeding on the Alaska Peninsula Author: Mehall-Niswander, Angela C. Diurnal time budgets and habitat use patterns of breeding Ugashik marbled godwits (Limosa fedoa beringiae) were studied on the north-central portion of the Alaska Peninsula during spring and summer 1995-1996. Marbled godwits were observed from blinds and behaviors were described for the four phases of the breeding season: pair-formation, egg-laying, incubation and post-hatching. During pair-formation, males spent the majority of time performing flight displays (40.2%), most notably the ceremonial flight (30.7%). Males spent 34.3% of the egg-laying period guarding their mates probably to reduce the threat of cuckoldry. Females incubated during the daytime and males incubated at night. Off-duty males were engaged in maintenance activities (49.4%) or were alert/erect (22.7%). Four marbled godwit nests and the first newly hatched, downy marbled godwit chicks ever recorded in Alaska were found within the study site. One parent guarded the chicks which allowed the other to forage in nearby wetlands. Males performed male-exit flight as they prepared to depart for coastal staging lagoons approximately three weeks after their chicks hatched. Interspecific and intraspecific hostility peaked during the post-hatching period although aggressiveness towards neighboring shorebirds decreased. Godwits may benefit from the aggressive nature of some neighboring shorebirds and more timid species may receive a similar benefit from nesting close to godwit semi-colonies. The scattering of nests in loose semi-colonies may reduce predation by offering both nest concealment and group defense. Cover types and microhabitat characteristics were compared between sites used by marbled godwits ("present") and paired sites where no godwits were observed throughout the breeding season ("absent"), and among sites used for broodrearing, foraging, ground display and nesting. Logistic regression models predicted the probability of godwit occurrence or the probability of a godwit broodrearing, foraging, displaying or nesting based upon significant site features. Results indicate that different cover types were used for broodrearing, foraging, ground display and nesting, and cover types differed between present and absent sites. Microhabitat characteristics were different between present and absent sites, and they varied among the different use sites. The odds of finding a godwit at a site or the odds of finding a godwit broodrearing, foraging, displaying or nesting changed with changes in the significant microhabitat characteristics. As the percent shrub cover increased the odds of finding a brood or a nest increased 2.65-fold and 1.95-fold, respectively. The vegetation at broodrearing sites was taller (1.6 dm) than the vegetation at the other use sites, while the vegetation at nest sites was considerably shorter (1.3 dm) and denser. The probability of finding a godwit foraging increased with increasing forb cover and water depth, and decreasing shrub and moss cover and site roughness. Godwits used the periphery of wetlands for ground display. These grassy areas were typically transition zones between the wetland itself and the drier shrub communities. Close

• 1802. [Article] Over-winter demography of the gray-tailed vole (Microtus canicaudus) in fragmented and continuous habitats

  Large scale disruption of natural habitats worldwide has led to concern over the effects of habitat fragmentation on wildlife populations. Small scale experiments may be a useful tool for discovering effects ...

  Citation × Citation Citation Abstract Copy Title: Over-winter demography of the gray-tailed vole (Microtus canicaudus) in fragmented and continuous habitats Author: Brunkal, Heidi L. Large scale disruption of natural habitats worldwide has led to concern over the effects of habitat fragmentation on wildlife populations. Small scale experiments may be a useful tool for discovering effects of fragmentation over larger landscape scales. I sought to explore the potential for using voles as an experimental model system, at a small scale, to discover mechanisms that may affect other species at different spatial scales. I compared over-winter demography of gray-tailed voles, Microtus canicaudus, in two experimental landscapes, consisting of fragmented and continuous habitat, to assess the effects of habitat fragmentation. I chose winter as the time frame of the experiment because it poses harsh conditions for voles and because seasonal bottlenecks may affect population persistence. Population size, population growth rates, reproduction, recruitment, survival and movements, were monitored using mark-recapture methods in 8, 0.2-ha enclosures planted with alfalfa. The habitat within the enclosures was manipulated into 2 configurations of equal area, 1 large continuous patch (625 m²), and a mosaic of 25 small patches (each 25 m²), prior to the introduction of 12 pairs of animals/enclosure. I hypothesized that population size and growth rates, reproduction, recruitment, and survival would be greater for vole populations in continuous habitats than for populations in fragmented habitats. Additionally, I hypothesized that movements would be more restricted within fragmented habitat because the voles would perceive the area between habitat patches as a barrier. I did not detect significant differences between vole populations in continuous and fragmented treatments. However, populations residing in fragmented habitat showed higher variability over the study period. Populations in both treatments decreased throughout the winter period and all became extinct by the end of the study. Reproduction occurred only during the fall period, and there were no significant differences between treatments. Movements were not different between treatments, or between male and female voles, but movements did increase over time. Survival appeared to be higher for male voles in continuous habitat than in fragmented habitat, but female vole survival was similar between treatments. Survival was influenced by weather conditions, and predation. These results contrast with a previous experiment during the summer season, and indicate that seasonal bottlenecks may be important to consider when studying habitat fragmentation. Extinction of populations in both treatments demonstrates that small populations are extremely vulnerable to both environmental and demographic stochastic events. Title: Over-winter demography of the gray-tailed vole (Microtus canicaudus) in fragmented and continuous habitats Author: Brunkal, Heidi L. Large scale disruption of natural habitats worldwide has led to concern over the effects of habitat fragmentation on wildlife populations. Small scale experiments may be a useful tool for discovering effects of fragmentation over larger landscape scales. I sought to explore the potential for using voles as an experimental model system, at a small scale, to discover mechanisms that may affect other species at different spatial scales. I compared over-winter demography of gray-tailed voles, Microtus canicaudus, in two experimental landscapes, consisting of fragmented and continuous habitat, to assess the effects of habitat fragmentation. I chose winter as the time frame of the experiment because it poses harsh conditions for voles and because seasonal bottlenecks may affect population persistence. Population size, population growth rates, reproduction, recruitment, survival and movements, were monitored using mark-recapture methods in 8, 0.2-ha enclosures planted with alfalfa. The habitat within the enclosures was manipulated into 2 configurations of equal area, 1 large continuous patch (625 m²), and a mosaic of 25 small patches (each 25 m²), prior to the introduction of 12 pairs of animals/enclosure. I hypothesized that population size and growth rates, reproduction, recruitment, and survival would be greater for vole populations in continuous habitats than for populations in fragmented habitats. Additionally, I hypothesized that movements would be more restricted within fragmented habitat because the voles would perceive the area between habitat patches as a barrier. I did not detect significant differences between vole populations in continuous and fragmented treatments. However, populations residing in fragmented habitat showed higher variability over the study period. Populations in both treatments decreased throughout the winter period and all became extinct by the end of the study. Reproduction occurred only during the fall period, and there were no significant differences between treatments. Movements were not different between treatments, or between male and female voles, but movements did increase over time. Survival appeared to be higher for male voles in continuous habitat than in fragmented habitat, but female vole survival was similar between treatments. Survival was influenced by weather conditions, and predation. These results contrast with a previous experiment during the summer season, and indicate that seasonal bottlenecks may be important to consider when studying habitat fragmentation. Extinction of populations in both treatments demonstrates that small populations are extremely vulnerable to both environmental and demographic stochastic events. Close

• 1803. [Article] Behavioral ecology of marbled murrelets (Brachyramphus marmoratus) in forest and marine ecosystems of Oregon

  Marbled Murrelets (Brachyramphus marmoratus) are threatened seabirds that are prone to disturbance both at sea and at old-growth forest nesting areas. I examined murrelet behavior and activity patterns ...

  Citation × Citation Citation Abstract Copy Title: Behavioral ecology of marbled murrelets (Brachyramphus marmoratus) in forest and marine ecosystems of Oregon Author: Jodice, Patrick G. R., 1961- Marbled Murrelets (Brachyramphus marmoratus) are threatened seabirds that are prone to disturbance both at sea and at old-growth forest nesting areas. I examined murrelet behavior and activity patterns in forest and marine ecosystems of Oregon. Diving behavior was studied during the 1995 and 1996 breeding seasons and was compared to predictions from optimal breathing models, which predicted a strong relationship between dive times and preceding pause times. Diving patterns appeared to fit these predictions more in 1996 than 1995 suggesting that diving behavior was affected more by annual changes in environmental conditions than by physiological constraints on breathing and diving as predicted by optimal breathing models. Activity patterns at inland nest sites were monitored on a near-daily basis during three breeding seasons to assess the relationships between activity and both weather and date. Daily activity was highly variable within and among sites and years and I observed greater variability in activity levels than has been previously reported for this species. Activity varied greatly during all portions of the breeding season and analyses revealed that weather and date variates explained little of the variability present. It also appeared that variability in activity during the breeding season was not due entirely to breeding phenology; however, activity of nonbreeding birds attending nesting stands may contribute to daily variability. Inland activity data also were used to assess the feasibility of developing long-term monitoring strategies based on counts of daily detections. I determined how effectively various survey strategies estimated measures of daily mean and standard deviation of detection counts of murrelets within a breeding season. Results indicated that it would be difficult to obtain reliable estimates of murrelet detections with sampling efforts up to 14 days/season. However, estimates of mean and standard deviation for daily detections during a breeding season may be reliably estimated to within ± 50% with similar or less effort. The power of survey strategies to detect annual declines in detections of 25% and 50% were very low and moderate, respectively, except when variability was quite low. Title: Behavioral ecology of marbled murrelets (Brachyramphus marmoratus) in forest and marine ecosystems of Oregon Author: Jodice, Patrick G. R., 1961- Marbled Murrelets (Brachyramphus marmoratus) are threatened seabirds that are prone to disturbance both at sea and at old-growth forest nesting areas. I examined murrelet behavior and activity patterns in forest and marine ecosystems of Oregon. Diving behavior was studied during the 1995 and 1996 breeding seasons and was compared to predictions from optimal breathing models, which predicted a strong relationship between dive times and preceding pause times. Diving patterns appeared to fit these predictions more in 1996 than 1995 suggesting that diving behavior was affected more by annual changes in environmental conditions than by physiological constraints on breathing and diving as predicted by optimal breathing models. Activity patterns at inland nest sites were monitored on a near-daily basis during three breeding seasons to assess the relationships between activity and both weather and date. Daily activity was highly variable within and among sites and years and I observed greater variability in activity levels than has been previously reported for this species. Activity varied greatly during all portions of the breeding season and analyses revealed that weather and date variates explained little of the variability present. It also appeared that variability in activity during the breeding season was not due entirely to breeding phenology; however, activity of nonbreeding birds attending nesting stands may contribute to daily variability. Inland activity data also were used to assess the feasibility of developing long-term monitoring strategies based on counts of daily detections. I determined how effectively various survey strategies estimated measures of daily mean and standard deviation of detection counts of murrelets within a breeding season. Results indicated that it would be difficult to obtain reliable estimates of murrelet detections with sampling efforts up to 14 days/season. However, estimates of mean and standard deviation for daily detections during a breeding season may be reliably estimated to within ± 50% with similar or less effort. The power of survey strategies to detect annual declines in detections of 25% and 50% were very low and moderate, respectively, except when variability was quite low. Close

• 1804. [Article] Isolation and characterization of a new reovirus from chum salmon (Oncorhynchus keta)

  This report describes the isolation of a new virus from adult chum salmon (Oncorhynchus keta) returning to the Tokushibetsu Hatchery, Hokkaido, Japan. The agent was isolated in the CHSE-214 cell line derived ...

  Citation × Citation Citation Abstract Copy Title: Isolation and characterization of a new reovirus from chum salmon (Oncorhynchus keta) Author: Winton, James R. This report describes the isolation of a new virus from adult chum salmon (Oncorhynchus keta) returning to the Tokushibetsu Hatchery, Hokkaido, Japan. The agent was isolated in the CHSE-214 cell line derived from chinook salmon (Oncorhynchus tshawytscha). The virus replicated in selected fish cell lines incubated between 10 and 20°C and produced a unique cytopathic effect characterized by the formation of circular plaque-like areas of cytoplasmic fusion. The nuclei of the cells were not affected. Physical and chemical studies have shown the agent, tentatively named chum salmon virus, to be a member of the family Reoviridae and distinct from any known virus of fish. Electron microscopy of negatively stained particles revealed a naked icosahedral virion 75 nm in diameter with a clearly defined double capsid. Treatment with α-chymotrypsin removed the outer capsid yielding 50-55 nm subviral particles with enhanced infectivity. Viral infectivity was not reduced by treatment with ether or chloroform. The virus was resistant to freeze-thaw and pH 3, but unstable at 56°C. It did not hemagglutinate human type 0 erythrocytes. No cross-neutralization was observed with antiserum against reovirus types 1, 2 or 3 or against infectious pancreatic necrosis virus. Viral replication was not inhibited by 5-fluoro-2'-deoxyuridine and infected cells stained with acridine orange showed typical reoviruslike cytoplasmic inclusions. Polyacrylamide gel electrophoresis of the viral genome revealed 10 segments of double-stranded RNA ranging in weight from 2.6 X 10⁶ to 0.32 X 10⁶ daltons with a total genome weight of 15.3 X 10⁶ daltons. Analysis of virion polypeptides on SDSpolyacrylamide gels indicated five major virion proteins with molecular weights of 145,000, 130,000, 75,000, 43,000 and 33,000 daltons were present in the intact virion. Two minor polypeptides of 80,000 and 30,000 daltons were also present. The density of the intact virion in CsC1 was 1.33 g/cc. The virus had limited pathogenicity for salmonid fish. Chum and chinook salmon infected with the virus exhibited a focal necrotizing hepatitis. No mortality could be attributed to these lesions which were active sites of viral synthesis. Rainbow trout (Salmo gairdneri) and kokanee salmon (Oncorhynchus nerka) showed no pathological changes in any organ system examined. The virus replicated in all four species tested. Title: Isolation and characterization of a new reovirus from chum salmon (Oncorhynchus keta) Author: Winton, James R. This report describes the isolation of a new virus from adult chum salmon (Oncorhynchus keta) returning to the Tokushibetsu Hatchery, Hokkaido, Japan. The agent was isolated in the CHSE-214 cell line derived from chinook salmon (Oncorhynchus tshawytscha). The virus replicated in selected fish cell lines incubated between 10 and 20°C and produced a unique cytopathic effect characterized by the formation of circular plaque-like areas of cytoplasmic fusion. The nuclei of the cells were not affected. Physical and chemical studies have shown the agent, tentatively named chum salmon virus, to be a member of the family Reoviridae and distinct from any known virus of fish. Electron microscopy of negatively stained particles revealed a naked icosahedral virion 75 nm in diameter with a clearly defined double capsid. Treatment with α-chymotrypsin removed the outer capsid yielding 50-55 nm subviral particles with enhanced infectivity. Viral infectivity was not reduced by treatment with ether or chloroform. The virus was resistant to freeze-thaw and pH 3, but unstable at 56°C. It did not hemagglutinate human type 0 erythrocytes. No cross-neutralization was observed with antiserum against reovirus types 1, 2 or 3 or against infectious pancreatic necrosis virus. Viral replication was not inhibited by 5-fluoro-2'-deoxyuridine and infected cells stained with acridine orange showed typical reoviruslike cytoplasmic inclusions. Polyacrylamide gel electrophoresis of the viral genome revealed 10 segments of double-stranded RNA ranging in weight from 2.6 X 10⁶ to 0.32 X 10⁶ daltons with a total genome weight of 15.3 X 10⁶ daltons. Analysis of virion polypeptides on SDSpolyacrylamide gels indicated five major virion proteins with molecular weights of 145,000, 130,000, 75,000, 43,000 and 33,000 daltons were present in the intact virion. Two minor polypeptides of 80,000 and 30,000 daltons were also present. The density of the intact virion in CsC1 was 1.33 g/cc. The virus had limited pathogenicity for salmonid fish. Chum and chinook salmon infected with the virus exhibited a focal necrotizing hepatitis. No mortality could be attributed to these lesions which were active sites of viral synthesis. Rainbow trout (Salmo gairdneri) and kokanee salmon (Oncorhynchus nerka) showed no pathological changes in any organ system examined. The virus replicated in all four species tested. Close

• 1805. [Article] Diethylnitrosamine, ethylnitrosourea, and dimethylbenz(a)anthracene DNA binding studies in the rainbow trout

  Dimethylbenz (a) anthracene (EMBA), a carcinogen that requires metabolic activation to produce active metabolites capable of binding to DNA, has been studied in the trout and other fish. Polycyclic aromatic ...

  Citation × Citation Citation Abstract Copy Title: Diethylnitrosamine, ethylnitrosourea, and dimethylbenz(a)anthracene DNA binding studies in the rainbow trout Author: Van Winkle, Samina Dimethylbenz (a) anthracene (EMBA), a carcinogen that requires metabolic activation to produce active metabolites capable of binding to DNA, has been studied in the trout and other fish. Polycyclic aromatic hydrocarbons (PAH) are of importance as they are ubiquitous in the environment and their carcinogenic effects in fish from contaminated waters are an important indication of the pollution risks to man. Since such pollution risk assessment presents the involvement of multiple agents, the study of the modulation of PAH-DNA binding produced by other agents is important. In this study the effect, of dietary pretreatment at 500 ppm, 100 ppm and 2000 ppn, using BNF, Aroclor 1254, or indole-3-carbinol (I3C) respectively on DMBA-DNA binding was examined. To study the effect of age on sensitivity to DMBA-DNA binding, adult trout and fry were used in two separate studies. The fish were fed treatment diet for at least two weeks. Fry were then injected with [³H] DMBA, at 22.4 μCi/3.9 x 10⁻² μmole/fish and adult trout at 284 μCi/1.58 μmole/fish. Liver DNA was isolated, purified and binding of radioactivity to DNA was examined and computed as the covalent binding index (CBI). Mean CBI for control dietary group vising adult trout was 1000 fold lower than for fry. Statistical analysis of covalent binding index for the treatment groups revealed that a statistically significant (p < 0.05) inhibition in DNA-DMBA binding response in adult trout and fry was produced fcy the DNF dietary treatment only. Diethylnitrosamine (DENA), a potent hepatocarcinogen in several animal species belongs also to the class of compounds that require metabolic activation. Dietary treatment and continuous exposure of trout to the carcinogen in water, have produced hepatocellular carcinctnas. The water exposure also produced a dose related DNA ethylation of the O⁶ position of guanine, believed to be the promutagenic adduct produced after DENA exposure. This study examines two other routes of exposure to DENA, in vitro hepatocyte incubations and i.p. injection. Adult trout and fry were injected with [³H] DENA. Adult fish received 3.3, 16.5, and 33 mg/kg DENA, and fry received 10, 50 and 100 mg/kg. Hepatocyte incubation was performed with doses up to 220 μM [³H] DENA, or 1 mM unlabelled DENA. DNA from fish livers and from hepatocyte pellets was isolated, purified and examined for radioactive binding of the DENA metabolites or in the case of the unlabelled DENA, was analyzed for O⁶ and N7 adduct using an HPIC technique with fluorescence detection. O⁶-EtG adduct after DENA exposure, in DNA of hepatocytes obtained from trout pretreated with beta-naphthoflavone (BNF, a known inducer of cytodhrcme P-450 dependent enzyme activities involved in the activation of xenobiotics) was below the limits of detection of the HPDC-fluorescenoe detection procedure used. To examine further if the lack of DNA binding and absence of the O⁶-EtG adduct was due to rapid repair, the persistence of O⁶-EtG after exposure to 40 nM ethylnitrosourea (ENU, a direct ethylating agent) was studied in hepatocytes at 2, 4, and 5 hours after treatment. The activity of the alkyltransferase protein involved in the repair of alkylguanines also was determined using liver extracts from adult rainbow trout. The studies did not reveal a significantly high rate of repair. It is concluded that i.p. injection and in vitro hepatocyte incubations are not a good method for studying the kinetics of activation and DNA binding of DENA in the rainbow trout. The i.p. route may lead to substantial loss of the dose of the carcinogen administered and hepatocyte incubations are limited by the toxic effects of increasing carcinogen concentration. The reasons mentioned above, coupled with low levels of metabolism of nitrosamines in trout results in the inability to detect and study the appearance, persistence and repair of the O⁶-EtG adduct. Title: Diethylnitrosamine, ethylnitrosourea, and dimethylbenz(a)anthracene DNA binding studies in the rainbow trout Author: Van Winkle, Samina Dimethylbenz (a) anthracene (EMBA), a carcinogen that requires metabolic activation to produce active metabolites capable of binding to DNA, has been studied in the trout and other fish. Polycyclic aromatic hydrocarbons (PAH) are of importance as they are ubiquitous in the environment and their carcinogenic effects in fish from contaminated waters are an important indication of the pollution risks to man. Since such pollution risk assessment presents the involvement of multiple agents, the study of the modulation of PAH-DNA binding produced by other agents is important. In this study the effect, of dietary pretreatment at 500 ppm, 100 ppm and 2000 ppn, using BNF, Aroclor 1254, or indole-3-carbinol (I3C) respectively on DMBA-DNA binding was examined. To study the effect of age on sensitivity to DMBA-DNA binding, adult trout and fry were used in two separate studies. The fish were fed treatment diet for at least two weeks. Fry were then injected with [³H] DMBA, at 22.4 μCi/3.9 x 10⁻² μmole/fish and adult trout at 284 μCi/1.58 μmole/fish. Liver DNA was isolated, purified and binding of radioactivity to DNA was examined and computed as the covalent binding index (CBI). Mean CBI for control dietary group vising adult trout was 1000 fold lower than for fry. Statistical analysis of covalent binding index for the treatment groups revealed that a statistically significant (p < 0.05) inhibition in DNA-DMBA binding response in adult trout and fry was produced fcy the DNF dietary treatment only. Diethylnitrosamine (DENA), a potent hepatocarcinogen in several animal species belongs also to the class of compounds that require metabolic activation. Dietary treatment and continuous exposure of trout to the carcinogen in water, have produced hepatocellular carcinctnas. The water exposure also produced a dose related DNA ethylation of the O⁶ position of guanine, believed to be the promutagenic adduct produced after DENA exposure. This study examines two other routes of exposure to DENA, in vitro hepatocyte incubations and i.p. injection. Adult trout and fry were injected with [³H] DENA. Adult fish received 3.3, 16.5, and 33 mg/kg DENA, and fry received 10, 50 and 100 mg/kg. Hepatocyte incubation was performed with doses up to 220 μM [³H] DENA, or 1 mM unlabelled DENA. DNA from fish livers and from hepatocyte pellets was isolated, purified and examined for radioactive binding of the DENA metabolites or in the case of the unlabelled DENA, was analyzed for O⁶ and N7 adduct using an HPIC technique with fluorescence detection. O⁶-EtG adduct after DENA exposure, in DNA of hepatocytes obtained from trout pretreated with beta-naphthoflavone (BNF, a known inducer of cytodhrcme P-450 dependent enzyme activities involved in the activation of xenobiotics) was below the limits of detection of the HPDC-fluorescenoe detection procedure used. To examine further if the lack of DNA binding and absence of the O⁶-EtG adduct was due to rapid repair, the persistence of O⁶-EtG after exposure to 40 nM ethylnitrosourea (ENU, a direct ethylating agent) was studied in hepatocytes at 2, 4, and 5 hours after treatment. The activity of the alkyltransferase protein involved in the repair of alkylguanines also was determined using liver extracts from adult rainbow trout. The studies did not reveal a significantly high rate of repair. It is concluded that i.p. injection and in vitro hepatocyte incubations are not a good method for studying the kinetics of activation and DNA binding of DENA in the rainbow trout. The i.p. route may lead to substantial loss of the dose of the carcinogen administered and hepatocyte incubations are limited by the toxic effects of increasing carcinogen concentration. The reasons mentioned above, coupled with low levels of metabolism of nitrosamines in trout results in the inability to detect and study the appearance, persistence and repair of the O⁶-EtG adduct. Close

• 1806. [Article] The herbicide HOE 23408; soil persistence, spring wheat cultivar tolerance, and interaction with broadleaf herbicides

  HOE 23408 [ 4-(2' , 4'-dichlorophenoxy)-phenoxy-u-propionic methylester.1 is a promising new compound for control of wild oats and other grass weeds in small grains. Several factors influencing its use ...

  Citation × Citation Citation Abstract Copy Title: The herbicide HOE 23408; soil persistence, spring wheat cultivar tolerance, and interaction with broadleaf herbicides Author: Ivackovich, Branislav D. HOE 23408 [ 4-(2' , 4'-dichlorophenoxy)-phenoxy-u-propionic methylester.1 is a promising new compound for control of wild oats and other grass weeds in small grains. Several factors influencing its use for this purpose were investigated. Greenhouse bioassay studies were conducted in 1975 to determine relative persistence of HOE 23408 in four western Oregon soils following application in the fall and winter. -Wild oats (Avena fatua L.) were used as a test plant. Soil from each of three application timings at all four locations contained measurable amounts of herbicide. Generally, residue levels in soil treated at the same herbicide rate approximately 1, 2, and 4 months before sampling were similar. Possibly less herbicide reached the soil from postemergence treatments, compensating for the longer degradation time of the preemergence treatments. Variation in residue levels among locations occurred. This may be explained by differences in smoothness of seedbeds and amounts of plant residue at the various locations. A study was conducted to determine persistence of HOE 23408 applied to bare soil on April 29, 1975. Wild oats and corn (Zea mays L.) were used as bioassay plants. Evaluation of plants seeded into the plots at intervals showed a gradual reduction in levels of herbicide through the season. At 1 lb/A, neither species planted 9 weeks after application was injured, indicating that no significant carry-over can be expected from this rate applied in spring wheat. Two and 4 lb/A persisted longer, causing injury to test plants seeded 9 weeks after treatment. A field experiment was established to evaluate the effect of combining each of four commercially used broadleaf herbicides with 1 and 2 lb/A of HOE 23408 on control of wild oats and barnyardgrass (Echinochloa crus-galli (L.) Beauv. ) and on yield of Fielder spring wheat. The addition of bromoxynil improved the effect of HOE 23408 on wild oats but reduced its effectiveness on barnyardgrass. Addition of 2,4-D LV ester, MCPA LV ester, or dicamba amine reduced its activity on both wild oats and barnyardgrass. Delaying the application of 2,4-D for 3 or 7 days eliminated the antagonistic effect but a delay of only 1 day was not sufficient. No detrimental effect on yield was observed from any treatment. A tolerance study was conducted in three commercially used spring wheat cultivars (Waldron, Twin, and WS-1). Excellent tolerance to HOE 23408 was observed in all cultivars, even when the rate was increased from 1 lb/A (proposed use rate) to 4 lb/A. Title: The herbicide HOE 23408; soil persistence, spring wheat cultivar tolerance, and interaction with broadleaf herbicides Author: Ivackovich, Branislav D. HOE 23408 [ 4-(2' , 4'-dichlorophenoxy)-phenoxy-u-propionic methylester.1 is a promising new compound for control of wild oats and other grass weeds in small grains. Several factors influencing its use for this purpose were investigated. Greenhouse bioassay studies were conducted in 1975 to determine relative persistence of HOE 23408 in four western Oregon soils following application in the fall and winter. -Wild oats (Avena fatua L.) were used as a test plant. Soil from each of three application timings at all four locations contained measurable amounts of herbicide. Generally, residue levels in soil treated at the same herbicide rate approximately 1, 2, and 4 months before sampling were similar. Possibly less herbicide reached the soil from postemergence treatments, compensating for the longer degradation time of the preemergence treatments. Variation in residue levels among locations occurred. This may be explained by differences in smoothness of seedbeds and amounts of plant residue at the various locations. A study was conducted to determine persistence of HOE 23408 applied to bare soil on April 29, 1975. Wild oats and corn (Zea mays L.) were used as bioassay plants. Evaluation of plants seeded into the plots at intervals showed a gradual reduction in levels of herbicide through the season. At 1 lb/A, neither species planted 9 weeks after application was injured, indicating that no significant carry-over can be expected from this rate applied in spring wheat. Two and 4 lb/A persisted longer, causing injury to test plants seeded 9 weeks after treatment. A field experiment was established to evaluate the effect of combining each of four commercially used broadleaf herbicides with 1 and 2 lb/A of HOE 23408 on control of wild oats and barnyardgrass (Echinochloa crus-galli (L.) Beauv. ) and on yield of Fielder spring wheat. The addition of bromoxynil improved the effect of HOE 23408 on wild oats but reduced its effectiveness on barnyardgrass. Addition of 2,4-D LV ester, MCPA LV ester, or dicamba amine reduced its activity on both wild oats and barnyardgrass. Delaying the application of 2,4-D for 3 or 7 days eliminated the antagonistic effect but a delay of only 1 day was not sufficient. No detrimental effect on yield was observed from any treatment. A tolerance study was conducted in three commercially used spring wheat cultivars (Waldron, Twin, and WS-1). Excellent tolerance to HOE 23408 was observed in all cultivars, even when the rate was increased from 1 lb/A (proposed use rate) to 4 lb/A. Close

• 1807. [Article] Studies on host range, fine structure, and nucleic acids of lactic streptococcus bacteriophages

  The most frequent cause of insufficient acid production during fermentation of dairy products is bacteriophage infection of lactic starter cultures. Previously, efforts to minimize this problem have dealt ...

  Citation × Citation Citation Abstract Copy Title: Studies on host range, fine structure, and nucleic acids of lactic streptococcus bacteriophages Author: Nyiendo, Joanne Annette The most frequent cause of insufficient acid production during fermentation of dairy products is bacteriophage infection of lactic starter cultures. Previously, efforts to minimize this problem have dealt primarily with the host range relationships of the viruses and susceptibility patterns of the lactic streptococci. This study was undertaken to characterize the host range, morphology, and nucleic acid types of 35 lactic streptococcus bacteriophages; and to investigate the interrelationship between these characters. Preliminary experiments revealed a simple procedure for obtaining high titer phage preparations. In addition, a simple procedure for storage of stock lysates was found to be effective in maintaining phage viability for more than two years. Host range determinations showed that considerably more hosts were lysed at high than at low titer. Groupings of phage were more apparent with low titer host range patterns. Several hosts that plated heterologous phages at low efficiency of pla.ting (E. O. P. ) were further investigated. A single cycle of growth through these hosts produced progeny phage that plated with low E. 0. P. on the original hosts, due either to host controlled modification or host range mutation. Electron microscopy studies revealed phages of the same general shape, differing only in size of the component structures. All of the phages examined had non-contractile tails with a tail end plate structure, typical of the double stranded DNA phages of Bradleys Group B. Head size ranged from 320-850 A in diameter. Tail lengths ranged from 850-5200 X. Six types of ta.11 end plate, structures were observed. The presence of a collar was observed for nine of the lactic phages. Ten separate morphological groups were characterized on the basis of similarity in head size and shape, tail length, tail plate structure, and the presence or absence of a collar. Two phage species, w401x1 and w407x1, were unique from the others with respect to head size and tail length. Head diameters ranged from 700-850 X and tail lengths from 2000-5200 X . The most striking feature of these two phages was the long winding tail of variable length. In addition, these two phages did not form plaques on lawns of the strains which gave rise to the lysate. An extensive search for an indicator strain was not made. The morphology groups showed no correlation with groups based on host range pattern. The buoyant density of these phages covers a wide range, from 1. 428 to 1. 531 g /cc. On the basis of the DNA melting profile, all of the phages in this study proved to be double stranded. The GC base composition ranged from 32. 7 to 40.0 percent. Genome sizes of the lactic phages were determined on the basis of renaturation kinetics. Genome sizes ranged from 6 to 24 x 10⁶ daltons. Renaturation kinetics were also used to assess polynucleotide similarity among the lactic phages. DNA homology ranged from zero to 100 percent. An orderly relationship between percent homology, GC base composition, morphology, and host range pattern was not revealed. Title: Studies on host range, fine structure, and nucleic acids of lactic streptococcus bacteriophages Author: Nyiendo, Joanne Annette The most frequent cause of insufficient acid production during fermentation of dairy products is bacteriophage infection of lactic starter cultures. Previously, efforts to minimize this problem have dealt primarily with the host range relationships of the viruses and susceptibility patterns of the lactic streptococci. This study was undertaken to characterize the host range, morphology, and nucleic acid types of 35 lactic streptococcus bacteriophages; and to investigate the interrelationship between these characters. Preliminary experiments revealed a simple procedure for obtaining high titer phage preparations. In addition, a simple procedure for storage of stock lysates was found to be effective in maintaining phage viability for more than two years. Host range determinations showed that considerably more hosts were lysed at high than at low titer. Groupings of phage were more apparent with low titer host range patterns. Several hosts that plated heterologous phages at low efficiency of pla.ting (E. O. P. ) were further investigated. A single cycle of growth through these hosts produced progeny phage that plated with low E. 0. P. on the original hosts, due either to host controlled modification or host range mutation. Electron microscopy studies revealed phages of the same general shape, differing only in size of the component structures. All of the phages examined had non-contractile tails with a tail end plate structure, typical of the double stranded DNA phages of Bradleys Group B. Head size ranged from 320-850 A in diameter. Tail lengths ranged from 850-5200 X. Six types of ta.11 end plate, structures were observed. The presence of a collar was observed for nine of the lactic phages. Ten separate morphological groups were characterized on the basis of similarity in head size and shape, tail length, tail plate structure, and the presence or absence of a collar. Two phage species, w401x1 and w407x1, were unique from the others with respect to head size and tail length. Head diameters ranged from 700-850 X and tail lengths from 2000-5200 X . The most striking feature of these two phages was the long winding tail of variable length. In addition, these two phages did not form plaques on lawns of the strains which gave rise to the lysate. An extensive search for an indicator strain was not made. The morphology groups showed no correlation with groups based on host range pattern. The buoyant density of these phages covers a wide range, from 1. 428 to 1. 531 g /cc. On the basis of the DNA melting profile, all of the phages in this study proved to be double stranded. The GC base composition ranged from 32. 7 to 40.0 percent. Genome sizes of the lactic phages were determined on the basis of renaturation kinetics. Genome sizes ranged from 6 to 24 x 10⁶ daltons. Renaturation kinetics were also used to assess polynucleotide similarity among the lactic phages. DNA homology ranged from zero to 100 percent. An orderly relationship between percent homology, GC base composition, morphology, and host range pattern was not revealed. Close

• 1808. [Article] In vitro transcription in the yeast: Saccharomyces cerevisiae

  The structure and transcriptional activity of intranuclear and isolated chromatin from logarithmically growing yeast cells has been compared to chromatin from cells which have entered the stationary phase ...

  Citation × Citation Citation Abstract Copy Title: In vitro transcription in the yeast: Saccharomyces cerevisiae Author: Ide, Gregory James The structure and transcriptional activity of intranuclear and isolated chromatin from logarithmically growing yeast cells has been compared to chromatin from cells which have entered the stationary phase and ceased growing. Both chromatins show a similar nucleosomal repeat pattern and a 160 by repeat size when digested with staphlococcal nuclease. The rate of DNase I digestion of growing phase is greater than in stationary. Growing phase nuclei are also 5 to 20 times as active as stationary in the amount of endogenous transcription. Analysis of elongating transcripts indicates the transcriptional differences between growing and stationary are due to differences in in vivo initiation. The DNase I susceptability and transcriptional differences noted in nuclei are maintained in sucrose gradient isolated oligonucleosomes and mononucleosomes from the two states. As an adjunct to structural and transcriptional studies of yeast,a rapid technique for isolation of yeast nuclei has been developed. Briefly, the method consists of layering of the 18% ficoll lysate prepared by the method described in Lohr and Ide (1979), on an isopycnic density gradient of 1M sorbitol, 0.5mM CaC1₂ dissolved in a solvent of 35% Percoll (Pharmacia) 65% H₂O, pH 6.5. The gradient is pre-formed before loading by spinning 34ml of the gradient solution contained in a 50ml tube in an SS-34 angle rotor at 37,000 xg for 50 minutes. Six ml of the 18% ficoll lystate is diluted with 6m1 1M Sorbitol 0.5mM CaC1₂ and then layered on this gradient. Nuclei are banded free of cell debris by a 7,500 rpm spin in an HB4 swinging bucket rotor for 15 minutes. The resulting band of nuclei is washed by dilution with 2 volumes 1M Sorbitol, 0.5mM CaC1₂ pH 6.5 and pelleted at 4300 xg for 5 minutes. Nuclei isolated by this method will incorporate 20 to 40 picomoles UTP into RNA per ug template DNA in a 15 minute synthesis. The nuclei are substantially free of cytoplasmic contamination as measured by alcohol dehydrogenase activities. Transcription initiation in isolated yeast nuclei by endogenous RNA polymerase has been studied using nucleoside 5'-[γ-S] triphosphates as affinity probes. In vitro initiated RNA can be separated from bulk RNA on a mercury agarose affinity column. Activity that transfers the [γ-S] group to other nucleotides or other RNA molecules (often troublesome in other systems) cannot be detected. Analysis of the in vitro initiated RNA shows that 5S and pre t-RNA are initiated in vitro by endogenous RNA polymerase III. Endogenous RNA polymerase III also initiates a discrete distribution of RNA species as large as 28S. The RNA populations initiated with 5'-[γ-S] adenosine 5' triphosphate and 5'[γ-S] guanosine 5' triphosphate are different. Title: In vitro transcription in the yeast: Saccharomyces cerevisiae Author: Ide, Gregory James The structure and transcriptional activity of intranuclear and isolated chromatin from logarithmically growing yeast cells has been compared to chromatin from cells which have entered the stationary phase and ceased growing. Both chromatins show a similar nucleosomal repeat pattern and a 160 by repeat size when digested with staphlococcal nuclease. The rate of DNase I digestion of growing phase is greater than in stationary. Growing phase nuclei are also 5 to 20 times as active as stationary in the amount of endogenous transcription. Analysis of elongating transcripts indicates the transcriptional differences between growing and stationary are due to differences in in vivo initiation. The DNase I susceptability and transcriptional differences noted in nuclei are maintained in sucrose gradient isolated oligonucleosomes and mononucleosomes from the two states. As an adjunct to structural and transcriptional studies of yeast,a rapid technique for isolation of yeast nuclei has been developed. Briefly, the method consists of layering of the 18% ficoll lysate prepared by the method described in Lohr and Ide (1979), on an isopycnic density gradient of 1M sorbitol, 0.5mM CaC1₂ dissolved in a solvent of 35% Percoll (Pharmacia) 65% H₂O, pH 6.5. The gradient is pre-formed before loading by spinning 34ml of the gradient solution contained in a 50ml tube in an SS-34 angle rotor at 37,000 xg for 50 minutes. Six ml of the 18% ficoll lystate is diluted with 6m1 1M Sorbitol 0.5mM CaC1₂ and then layered on this gradient. Nuclei are banded free of cell debris by a 7,500 rpm spin in an HB4 swinging bucket rotor for 15 minutes. The resulting band of nuclei is washed by dilution with 2 volumes 1M Sorbitol, 0.5mM CaC1₂ pH 6.5 and pelleted at 4300 xg for 5 minutes. Nuclei isolated by this method will incorporate 20 to 40 picomoles UTP into RNA per ug template DNA in a 15 minute synthesis. The nuclei are substantially free of cytoplasmic contamination as measured by alcohol dehydrogenase activities. Transcription initiation in isolated yeast nuclei by endogenous RNA polymerase has been studied using nucleoside 5'-[γ-S] triphosphates as affinity probes. In vitro initiated RNA can be separated from bulk RNA on a mercury agarose affinity column. Activity that transfers the [γ-S] group to other nucleotides or other RNA molecules (often troublesome in other systems) cannot be detected. Analysis of the in vitro initiated RNA shows that 5S and pre t-RNA are initiated in vitro by endogenous RNA polymerase III. Endogenous RNA polymerase III also initiates a discrete distribution of RNA species as large as 28S. The RNA populations initiated with 5'-[γ-S] adenosine 5' triphosphate and 5'[γ-S] guanosine 5' triphosphate are different. Close

• 1809. [Article] Genetic mapping of Cuphea lanceolata : molecular-marker linkage to quantitative-trait loci affecting seed capric acid, seed oil, and embryo development

  Cuphea is an herbaceous genus having species whose seed storage lipids are predominantly medium-chain triglycerides (MCTs). Cuphea lanceolate Ait, and Cuphea viscosissima Jacq. are central to the breeding ...

  Citation × Citation Citation Abstract Copy Title: Genetic mapping of Cuphea lanceolata : molecular-marker linkage to quantitative-trait loci affecting seed capric acid, seed oil, and embryo development Author: Webb, David M. (David Morton), 1954- Cuphea is an herbaceous genus having species whose seed storage lipids are predominantly medium-chain triglycerides (MCTs). Cuphea lanceolate Ait, and Cuphea viscosissima Jacq. are central to the breeding of Cuphea as a new commercial source of MCTs. The objectives of this thesis were to develop a reliable method to extract DNA from Cuphea, to construct a molecular-marker linkage map of C. lanceolate, and to evaluate quantitative-trait loci (QTL) affecting seed capric acid content, seed oil content, and embryo development in C. lanceolate. We used allozyme and restriction-fragment- length-polymorphism (RFLP) markers to study Cuphea because molecular markers are the best method available to investigate the Mendelian genetics underlying quantitative traits, and are useful in breeding. Adequate yield of clean DNA is essential for RFLP mapping. We tried numerous DNA extraction methods that failed to remove contaminants that interfere with restriction digests of Cuphea DNA. The method described here was developed to remove those contaminants and maintain relatively high DNA yields. In this method, the critical step in purification consists of washing the DNA with phenol while it is complexed with CTAB and dissolved in 1 M NaCl. An RFLP and allozyme linkage map of C. lanceolate was constructed having 37 markers in six linkage groups with a total distance of 288 cM. Levels of polymorphism were estimated for three lines of C. lanceolate and one line of C. viscosissima using 84 random genomic clones and two restriction enzymes, EcoRI and HindIII. Twenty-nine percent of the probes detected RFLPs between C. lanceolate lines, whereas 63% of the probes detected RFLPs between C. lanceolate and C. viscosissima lines. Thirty RFLP and four allozyme markers were used to locate on the C. lanceolata linkage map QTL affecting seed capric acid content, seed oil content, and embryo development. Three unlinked QTL explained 19.4% of the phenotypic variation in capric acid content in F₂ seed. Seed oil content and seed weight were measured on seed from field-grown F₂ plants. Seed weight was indicative of embryo size (development). Four unlinked QTL explained 33.9% of the phenotypic variation in embryo size. One of these QTL, which explained 20.3% of the variation, may have been a chromosomal deletion detected by a marker having a null allele. Three QTL pleiotropically affected seed oil by affecting embryo size. The one QTL that only affected seed oil accounted for 2.8% of the phenotypic variation. Title: Genetic mapping of Cuphea lanceolata : molecular-marker linkage to quantitative-trait loci affecting seed capric acid, seed oil, and embryo development Author: Webb, David M. (David Morton), 1954- Cuphea is an herbaceous genus having species whose seed storage lipids are predominantly medium-chain triglycerides (MCTs). Cuphea lanceolate Ait, and Cuphea viscosissima Jacq. are central to the breeding of Cuphea as a new commercial source of MCTs. The objectives of this thesis were to develop a reliable method to extract DNA from Cuphea, to construct a molecular-marker linkage map of C. lanceolate, and to evaluate quantitative-trait loci (QTL) affecting seed capric acid content, seed oil content, and embryo development in C. lanceolate. We used allozyme and restriction-fragment- length-polymorphism (RFLP) markers to study Cuphea because molecular markers are the best method available to investigate the Mendelian genetics underlying quantitative traits, and are useful in breeding. Adequate yield of clean DNA is essential for RFLP mapping. We tried numerous DNA extraction methods that failed to remove contaminants that interfere with restriction digests of Cuphea DNA. The method described here was developed to remove those contaminants and maintain relatively high DNA yields. In this method, the critical step in purification consists of washing the DNA with phenol while it is complexed with CTAB and dissolved in 1 M NaCl. An RFLP and allozyme linkage map of C. lanceolate was constructed having 37 markers in six linkage groups with a total distance of 288 cM. Levels of polymorphism were estimated for three lines of C. lanceolate and one line of C. viscosissima using 84 random genomic clones and two restriction enzymes, EcoRI and HindIII. Twenty-nine percent of the probes detected RFLPs between C. lanceolate lines, whereas 63% of the probes detected RFLPs between C. lanceolate and C. viscosissima lines. Thirty RFLP and four allozyme markers were used to locate on the C. lanceolata linkage map QTL affecting seed capric acid content, seed oil content, and embryo development. Three unlinked QTL explained 19.4% of the phenotypic variation in capric acid content in F₂ seed. Seed oil content and seed weight were measured on seed from field-grown F₂ plants. Seed weight was indicative of embryo size (development). Four unlinked QTL explained 33.9% of the phenotypic variation in embryo size. One of these QTL, which explained 20.3% of the variation, may have been a chromosomal deletion detected by a marker having a null allele. Three QTL pleiotropically affected seed oil by affecting embryo size. The one QTL that only affected seed oil accounted for 2.8% of the phenotypic variation. Close

• 1810. [Article] Essays on nursery labor, sales contracts, and price discovery

  Oregon's nursery and greenhouse industry has ranked the first in the State's agricultural for 18 years. The majority of nursery sales from the Pacific Northwest come from Oregon. Due to data limitations, ...

  Citation × Citation Citation Abstract Copy Title: Essays on nursery labor, sales contracts, and price discovery Author: Li, Cheng Oregon's nursery and greenhouse industry has ranked the first in the State's agricultural for 18 years. The majority of nursery sales from the Pacific Northwest come from Oregon. Due to data limitations, empirical study of the Oregon nursery industry is rare. The present dissertation consists of three essays that analyze the demand and supply of inputs and outputs and the relationship between producers and retailers in the Oregon nursery industry. Chapter 2 identifies the major factors affecting farm labor supply and demand and evaluates their relative importance in the Oregon nursery industry from 1991 to 2008. Empirical results show that border control effort doesn't have an influential role in labor supply, while the Oregon and Mexican minimum wage do. It is because of the substantial gap between the U.S. and Mexican economies, reflected for an example in the minimum wage gap, which attracts a continual flow of immigrants. Risk of border apprehension is not great enough to prevent the flow. Increases in Oregon minimum wage is more effective than border apprehension policies in boosting the average wage and in reducing the number of hours that illegal immigrants work in the nursery sector. Chapter 3 investigates producers' and retailers' choices of, and reactions to, various contract types in the Oregon nursery industry from 2005 to 2010. As new and fast-growing retailers in the industry, big-box stores are less likely than independent retailers to make pre-order contracts with the producer. However, once a pre-order contract is chosen, big-box stores demand more days of pre-order interval than independent retailers do. Transactions with independent retailers exhibit – on average over the sample range – scale economies and scope diseconomies. Boosting per-transaction revenue scale and the number of species sold to big-box stores enhances transaction efficiency. Chapter 4 examines the interaction between supply and demand in Oregon nursery products. The result indicates that the production and transaction costs are major drivers on the supply side, while transportation costs and consumer demand for nursery products play important roles on the demand side. At the genus level, the supply elasticities of coniferous plants are larger than those of deciduous plants, which in turn are higher than those of flowering plants. The demand elasticities are the lowest in coniferous trees followed by deciduous plants, then flowering plants. Price discounts on plants with high demand elasticities would significantly boost sales and enlarge the market, while those on plants with low demand elasticities would have less sales impact. Empirically, patenting seems to bring no direct signs of greater profitability. The wholesale nursery may wish to reconsider the pricing and marketing policies of its patented plants to differentiate them more effectively from its non-patented plants. Title: Essays on nursery labor, sales contracts, and price discovery Author: Li, Cheng Oregon's nursery and greenhouse industry has ranked the first in the State's agricultural for 18 years. The majority of nursery sales from the Pacific Northwest come from Oregon. Due to data limitations, empirical study of the Oregon nursery industry is rare. The present dissertation consists of three essays that analyze the demand and supply of inputs and outputs and the relationship between producers and retailers in the Oregon nursery industry. Chapter 2 identifies the major factors affecting farm labor supply and demand and evaluates their relative importance in the Oregon nursery industry from 1991 to 2008. Empirical results show that border control effort doesn't have an influential role in labor supply, while the Oregon and Mexican minimum wage do. It is because of the substantial gap between the U.S. and Mexican economies, reflected for an example in the minimum wage gap, which attracts a continual flow of immigrants. Risk of border apprehension is not great enough to prevent the flow. Increases in Oregon minimum wage is more effective than border apprehension policies in boosting the average wage and in reducing the number of hours that illegal immigrants work in the nursery sector. Chapter 3 investigates producers' and retailers' choices of, and reactions to, various contract types in the Oregon nursery industry from 2005 to 2010. As new and fast-growing retailers in the industry, big-box stores are less likely than independent retailers to make pre-order contracts with the producer. However, once a pre-order contract is chosen, big-box stores demand more days of pre-order interval than independent retailers do. Transactions with independent retailers exhibit – on average over the sample range – scale economies and scope diseconomies. Boosting per-transaction revenue scale and the number of species sold to big-box stores enhances transaction efficiency. Chapter 4 examines the interaction between supply and demand in Oregon nursery products. The result indicates that the production and transaction costs are major drivers on the supply side, while transportation costs and consumer demand for nursery products play important roles on the demand side. At the genus level, the supply elasticities of coniferous plants are larger than those of deciduous plants, which in turn are higher than those of flowering plants. The demand elasticities are the lowest in coniferous trees followed by deciduous plants, then flowering plants. Price discounts on plants with high demand elasticities would significantly boost sales and enlarge the market, while those on plants with low demand elasticities would have less sales impact. Empirically, patenting seems to bring no direct signs of greater profitability. The wholesale nursery may wish to reconsider the pricing and marketing policies of its patented plants to differentiate them more effectively from its non-patented plants. Close

• 1811. [Article] The distribution of organic bases in reverse phase liquid chromatography : a study of mechanisms

  The distribution of hydrophobic ionogenic organic compounds (HIOC's) between aqueous and nonaqueous phases has been investigated. The HIOC's are aniline and methyl substituted anilines. The aqueous phases ...

  Citation × Citation Citation Abstract Copy Title: The distribution of organic bases in reverse phase liquid chromatography : a study of mechanisms Author: Jayasinghe, Dudley Shelton The distribution of hydrophobic ionogenic organic compounds (HIOC's) between aqueous and nonaqueous phases has been investigated. The HIOC's are aniline and methyl substituted anilines. The aqueous phases are methanol-water mixed solvents with varying pH and ionic strength. The nonaqueous phases are silica and alkyl derivatized silica with ethyl- (C-2), octyl- (C-8), and octadecyl- (C-18) silanes. A gas-liquid equilibration method has been developed to determine the Henry's law constants and the activity coefficients of methyl anilines in methanol-water mixed solvents. The logarithm of the Henry's law constants vary quadratically with the volume fraction of methanol. The chromatographic study has been performed to investigate the effect of three mobile phase factors, fraction of methanol, pH, and ionic strength, on the retention of methyl anilines on different stationary phases. The logarithm of mass distribution ratios, log k's, of methyl anilines vary linearly with the volume fraction of methanol. The ratios of H / k' of methyl anilines increase with increase in methanol in the mobile phase, indicating an increase in the activity coefficients in the stationary phases. This observation is found to be true for different methyl anilines in different stationary phases. A partition model is presented to describe the effect of pH and ionic strength on the retention of HIOC's in the mobile phase. The variation in log k' among neutral and ionic methyl anilines can be explained by linear free energy relationships. Equations are established to predict retention of neutral or ionized methyl anilines from their octanol-water partition coefficients at any methanol content in the mobile phase. Acid dissociation constants of methyl anilines determined from the dependence of log k' on pH are in close agrement with those determined by potentiometric titrations. The effect of ionic strength on the retention of both neutral and ionic species of methyl anilines is negligible. That is, the contribution from electrostatic energy and salting out effect are not significant. The chromatographic study is extended to study the retention of methyl anilines on silica as a function of pH and methanol at a constant ionic strength. The dependence of retention on pH is qualitatively interpreted from an ion exchange reaction between the dissociated silanol groups in the surface and the ionized methyl anilines. The effect of methanol on the retention of methyl anilines and of pyridine on silica is described by a quadratic relationship between the log k' and volume fraction of methanol. Title: The distribution of organic bases in reverse phase liquid chromatography : a study of mechanisms Author: Jayasinghe, Dudley Shelton The distribution of hydrophobic ionogenic organic compounds (HIOC's) between aqueous and nonaqueous phases has been investigated. The HIOC's are aniline and methyl substituted anilines. The aqueous phases are methanol-water mixed solvents with varying pH and ionic strength. The nonaqueous phases are silica and alkyl derivatized silica with ethyl- (C-2), octyl- (C-8), and octadecyl- (C-18) silanes. A gas-liquid equilibration method has been developed to determine the Henry's law constants and the activity coefficients of methyl anilines in methanol-water mixed solvents. The logarithm of the Henry's law constants vary quadratically with the volume fraction of methanol. The chromatographic study has been performed to investigate the effect of three mobile phase factors, fraction of methanol, pH, and ionic strength, on the retention of methyl anilines on different stationary phases. The logarithm of mass distribution ratios, log k's, of methyl anilines vary linearly with the volume fraction of methanol. The ratios of H / k' of methyl anilines increase with increase in methanol in the mobile phase, indicating an increase in the activity coefficients in the stationary phases. This observation is found to be true for different methyl anilines in different stationary phases. A partition model is presented to describe the effect of pH and ionic strength on the retention of HIOC's in the mobile phase. The variation in log k' among neutral and ionic methyl anilines can be explained by linear free energy relationships. Equations are established to predict retention of neutral or ionized methyl anilines from their octanol-water partition coefficients at any methanol content in the mobile phase. Acid dissociation constants of methyl anilines determined from the dependence of log k' on pH are in close agrement with those determined by potentiometric titrations. The effect of ionic strength on the retention of both neutral and ionic species of methyl anilines is negligible. That is, the contribution from electrostatic energy and salting out effect are not significant. The chromatographic study is extended to study the retention of methyl anilines on silica as a function of pH and methanol at a constant ionic strength. The dependence of retention on pH is qualitatively interpreted from an ion exchange reaction between the dissociated silanol groups in the surface and the ionized methyl anilines. The effect of methanol on the retention of methyl anilines and of pyridine on silica is described by a quadratic relationship between the log k' and volume fraction of methanol. Close

• 1812. [Article] Chronic exposure of rodents to indole-3-carbinol and 3,3'-diindolylmethane : implications for drug metabolism, chemoprevention and human health

  Indole-3-carbinol (I3C) is a naturally occurring plant alkaloid, found in significant concentrations in cruciferous vegetables such as broccoli and Brussels sprouts. I3C is an unstable compound that undergoes ...

  Citation × Citation Citation Abstract Copy Title: Chronic exposure of rodents to indole-3-carbinol and 3,3'-diindolylmethane : implications for drug metabolism, chemoprevention and human health Author: Leibelt, Dustin A. Indole-3-carbinol (I3C) is a naturally occurring plant alkaloid, found in significant concentrations in cruciferous vegetables such as broccoli and Brussels sprouts. I3C is an unstable compound that undergoes rapid oligomerization in an acidic environment to form higher order condensation products (I3C-ACPs), such as 3-3'-diindolylmethane (DIM). Both I3C and DIM are marketed as dietary supplements and are under investigation as potential chemopreventive agents, despite limited data on the effects of chronic exposure. Previous studies have demonstrated that the chemopreventive potential of I3C and DIM in animal studies is dependent on species, strain, tissue and timing of treatment relative to carcinogen exposure, and long-term post-initiation exposure can even promote tumors. The majority of biological effects from I3C are the result of the abilities DIM and other I3C-ACPs to bind to the aryl hydrocarbon receptor and the subsequent induction of phase I and phase II enzymes. Phase I and phase II enzyme induction in many cases leads to protection from carcinogens by increasing the rate of metabolism and excretion but in some cases enhances carcinogenicity by increasing the rate of bioactivation. It has been demonstrated that modulation of enzyme levels can also result in altered metabolism of compounds that could affect efficacy and toxicity of pharmaceuticals and xenobiotics. The current work utilizes chronic dietary I3C and DIM exposures in rodent models to further elucidate the effect these compounds might have on health, drug metabolism and carcinogenesis. The reduced weight of Fischer 344 rats treated with 2500 ppm I3C for 1 year may be indicative of adverse effects but toxicity was not confirmed by blood chemistry or histopathological examination. Furthermore, no toxicity was observed after a comparable treatment of Sprague-Dawley rats. As observed after acute and sub-chronic exposures to I3C and DIM, we documented significant induction of cytochrome P450 enzymes and a related modification to drug metabolism in liver slice incubations. Evidence is also provided that may suggest that tumor modulation in mice may occur through an estrogenic mechanism. Further studies should be completed to determine the potential for similar responses in humans. Title: Chronic exposure of rodents to indole-3-carbinol and 3,3'-diindolylmethane : implications for drug metabolism, chemoprevention and human health Author: Leibelt, Dustin A. Indole-3-carbinol (I3C) is a naturally occurring plant alkaloid, found in significant concentrations in cruciferous vegetables such as broccoli and Brussels sprouts. I3C is an unstable compound that undergoes rapid oligomerization in an acidic environment to form higher order condensation products (I3C-ACPs), such as 3-3'-diindolylmethane (DIM). Both I3C and DIM are marketed as dietary supplements and are under investigation as potential chemopreventive agents, despite limited data on the effects of chronic exposure. Previous studies have demonstrated that the chemopreventive potential of I3C and DIM in animal studies is dependent on species, strain, tissue and timing of treatment relative to carcinogen exposure, and long-term post-initiation exposure can even promote tumors. The majority of biological effects from I3C are the result of the abilities DIM and other I3C-ACPs to bind to the aryl hydrocarbon receptor and the subsequent induction of phase I and phase II enzymes. Phase I and phase II enzyme induction in many cases leads to protection from carcinogens by increasing the rate of metabolism and excretion but in some cases enhances carcinogenicity by increasing the rate of bioactivation. It has been demonstrated that modulation of enzyme levels can also result in altered metabolism of compounds that could affect efficacy and toxicity of pharmaceuticals and xenobiotics. The current work utilizes chronic dietary I3C and DIM exposures in rodent models to further elucidate the effect these compounds might have on health, drug metabolism and carcinogenesis. The reduced weight of Fischer 344 rats treated with 2500 ppm I3C for 1 year may be indicative of adverse effects but toxicity was not confirmed by blood chemistry or histopathological examination. Furthermore, no toxicity was observed after a comparable treatment of Sprague-Dawley rats. As observed after acute and sub-chronic exposures to I3C and DIM, we documented significant induction of cytochrome P450 enzymes and a related modification to drug metabolism in liver slice incubations. Evidence is also provided that may suggest that tumor modulation in mice may occur through an estrogenic mechanism. Further studies should be completed to determine the potential for similar responses in humans. Close

• 1813. [Article] Conditioning of northern Great Basin grasses with livestock grazing

  Because forage quality of cool season grasses declines to sub-maintenance levels for ruminants late in the growing season in the northern Great Basin, there is a need to elevate protein levels and digestibility ...

  Citation × Citation Citation Abstract Copy Title: Conditioning of northern Great Basin grasses with livestock grazing Author: Aguilera, Lisa M. Because forage quality of cool season grasses declines to sub-maintenance levels for ruminants late in the growing season in the northern Great Basin, there is a need to elevate protein levels and digestibility of grasses for both wild and domestic ruminants in late summer. Anderson and Scherzinger (1975) proposed using livestock forage conditioning early in the growing season to elevate forage quality of grasses for use later in the year. We tested their forage conditioning hypothesis among 6 grasses with cattle grazing applied at 3 stages in phenology (vegetative, boot, and anthesis) on the Northern Great Basin Experimental Range near Burns, Oregon. Forage quality of regrowth was compared among grazing treatments and with herbage from grasses rested throughout the growing season (ungrazed controls). Indices were: crude protein, in vitro dry matter digestibility, and yield sampled in late July and early September of 1997 and 1998. Grasses included: crested wheatgrass (Agropyron desertorum (Fischer ex Link) Schultes), bluebunch wheatgrass (Agropyron spicatum (Pursh) Scribn. & Smith), bottlebrush squirreltail (Sitanion hysterix (Nutt.) J.G.Smith), Idaho fescue (Festuca idahoensis Elmer), Thurber needlegrass (Stipa thurberiana Piper), and basin wildrye (Elymus cinereus Scribn. & Merr). In both years,grasses showed the expected seasonal decline in forage quality (CP and IVDMD) as the season advanced. A positive response to conditioning occurred with crude protein of regrowth (x = 7.2 %) in 1997 with a treatment x species interaction (P< 0.003) and in 1998 (x = 4.6 %) with a significant treatment effect (P<0.001). In vitro dry matter digestibility of regrowth increased for boot and anthesis grazing treatments in 1997 (x = 50.4 %) (P<0.008), and for vegetative and boot grazing treatments in July samples of 1998 (x = 43.0 %) (P<0.007). Soil moisture content when grasses were grazed was a poor predictor of subsequent regrowth yields. In conclusion, forage-conditioning efforts appeared to be more successful in the drier of the 2 years. Bottlebrush squirreltail and Thurber needlegrass responded most favorably to forage conditioning treatments, while Idaho fescue and bluebunch wheatgrass exhibited the fewest favorable responses. Title: Conditioning of northern Great Basin grasses with livestock grazing Author: Aguilera, Lisa M. Because forage quality of cool season grasses declines to sub-maintenance levels for ruminants late in the growing season in the northern Great Basin, there is a need to elevate protein levels and digestibility of grasses for both wild and domestic ruminants in late summer. Anderson and Scherzinger (1975) proposed using livestock forage conditioning early in the growing season to elevate forage quality of grasses for use later in the year. We tested their forage conditioning hypothesis among 6 grasses with cattle grazing applied at 3 stages in phenology (vegetative, boot, and anthesis) on the Northern Great Basin Experimental Range near Burns, Oregon. Forage quality of regrowth was compared among grazing treatments and with herbage from grasses rested throughout the growing season (ungrazed controls). Indices were: crude protein, in vitro dry matter digestibility, and yield sampled in late July and early September of 1997 and 1998. Grasses included: crested wheatgrass (Agropyron desertorum (Fischer ex Link) Schultes), bluebunch wheatgrass (Agropyron spicatum (Pursh) Scribn. & Smith), bottlebrush squirreltail (Sitanion hysterix (Nutt.) J.G.Smith), Idaho fescue (Festuca idahoensis Elmer), Thurber needlegrass (Stipa thurberiana Piper), and basin wildrye (Elymus cinereus Scribn. & Merr). In both years,grasses showed the expected seasonal decline in forage quality (CP and IVDMD) as the season advanced. A positive response to conditioning occurred with crude protein of regrowth (x = 7.2 %) in 1997 with a treatment x species interaction (P< 0.003) and in 1998 (x = 4.6 %) with a significant treatment effect (P<0.001). In vitro dry matter digestibility of regrowth increased for boot and anthesis grazing treatments in 1997 (x = 50.4 %) (P<0.008), and for vegetative and boot grazing treatments in July samples of 1998 (x = 43.0 %) (P<0.007). Soil moisture content when grasses were grazed was a poor predictor of subsequent regrowth yields. In conclusion, forage-conditioning efforts appeared to be more successful in the drier of the 2 years. Bottlebrush squirreltail and Thurber needlegrass responded most favorably to forage conditioning treatments, while Idaho fescue and bluebunch wheatgrass exhibited the fewest favorable responses. Close

• 1814. [Article] Role of priority effects and habitat complexity in coral-reef fish communities

  Understanding the processes that influence the composition of animal communities is a central goal in ecology. Interactions between established residents and colonizing juveniles that affect the subsequent ...

  Citation × Citation Citation Abstract Copy Title: Role of priority effects and habitat complexity in coral-reef fish communities Author: Almany, Glenn R. Understanding the processes that influence the composition of animal communities is a central goal in ecology. Interactions between established residents and colonizing juveniles that affect the subsequent survival of juveniles may influence community composition. In a series of experiments on coral reef fish communities in the Bahamas and Australia, I tested whether and how interactions between colonizing juveniles and established residents, such as predators and territorial competitors, affected recruitment, and whether these interactions were modified by habitat complexity. In the Bahamas, I factorially manipulated the presence and absence of resident piscivores and territorial damselfishes on 16 spatially isolated patch reefs and found that both groups had strong, species-specific effects on subsequent recruitment. In a second experiment, I tested whether the aforementioned effects of residents were due to direct interactions between residents and juveniles or were the result of differential juvenile settlement. This was accomplished by repeating the first experiment, except this time placing piscivores and damselfishes within cages to prevent direct interactions. I found no evidence for differential settlement, suggesting that effects of residents were due to direct interactions between residents and juveniles after settlement. In a third experiment, I cross-factored the presence and absence of piscivores and damselfishes with two levels of habitat complexity. I found that juvenile abundance was strongly influenced by prior residents and that effects of residents did not differ with habitat complexity. In contrast, the abundance of adult fish was strongly influenced by habitat complexity but not residents. In Australia, I factorially manipulated the presence and absence of resident predators and potential competitors on 20 reefs to determine whether these fish communities were influenced by resident-juvenile interactions comparable to those in the Bahamas. Results were similar to those obtained with the same experimental design in the Bahamas, indicating that priority effects may be a common feature of coral reef fish communities. These studies illustrate the importance of both habitat complexity and interactions between resident fishes and newly settled juveniles in coral reef fish communities, and provide a means of qualitatively predicting the future composition of these communities based on their current structure. Title: Role of priority effects and habitat complexity in coral-reef fish communities Author: Almany, Glenn R. Understanding the processes that influence the composition of animal communities is a central goal in ecology. Interactions between established residents and colonizing juveniles that affect the subsequent survival of juveniles may influence community composition. In a series of experiments on coral reef fish communities in the Bahamas and Australia, I tested whether and how interactions between colonizing juveniles and established residents, such as predators and territorial competitors, affected recruitment, and whether these interactions were modified by habitat complexity. In the Bahamas, I factorially manipulated the presence and absence of resident piscivores and territorial damselfishes on 16 spatially isolated patch reefs and found that both groups had strong, species-specific effects on subsequent recruitment. In a second experiment, I tested whether the aforementioned effects of residents were due to direct interactions between residents and juveniles or were the result of differential juvenile settlement. This was accomplished by repeating the first experiment, except this time placing piscivores and damselfishes within cages to prevent direct interactions. I found no evidence for differential settlement, suggesting that effects of residents were due to direct interactions between residents and juveniles after settlement. In a third experiment, I cross-factored the presence and absence of piscivores and damselfishes with two levels of habitat complexity. I found that juvenile abundance was strongly influenced by prior residents and that effects of residents did not differ with habitat complexity. In contrast, the abundance of adult fish was strongly influenced by habitat complexity but not residents. In Australia, I factorially manipulated the presence and absence of resident predators and potential competitors on 20 reefs to determine whether these fish communities were influenced by resident-juvenile interactions comparable to those in the Bahamas. Results were similar to those obtained with the same experimental design in the Bahamas, indicating that priority effects may be a common feature of coral reef fish communities. These studies illustrate the importance of both habitat complexity and interactions between resident fishes and newly settled juveniles in coral reef fish communities, and provide a means of qualitatively predicting the future composition of these communities based on their current structure. Close

• 1815. [Article] Liquor to liquor differences and the effects of liquor feed rate on the distribution of condensed phase combustion products of kraft black liquor solids burned in a laminar entrained-flow reactor

  Combustion properties of kraft black liquor solids were studied using a laminar entrained flow reactor. The tendency of black liquors to release fume (compounds containing Na⁺, K⁺, Cl⁻, SO₄²⁻, SO₃²⁻, S₂0₃²⁻ ...

  Citation × Citation Citation Abstract Copy Title: Liquor to liquor differences and the effects of liquor feed rate on the distribution of condensed phase combustion products of kraft black liquor solids burned in a laminar entrained-flow reactor Author: Train, Ron Combustion properties of kraft black liquor solids were studied using a laminar entrained flow reactor. The tendency of black liquors to release fume (compounds containing Na⁺, K⁺, Cl⁻, SO₄²⁻, SO₃²⁻, S₂0₃²⁻ and C0₃²⁻) during combustion were observed at 1000°C. Black liquor solids with a size fraction of 63 to 100 μm were burned in a mixture of 4% 0₂ and 96% N₂ at a residence time of 0.67 seconds. Combustion properties of one black liquor (liquor #3) were studied by varying the solids feed rate from 0.47 to 1.08 g/min (liquor feed rate study). Combustion properties of five North American and Finnish black liquors were studied at a target solids feed rate of 0.73 g/min (liquor to liquor study). Black liquor fuming was observed to be a decreasing function of solids feed rate and an increasing function of excess oxygen. The appearance of char residues varied from black and porous at high solids feed rates to white and dense at low solids feed rates. Combustion may have been enhanced at low solids feed rates by liquor swelling due to a combination of heat and mass transfer effects and limited at high solids feed rates by inter-particle and bulk gas mass transfer limitations. For the liquor to liquor study, black liquors were observed to release fume differently. Chars produced during this study varied in appearance, indicating that the black liquors had unique combustion properties. Variations in temperature and mass transfer effects resulting from liquor swelling properties were likely responsible for the variability in liquor fuming behavior. The liquors that contained the most NaCl and had the highest anionic equivalents as C0₃²⁻ (or other chemical species) produced the most fume. Sodium vaporization varied from 25.2% to 33.7%: Liquors #2 and #5 vaporized the most sodium and also had the lowest concentrations of measured anions in their char residues. Potassium and chloride enrichment factors for the five liquors were slightly lower than those of common industrial boilers. Liquor #3 had a concentration of Cl⁻ that was (roughly) an order of magnitude higher than the other liquors studied; however, it also had the lowest chloride enrichment factor. Title: Liquor to liquor differences and the effects of liquor feed rate on the distribution of condensed phase combustion products of kraft black liquor solids burned in a laminar entrained-flow reactor Author: Train, Ron Combustion properties of kraft black liquor solids were studied using a laminar entrained flow reactor. The tendency of black liquors to release fume (compounds containing Na⁺, K⁺, Cl⁻, SO₄²⁻, SO₃²⁻, S₂0₃²⁻ and C0₃²⁻) during combustion were observed at 1000°C. Black liquor solids with a size fraction of 63 to 100 μm were burned in a mixture of 4% 0₂ and 96% N₂ at a residence time of 0.67 seconds. Combustion properties of one black liquor (liquor #3) were studied by varying the solids feed rate from 0.47 to 1.08 g/min (liquor feed rate study). Combustion properties of five North American and Finnish black liquors were studied at a target solids feed rate of 0.73 g/min (liquor to liquor study). Black liquor fuming was observed to be a decreasing function of solids feed rate and an increasing function of excess oxygen. The appearance of char residues varied from black and porous at high solids feed rates to white and dense at low solids feed rates. Combustion may have been enhanced at low solids feed rates by liquor swelling due to a combination of heat and mass transfer effects and limited at high solids feed rates by inter-particle and bulk gas mass transfer limitations. For the liquor to liquor study, black liquors were observed to release fume differently. Chars produced during this study varied in appearance, indicating that the black liquors had unique combustion properties. Variations in temperature and mass transfer effects resulting from liquor swelling properties were likely responsible for the variability in liquor fuming behavior. The liquors that contained the most NaCl and had the highest anionic equivalents as C0₃²⁻ (or other chemical species) produced the most fume. Sodium vaporization varied from 25.2% to 33.7%: Liquors #2 and #5 vaporized the most sodium and also had the lowest concentrations of measured anions in their char residues. Potassium and chloride enrichment factors for the five liquors were slightly lower than those of common industrial boilers. Liquor #3 had a concentration of Cl⁻ that was (roughly) an order of magnitude higher than the other liquors studied; however, it also had the lowest chloride enrichment factor. Close

• 1816. [Article] Heritability estimates for seed and plant characteristics in white clover (Trifolium repens L.)

  Genetic differences, extent of hybrid vigor, nature of gene action, heritability estimates, and associations among characteristics, and between progenies and their respective mid-parents were determined for ...

  Citation × Citation Citation Abstract Copy Title: Heritability estimates for seed and plant characteristics in white clover (Trifolium repens L.) Author: Kim, Dal Ung Genetic differences, extent of hybrid vigor, nature of gene action, heritability estimates, and associations among characteristics, and between progenies and their respective mid-parents were determined for seed and plant characteristics in white clover (Trifolium repens L.). Ten seed and seedling vigor characteristics, including seed weight, ATP content in seed, seed respiration, and seedling vigor index were studied for a diallel cross consisting of 28 single crosses, five test-crosses, four checks, and eight open-pollinated seed and seedlings. Twenty-three plant characteristics on stolon, petiole, leaf, and forage were examined on the eight clones diallel cross, five test-crosses, three checks, the eight parental clones of single crosses, and six parent clones of the test-crosses. These 14 parent clones for this study were assembled on the basis of diverse morphology and origin. Most seed and seedling vigor characteristics, except RQ values, and most plant characteristics, except internode length, LAR and diurnal ratio in SLW, expressed significant differences among and within most groups of progenies and parental clones. All seed and seedling vigor characteristics, except RQ values, responded primarily to the nonadditive type of gene action. This suggests that the plant breeder should design his breeding program to develop varieties where hybrid vigor can be used to advantage. Among the criteria used in this study to measure seed and seedling vigor, ATP content per seed was closely associated with seedling vigor index and with certain plant characteristics, including forage yield per plant. The associations of seed weight with other seed and seedling vigor characteristics were negative or poor. Most plant characteristics showed apparent hybrid vigor when progenies were compared with their respective mid-parents. With few exceptions, most plant characteristics, stolon, petiole, leaf and forage yield per plant, responded primarily to the nonadditive gene system. This indicated that the plant breeder may use the hybrid approach to white clover variety development. The exceptions were leaf ratio and SLW which responded primarily to additive gene action, and area and dry weight per leaf appeared to respond equally to additive and nonadditive gene action. Genetic differences were more readily identified for stolon number and length when measurements were taken after 70 days of growth. Yield components, such as number, length, and diameter of stolon, petiole length, number of leaves per plant, and dry weight per leaf were closely related to each other. The leaf components of yield, dry weight per leaf and number of leaves per plant, had the highest direct and indirect effects on forage yields per plant among the yield components. This study showed nonadditive gene action primarily responsible for most seed and plant characteristics. Considering the ease of vegetative propagation in this species along with the self-incompatibility, mechanisms, it is suggested that parent geneotypes may be developed by some recurrent selection procedure, then crossed on a two clone synthetic basis to form experimental lines for testing purposes. Title: Heritability estimates for seed and plant characteristics in white clover (Trifolium repens L.) Author: Kim, Dal Ung Genetic differences, extent of hybrid vigor, nature of gene action, heritability estimates, and associations among characteristics, and between progenies and their respective mid-parents were determined for seed and plant characteristics in white clover (Trifolium repens L.). Ten seed and seedling vigor characteristics, including seed weight, ATP content in seed, seed respiration, and seedling vigor index were studied for a diallel cross consisting of 28 single crosses, five test-crosses, four checks, and eight open-pollinated seed and seedlings. Twenty-three plant characteristics on stolon, petiole, leaf, and forage were examined on the eight clones diallel cross, five test-crosses, three checks, the eight parental clones of single crosses, and six parent clones of the test-crosses. These 14 parent clones for this study were assembled on the basis of diverse morphology and origin. Most seed and seedling vigor characteristics, except RQ values, and most plant characteristics, except internode length, LAR and diurnal ratio in SLW, expressed significant differences among and within most groups of progenies and parental clones. All seed and seedling vigor characteristics, except RQ values, responded primarily to the nonadditive type of gene action. This suggests that the plant breeder should design his breeding program to develop varieties where hybrid vigor can be used to advantage. Among the criteria used in this study to measure seed and seedling vigor, ATP content per seed was closely associated with seedling vigor index and with certain plant characteristics, including forage yield per plant. The associations of seed weight with other seed and seedling vigor characteristics were negative or poor. Most plant characteristics showed apparent hybrid vigor when progenies were compared with their respective mid-parents. With few exceptions, most plant characteristics, stolon, petiole, leaf and forage yield per plant, responded primarily to the nonadditive gene system. This indicated that the plant breeder may use the hybrid approach to white clover variety development. The exceptions were leaf ratio and SLW which responded primarily to additive gene action, and area and dry weight per leaf appeared to respond equally to additive and nonadditive gene action. Genetic differences were more readily identified for stolon number and length when measurements were taken after 70 days of growth. Yield components, such as number, length, and diameter of stolon, petiole length, number of leaves per plant, and dry weight per leaf were closely related to each other. The leaf components of yield, dry weight per leaf and number of leaves per plant, had the highest direct and indirect effects on forage yields per plant among the yield components. This study showed nonadditive gene action primarily responsible for most seed and plant characteristics. Considering the ease of vegetative propagation in this species along with the self-incompatibility, mechanisms, it is suggested that parent geneotypes may be developed by some recurrent selection procedure, then crossed on a two clone synthetic basis to form experimental lines for testing purposes. Close

• 1817. [Article] Effects of single and multiple stressors on communities of wheat and wild oats

  Most plant toxicology tests developed in support of environmental laws use a single stress applied to an individual plant. While tests using individual species or stresses require fewer resources and are ...

  Citation × Citation Citation Abstract Copy Title: Effects of single and multiple stressors on communities of wheat and wild oats Author: Pfleeger, Thomas G. Most plant toxicology tests developed in support of environmental laws use a single stress applied to an individual plant. While tests using individual species or stresses require fewer resources and are easier to interpret, they are under increasing criticism for being unrealistic and missing important ecological interactions. The objective of this research was to increase our understanding of how plants and plant communities respond to a variety of stressors. Model plant communities of spring wheat (Triticum aestivum) and wild oats (Avena fatua) were planted at three densities and five proportions in the field. Puccinia recondita, the causal agent of wheat leaf rust, was inoculated on half of the plots. Disease severity was estimated as percent of wheat flag leaves covered by rust lesions. Plants were harvested at maturity and measured. Seeding density rarely had a significant influence on rust severity, probably because tiller density differed little as a result of compensation due to increased tillering at low seeding densities. In contrast, increasing the proportion of wheat in mixtures with wild oats consistently increased wheat leaf rust severity. There was no evidence to suggest that wild oats acted as a barrier to inoculum movement. Wild oats' effect on wheat leaf rust was probably through its competitive reduction of wheat tiller density. Both wheat and wild oats seed weight decreased as the proportion of wild oats increased in mixtures. This indicates that intraspecific competition was stronger in wild oats than was intraspecific competition with wheat in these mixtures. Wild oats generally did not respond to the presence of leaf rust on wheat, while wheat was negatively impacted. Thus, there was little competitive advantage to wild oats when its competitor (wheat) was diseased. A small subset of the field treatments was treated with ozone, because of the limited space available in the open-top ozone exposure chambers. Wheat height and aboveground biomass generally decreased with ozone exposure and with increasing disease severity in both years, while total grain weight decreased significantly only with disease and only in one year. There was no interaction between ozone and disease, regardless of cultivar, density, or plant response variable measured. There was little evidence that ozone exposure affected the severity of wheat leaf rust. In general, there seemed to be a lack of interactions among the different stressors and the results varied considerably depending on year and wheat cultivar. Title: Effects of single and multiple stressors on communities of wheat and wild oats Author: Pfleeger, Thomas G. Most plant toxicology tests developed in support of environmental laws use a single stress applied to an individual plant. While tests using individual species or stresses require fewer resources and are easier to interpret, they are under increasing criticism for being unrealistic and missing important ecological interactions. The objective of this research was to increase our understanding of how plants and plant communities respond to a variety of stressors. Model plant communities of spring wheat (Triticum aestivum) and wild oats (Avena fatua) were planted at three densities and five proportions in the field. Puccinia recondita, the causal agent of wheat leaf rust, was inoculated on half of the plots. Disease severity was estimated as percent of wheat flag leaves covered by rust lesions. Plants were harvested at maturity and measured. Seeding density rarely had a significant influence on rust severity, probably because tiller density differed little as a result of compensation due to increased tillering at low seeding densities. In contrast, increasing the proportion of wheat in mixtures with wild oats consistently increased wheat leaf rust severity. There was no evidence to suggest that wild oats acted as a barrier to inoculum movement. Wild oats' effect on wheat leaf rust was probably through its competitive reduction of wheat tiller density. Both wheat and wild oats seed weight decreased as the proportion of wild oats increased in mixtures. This indicates that intraspecific competition was stronger in wild oats than was intraspecific competition with wheat in these mixtures. Wild oats generally did not respond to the presence of leaf rust on wheat, while wheat was negatively impacted. Thus, there was little competitive advantage to wild oats when its competitor (wheat) was diseased. A small subset of the field treatments was treated with ozone, because of the limited space available in the open-top ozone exposure chambers. Wheat height and aboveground biomass generally decreased with ozone exposure and with increasing disease severity in both years, while total grain weight decreased significantly only with disease and only in one year. There was no interaction between ozone and disease, regardless of cultivar, density, or plant response variable measured. There was little evidence that ozone exposure affected the severity of wheat leaf rust. In general, there seemed to be a lack of interactions among the different stressors and the results varied considerably depending on year and wheat cultivar. Close

• 1818. [Article] Epiphytic yeasts isolated from apple leaves to control of gray and blue mold fruit rots of apple

  Eight phylloplane yeasts were isolated from backyard apple trees in Corvallis, OR. Yeast isolates were classified to genus or species level. All isolates were tested in vitro for antagonistic activity ...

  Citation × Citation Citation Abstract Copy Title: Epiphytic yeasts isolated from apple leaves to control of gray and blue mold fruit rots of apple Author: Falconi, Cesar E. Eight phylloplane yeasts were isolated from backyard apple trees in Corvallis, OR. Yeast isolates were classified to genus or species level. All isolates were tested in vitro for antagonistic activity against the postharvest pathogens Botrytis cinerea and Penicillium expansum. Of these isolates, Aureobasidium pullulans, Sporobolomyces roseus Rhodotorula sp., consistently reduced mycelial growth of B. cinerea and P. expansum in nutrient yeast dextrose agar (pH 4.5 or 7.0) incubated for 8 or 30 days at 24 or 1 C, respectively. These three yeasts also were evaluated for their ability to suppress spore germination of B. cinerea and P. expansum in a gradient of apple juice concentrations and to suppress development of gray and blue mold lesions in inoculated fruits of Golden Delicious apple. Germination of B. cinerea and P. expansum was reduced significantly (P≤0.05) when incubated with the yeast isolates in 100 or 50% apple juice, but not in 0, 1 or 10% apple juice. S. roseus and A. pullulans reduced significantly (P≤0.05) the size of gray mold lesions in wounded fruit stored at 5 C and 24 C by 63 to 72 and 81 to 90%, respectively, when compared to the nontreated control. Size of blue mold lesions in fruit stored at 5 and 24 C also were reduced significantly (P≤0.05) by 66 to 38 and 74 to 63%, respectively, when pre-treated with S. roseus and A. pullulans. In general, fruit rot suppression by some yeasts isolated in this study was similar in magnitude to suppression obtained by Cryptococcus laurentii isolate 87-108, a yeast with commercial potential to suppress postharvest rots of pome fruits. Pretreatment of apple wounds with washed cells of A. pullulans, S. roseus, Rhodotorula sp., resulted in disease suppression, but treatment of wounds with cell-free culture supernatant of these isolates did not affect lesion development. Population size of A. pullulans, S. roseus, and C. laurentii increased in apple wounds incubated at 5 or 24 C for up to 25 days, indicating that they colonized the wound site. Data collected in this study support the hypothesis that yeast isolates antagonize fruit pathogens by competing for nutrients in wounds on fruit surfaces. The isolates of A. pullulans and S. roseus show promise for commercial development. Title: Epiphytic yeasts isolated from apple leaves to control of gray and blue mold fruit rots of apple Author: Falconi, Cesar E. Eight phylloplane yeasts were isolated from backyard apple trees in Corvallis, OR. Yeast isolates were classified to genus or species level. All isolates were tested in vitro for antagonistic activity against the postharvest pathogens Botrytis cinerea and Penicillium expansum. Of these isolates, Aureobasidium pullulans, Sporobolomyces roseus Rhodotorula sp., consistently reduced mycelial growth of B. cinerea and P. expansum in nutrient yeast dextrose agar (pH 4.5 or 7.0) incubated for 8 or 30 days at 24 or 1 C, respectively. These three yeasts also were evaluated for their ability to suppress spore germination of B. cinerea and P. expansum in a gradient of apple juice concentrations and to suppress development of gray and blue mold lesions in inoculated fruits of Golden Delicious apple. Germination of B. cinerea and P. expansum was reduced significantly (P≤0.05) when incubated with the yeast isolates in 100 or 50% apple juice, but not in 0, 1 or 10% apple juice. S. roseus and A. pullulans reduced significantly (P≤0.05) the size of gray mold lesions in wounded fruit stored at 5 C and 24 C by 63 to 72 and 81 to 90%, respectively, when compared to the nontreated control. Size of blue mold lesions in fruit stored at 5 and 24 C also were reduced significantly (P≤0.05) by 66 to 38 and 74 to 63%, respectively, when pre-treated with S. roseus and A. pullulans. In general, fruit rot suppression by some yeasts isolated in this study was similar in magnitude to suppression obtained by Cryptococcus laurentii isolate 87-108, a yeast with commercial potential to suppress postharvest rots of pome fruits. Pretreatment of apple wounds with washed cells of A. pullulans, S. roseus, Rhodotorula sp., resulted in disease suppression, but treatment of wounds with cell-free culture supernatant of these isolates did not affect lesion development. Population size of A. pullulans, S. roseus, and C. laurentii increased in apple wounds incubated at 5 or 24 C for up to 25 days, indicating that they colonized the wound site. Data collected in this study support the hypothesis that yeast isolates antagonize fruit pathogens by competing for nutrients in wounds on fruit surfaces. The isolates of A. pullulans and S. roseus show promise for commercial development. Close

• 1819. [Article] Establishing irrigation criteria for cultivation of Veratrum californicum

  Veratrum californicum (common name: corn lily) is a wild plant species that grows in the Intermountain West, its range extending from British Columbia to Mexico. Corn lily is of interest because it has ...

  Citation × Citation Citation Abstract Copy Title: Establishing irrigation criteria for cultivation of Veratrum californicum Author: Doniger, Alison R. Veratrum californicum (common name: corn lily) is a wild plant species that grows in the Intermountain West, its range extending from British Columbia to Mexico. Corn lily is of interest because it has the potential to provide pharmaceutical precursors for use in the treatment of cancer. Pharmaceutical companies are currently running clinical trials of new drugs that use these precursors. As such, a sustainable supply of corn lily is needed if these drugs are ever to enter the market. Unfortunately, wild populations of corn lily will not be able to meet the market demand. Therefore, it is necessary that horticultural guidelines be established so that corn lily can be grown in an agricultural setting. Establishing irrigation criteria is one crucial component in this process, as corn lily grows in naturally wet areas and will most likely require supplemental irrigation in an agricultural setting. In order to determine the appropriate level of irrigation for corn lily, an appropriate range of irrigation levels to test in a field trial must be determined. Plant success as a function of irrigation level can then be measured. In order to determine what irrigation levels should be tested, the OSU Malheur Experiment Station monitored the natural environment of corn lily at a variety of locations over the course of four seasons. Results showed that for the majority of its growing season, corn lily occupies a narrow environmental niche where soil water tension ranges from 0 kPa to 30 kPa. With this information, irrigation levels ranging from 5 kPa to 30 kPa were chosen for irrigation trials. In 2009, corn lily plots were established at Ontario, Oregon and McCall, Idaho. Irrigation trials were run in 2010, 2011, and 2012 at Ontario and McCall. Plots were assigned to five irrigation treatments: 5 kPa (added halfway through the 2010 growing season), 10 kPa, 15 kPa, 20 kPa, and 30 kPa. Collectively, the data indicate that the 5 and 10 kPa treatments are most conducive to corn lily survival and growth. In addition, the observed data are consistent with the hypothesis that soil moisture levels in the first month of growth may be the most important determinant in plant growth and survival. Title: Establishing irrigation criteria for cultivation of Veratrum californicum Author: Doniger, Alison R. Veratrum californicum (common name: corn lily) is a wild plant species that grows in the Intermountain West, its range extending from British Columbia to Mexico. Corn lily is of interest because it has the potential to provide pharmaceutical precursors for use in the treatment of cancer. Pharmaceutical companies are currently running clinical trials of new drugs that use these precursors. As such, a sustainable supply of corn lily is needed if these drugs are ever to enter the market. Unfortunately, wild populations of corn lily will not be able to meet the market demand. Therefore, it is necessary that horticultural guidelines be established so that corn lily can be grown in an agricultural setting. Establishing irrigation criteria is one crucial component in this process, as corn lily grows in naturally wet areas and will most likely require supplemental irrigation in an agricultural setting. In order to determine the appropriate level of irrigation for corn lily, an appropriate range of irrigation levels to test in a field trial must be determined. Plant success as a function of irrigation level can then be measured. In order to determine what irrigation levels should be tested, the OSU Malheur Experiment Station monitored the natural environment of corn lily at a variety of locations over the course of four seasons. Results showed that for the majority of its growing season, corn lily occupies a narrow environmental niche where soil water tension ranges from 0 kPa to 30 kPa. With this information, irrigation levels ranging from 5 kPa to 30 kPa were chosen for irrigation trials. In 2009, corn lily plots were established at Ontario, Oregon and McCall, Idaho. Irrigation trials were run in 2010, 2011, and 2012 at Ontario and McCall. Plots were assigned to five irrigation treatments: 5 kPa (added halfway through the 2010 growing season), 10 kPa, 15 kPa, 20 kPa, and 30 kPa. Collectively, the data indicate that the 5 and 10 kPa treatments are most conducive to corn lily survival and growth. In addition, the observed data are consistent with the hypothesis that soil moisture levels in the first month of growth may be the most important determinant in plant growth and survival. Close

• 1820. [Article] The Use of Terrestrial Laser Scanning and Computer Vision in Tree Level Modeling

  Laser Scanning represents a new opportunity in forestry to effect meaningful change in the methods used for collection and analysis of inventory data. With the ability to collect spatial information in ...

  Citation × Citation Citation Abstract Copy Title: The Use of Terrestrial Laser Scanning and Computer Vision in Tree Level Modeling Author: Gabriel, Richard S. Laser Scanning represents a new opportunity in forestry to effect meaningful change in the methods used for collection and analysis of inventory data. With the ability to collect spatial information in 360 degrees, while fluidly tracking the sensor and building the final point cloud, large tracks of terrestrial LiDAR based measurements are now feasible. With the advancement in collection technology, advancement in analysis methods are necessary to utilize the surplus of information. This project investigates efficient methods for automated recognition and mapping of conifer structure within terrestrial based LiDAR point clouds. Chapter 2 develops a methodology for using terrestrial laser scanning to show that accurate predictive lower bole volumes can be obtained. This leads to more accurate taper equations which are crucial for the estimated stand volume of all trees. Advances in remote sensing technology such as LiDAR and computer vision are quickly approaching the point where semi-autonomous, or limited human interaction, inspection and modeling of tree structure using computers is possible. Model construction estimates were analyzed alongside the Hann 2011 curves. Estimates were shown to improve on the Hann equation using the Mean of Group Mean Equation and Logarithmic Function. Model performance improved the MSE, and showed the lowest bias of the equations tested. While total tree bole estimation was not possible, the results show that improvement of bole predicted diameters is certainly possible. Chapter 3 examined the potential for laser scanning to begin to automate log quality analysis in the field using a developed branch detection algorithm. Branch knots are an indicator tied to log value and are often difficult to properly estimate. Laser scanning offers an alternative to field estimation using Mobile Laser Scanning and computer vision. The developed algorithm performed very well identifying 94.4% of branches in the lower bole but was unable to extend further due to visual obstructions beyond the lower bole. While this paper focused on branch detection, there are many ancillary products from this workflow. Tree geolocation allows for mapping of spatial relationships, permits for better planning not only at harvest time, but also in silvicultural decisions. The concepts discussed in this thesis serve as a starting point for future work, forming the initial framework of computationally inexpensive, information rich processes for the semi-autonomous processing of LiDAR point clouds. Future research is needed into each of the methods to determine the viability of each over a landscape of varying tree forms and species. Title: The Use of Terrestrial Laser Scanning and Computer Vision in Tree Level Modeling Author: Gabriel, Richard S. Laser Scanning represents a new opportunity in forestry to effect meaningful change in the methods used for collection and analysis of inventory data. With the ability to collect spatial information in 360 degrees, while fluidly tracking the sensor and building the final point cloud, large tracks of terrestrial LiDAR based measurements are now feasible. With the advancement in collection technology, advancement in analysis methods are necessary to utilize the surplus of information. This project investigates efficient methods for automated recognition and mapping of conifer structure within terrestrial based LiDAR point clouds. Chapter 2 develops a methodology for using terrestrial laser scanning to show that accurate predictive lower bole volumes can be obtained. This leads to more accurate taper equations which are crucial for the estimated stand volume of all trees. Advances in remote sensing technology such as LiDAR and computer vision are quickly approaching the point where semi-autonomous, or limited human interaction, inspection and modeling of tree structure using computers is possible. Model construction estimates were analyzed alongside the Hann 2011 curves. Estimates were shown to improve on the Hann equation using the Mean of Group Mean Equation and Logarithmic Function. Model performance improved the MSE, and showed the lowest bias of the equations tested. While total tree bole estimation was not possible, the results show that improvement of bole predicted diameters is certainly possible. Chapter 3 examined the potential for laser scanning to begin to automate log quality analysis in the field using a developed branch detection algorithm. Branch knots are an indicator tied to log value and are often difficult to properly estimate. Laser scanning offers an alternative to field estimation using Mobile Laser Scanning and computer vision. The developed algorithm performed very well identifying 94.4% of branches in the lower bole but was unable to extend further due to visual obstructions beyond the lower bole. While this paper focused on branch detection, there are many ancillary products from this workflow. Tree geolocation allows for mapping of spatial relationships, permits for better planning not only at harvest time, but also in silvicultural decisions. The concepts discussed in this thesis serve as a starting point for future work, forming the initial framework of computationally inexpensive, information rich processes for the semi-autonomous processing of LiDAR point clouds. Future research is needed into each of the methods to determine the viability of each over a landscape of varying tree forms and species. Close

• 1821. [Article] The effects of predation on anuran metamorphosis

  Many organisms with complex life cycles undergo transition periods associated with increased vulnerability to predation. Several evolutionary adaptations have been proposed as antipredator defenses for ...

  Citation × Citation Citation Abstract Copy Title: The effects of predation on anuran metamorphosis Author: DeVito, Jill Many organisms with complex life cycles undergo transition periods associated with increased vulnerability to predation. Several evolutionary adaptations have been proposed as antipredator defenses for organisms during risky transition periods. These include: shortening of the transition period, parental care, cryptic coloration, and synchrony of risky transitions with large numbers of conspecifics. The results of my research support the hypothesis that synchrony of metamorphosis and emergence from the water and aggregation during the period of transformation may be antipredator defenses for the western toad (Bufo boreas). For some anuran species, synchronous metamorphosis may function as an antipredator adaptation by swamping predators during the period of transformation. I examined the levels of synchrony of emergence from the water of metamorphosing western toads (Bufo boreas) in the presence and absence of a live snake predator, the common garter snake (Thamnophis sirtalis) in a laboratory experiment. To compare between the treatments, I measured the time to emergence from the water, the number of metamorphs emerging together, and the level of aggregation (before and during emergence) of the toads in each treatment. There was a difference between the treatments when all three factors were considered. I attributed these differences to a behavioral response in which B. boreas emerged sooner in the presence of the predator, regardless of whether individual toads had reached the point at which they were physically better suited to the terrestrial environment than the larval environment. Since the Pacific treefrog (Hyla regilla) is also preyed upon by T. sirtalis during the vulnerable period of metamorphosis, I conducted a laboratory experiment to test the effects of the presence of T. sirtalis on 1) aggregation of larval and metamorphosing H. regilla, 2) time to metamorphosis, 3) synchrony of metamorphosis, 4) time to emergence from the water and 5) synchrony of emergence from the water. The only significant effect observed in this experiment was a difference between aggregation levels of H. regilla throughout the experiment. There was, however, a strong trend in which the variances around the mean times to metamorphosis and emergence of the frogs in the control treatments were larger than those in the predator treatments. This could indicate a trend toward synchrony of metamorphosis and emergence for H. regilla in the presence of snake predators. Title: The effects of predation on anuran metamorphosis Author: DeVito, Jill Many organisms with complex life cycles undergo transition periods associated with increased vulnerability to predation. Several evolutionary adaptations have been proposed as antipredator defenses for organisms during risky transition periods. These include: shortening of the transition period, parental care, cryptic coloration, and synchrony of risky transitions with large numbers of conspecifics. The results of my research support the hypothesis that synchrony of metamorphosis and emergence from the water and aggregation during the period of transformation may be antipredator defenses for the western toad (Bufo boreas). For some anuran species, synchronous metamorphosis may function as an antipredator adaptation by swamping predators during the period of transformation. I examined the levels of synchrony of emergence from the water of metamorphosing western toads (Bufo boreas) in the presence and absence of a live snake predator, the common garter snake (Thamnophis sirtalis) in a laboratory experiment. To compare between the treatments, I measured the time to emergence from the water, the number of metamorphs emerging together, and the level of aggregation (before and during emergence) of the toads in each treatment. There was a difference between the treatments when all three factors were considered. I attributed these differences to a behavioral response in which B. boreas emerged sooner in the presence of the predator, regardless of whether individual toads had reached the point at which they were physically better suited to the terrestrial environment than the larval environment. Since the Pacific treefrog (Hyla regilla) is also preyed upon by T. sirtalis during the vulnerable period of metamorphosis, I conducted a laboratory experiment to test the effects of the presence of T. sirtalis on 1) aggregation of larval and metamorphosing H. regilla, 2) time to metamorphosis, 3) synchrony of metamorphosis, 4) time to emergence from the water and 5) synchrony of emergence from the water. The only significant effect observed in this experiment was a difference between aggregation levels of H. regilla throughout the experiment. There was, however, a strong trend in which the variances around the mean times to metamorphosis and emergence of the frogs in the control treatments were larger than those in the predator treatments. This could indicate a trend toward synchrony of metamorphosis and emergence for H. regilla in the presence of snake predators. Close

• 1822. [Article] Characterization of the LeIAA family of auxin-regulated genes in tomato (Lycopericon esculentum, Mill.)

  The plant hormone auxin regulates many aspects of plant growth and development. At the cellular level, auxin can stimulate cell division, cell elongation, and cell differentiation. Little is known about ...

  Citation × Citation Citation Abstract Copy Title: Characterization of the LeIAA family of auxin-regulated genes in tomato (Lycopericon esculentum, Mill.) Author: Nebenfuhr, Andreas The plant hormone auxin regulates many aspects of plant growth and development. At the cellular level, auxin can stimulate cell division, cell elongation, and cell differentiation. Little is known about the molecular mechanisms that mediate auxin action at this level, although changes in gene expression have been implicated in each of them. An important step in elucidating the signal transduction steps involved in these responses is the identification of intermediates that respond to auxin treatment within a physiologically relevant range, and can be functionally linked to specific response(s). The Aux/IAA family of auxin-regulated genes, which has been identified in several species, may constitute such a group of signalling intermediates. This dissertation reports on the isolation and characterization of eleven tomato genes, LeIAA1 - 11, which are homologous to these Aux/IAA genes. Expression characteristics in response to exogenously-applied auxin were determined in segments of etiolated hypocotyls. The LeIAA genes fell into three kinetic classes and displayed differential responsiveness to the treatment. Comparison of auxin-induced expression in wild-type and the auxin-insensitive diageotropica (dgt) mutant revealed that induction of only a subset of genes was affected by the mutation while the other genes retained wild-type response levels in the mutant. This finding indicates that at least two signal transduction chains lead to auxin-induced gene expression, and the dgt gene product acts on only one of them. The expression pattern of nine LeIAA genes was determined in a wide variety of tissue samples in order to link individual LeIAA genes with specific physiological responses. To that end, a qualitative multiplex RT-PCR method was developed that allowed quick assessment of relative expression levels in a large number of small RNA samples. It was found that LeIAA10 expression was highest in tissues undergoing rapid growth, suggesting a role for this gene in the process of cell expansion. The expression of LeIAA1 1 was also variable during development, while LeIAA2 was strongly down-regulated after light treatment. These experiments demonstrated organ-preferential expression of LeIAA genes under the control of environmental factors and depending on developmental stages. The LeIAA genes may thus act as integrators of several other signals with the auxin stimulus. Title: Characterization of the LeIAA family of auxin-regulated genes in tomato (Lycopericon esculentum, Mill.) Author: Nebenfuhr, Andreas The plant hormone auxin regulates many aspects of plant growth and development. At the cellular level, auxin can stimulate cell division, cell elongation, and cell differentiation. Little is known about the molecular mechanisms that mediate auxin action at this level, although changes in gene expression have been implicated in each of them. An important step in elucidating the signal transduction steps involved in these responses is the identification of intermediates that respond to auxin treatment within a physiologically relevant range, and can be functionally linked to specific response(s). The Aux/IAA family of auxin-regulated genes, which has been identified in several species, may constitute such a group of signalling intermediates. This dissertation reports on the isolation and characterization of eleven tomato genes, LeIAA1 - 11, which are homologous to these Aux/IAA genes. Expression characteristics in response to exogenously-applied auxin were determined in segments of etiolated hypocotyls. The LeIAA genes fell into three kinetic classes and displayed differential responsiveness to the treatment. Comparison of auxin-induced expression in wild-type and the auxin-insensitive diageotropica (dgt) mutant revealed that induction of only a subset of genes was affected by the mutation while the other genes retained wild-type response levels in the mutant. This finding indicates that at least two signal transduction chains lead to auxin-induced gene expression, and the dgt gene product acts on only one of them. The expression pattern of nine LeIAA genes was determined in a wide variety of tissue samples in order to link individual LeIAA genes with specific physiological responses. To that end, a qualitative multiplex RT-PCR method was developed that allowed quick assessment of relative expression levels in a large number of small RNA samples. It was found that LeIAA10 expression was highest in tissues undergoing rapid growth, suggesting a role for this gene in the process of cell expansion. The expression of LeIAA1 1 was also variable during development, while LeIAA2 was strongly down-regulated after light treatment. These experiments demonstrated organ-preferential expression of LeIAA genes under the control of environmental factors and depending on developmental stages. The LeIAA genes may thus act as integrators of several other signals with the auxin stimulus. Close

• 1823. [Article] Influences of riparian canopy on aquatic communities in high desert streams of eastern Oregon

  Because riparian canopy controls most energy inputs to stream ecosystems, it directly affects the structure of aquatic food webs and the ecological processes that govern interactions among trophic levels. ...

  Citation × Citation Citation Abstract Copy Title: Influences of riparian canopy on aquatic communities in high desert streams of eastern Oregon Author: Tait, Cynthia K. Because riparian canopy controls most energy inputs to stream ecosystems, it directly affects the structure of aquatic food webs and the ecological processes that govern interactions among trophic levels. This study addresses the interdependence among riparian canopy, benthic community structure, and the carrying capacity of high desert streams for salmonid fishes. In streams in the lower John Day River Basin in eastern Oregon, algal, invertebrate, and fish communities were compared in reaches with varying densities of riparian canopy. Water temperatures varied with the density and upstream extent of canopy. Densely canopied sites were cool, while sites with high irradiances had temperatures exceeding the upper lethal limit for salmonids. Periphyton and grazer biomasses were greater in well-lighted sites, but 90% of grazer biomass consisted of Dicosmoecus gilvipes, a large caddisfly inedible by juvenile trout. Warmer water increased metabolic demands for salmonids, while the overwhelming dominance of Dicosmoecus in open sites shifted energy flow away from trout and shrunk their food base. High water temperatures, however, provided suitable habitat for many warmwater fishes which would otherwise not enter tributaries of this size. At higher elevation study sites in Camp Creek, light levels were higher and less variable than at the lower sites. Periphyton and invertebrate abundances were not correlated with irradiance. Rather, periphyton was maintained at low levels by grazers, particularly Dicosmoecus and snails. Manipulations of fish densities in enclosures showed that trout and dace had no negative impacts on numbers of invertebrate prey, and that grazers played a larger role in regulating lower trophic levels than did fish. Dicosmoecus acted as a keystone species in the benthic food web of Camp Creek by simultaneously influencing the trophic level both below and above its own. When irradiance was experimentally reduced under artificial canopies, periphyton standing crops were not different from those in open control pools after 4 wks. However, grazers were more abundant in open pools. The cropping of periphyton to uniform levels in both sunlight and shade indicated that mobile grazers targeted sites of varying productivities. Comparisons between benthic communities in Camp Creek and in a densely canopied reference stream suggested that benthic community structure shifted to accommodate changes in energy resources that occur when canopy density is altered. Title: Influences of riparian canopy on aquatic communities in high desert streams of eastern Oregon Author: Tait, Cynthia K. Because riparian canopy controls most energy inputs to stream ecosystems, it directly affects the structure of aquatic food webs and the ecological processes that govern interactions among trophic levels. This study addresses the interdependence among riparian canopy, benthic community structure, and the carrying capacity of high desert streams for salmonid fishes. In streams in the lower John Day River Basin in eastern Oregon, algal, invertebrate, and fish communities were compared in reaches with varying densities of riparian canopy. Water temperatures varied with the density and upstream extent of canopy. Densely canopied sites were cool, while sites with high irradiances had temperatures exceeding the upper lethal limit for salmonids. Periphyton and grazer biomasses were greater in well-lighted sites, but 90% of grazer biomass consisted of Dicosmoecus gilvipes, a large caddisfly inedible by juvenile trout. Warmer water increased metabolic demands for salmonids, while the overwhelming dominance of Dicosmoecus in open sites shifted energy flow away from trout and shrunk their food base. High water temperatures, however, provided suitable habitat for many warmwater fishes which would otherwise not enter tributaries of this size. At higher elevation study sites in Camp Creek, light levels were higher and less variable than at the lower sites. Periphyton and invertebrate abundances were not correlated with irradiance. Rather, periphyton was maintained at low levels by grazers, particularly Dicosmoecus and snails. Manipulations of fish densities in enclosures showed that trout and dace had no negative impacts on numbers of invertebrate prey, and that grazers played a larger role in regulating lower trophic levels than did fish. Dicosmoecus acted as a keystone species in the benthic food web of Camp Creek by simultaneously influencing the trophic level both below and above its own. When irradiance was experimentally reduced under artificial canopies, periphyton standing crops were not different from those in open control pools after 4 wks. However, grazers were more abundant in open pools. The cropping of periphyton to uniform levels in both sunlight and shade indicated that mobile grazers targeted sites of varying productivities. Comparisons between benthic communities in Camp Creek and in a densely canopied reference stream suggested that benthic community structure shifted to accommodate changes in energy resources that occur when canopy density is altered. Close

• 1824. [Article] Evaluation of tree forage as a nontraditional feedstuff for small livestock

  Five experiments were conducted to evaluate tree forage as a feedstuff for small livestock, using the foliage of black locust (Robinia pseudoacacia) and hybrid poplar (Populus spp.). In the first trial, ...

  Citation × Citation Citation Abstract Copy Title: Evaluation of tree forage as a nontraditional feedstuff for small livestock Author: Ayers, Anne Christine Five experiments were conducted to evaluate tree forage as a feedstuff for small livestock, using the foliage of black locust (Robinia pseudoacacia) and hybrid poplar (Populus spp.). In the first trial, rabbits were fed diets containing 40% alfalfa (control), and 10%, 20% and 40% poplar leaves (PL) from untrimmed or uncoppiced growth, and 10% and 20% PL from trimmed or coppiced growth. At the 20% level, crude protein (CP) was better digested for the coppiced PL than for the uncoppiced (p < .05). No significant difference was evident between treatments in the average daily gain (ADG) or feed efficiency, but dry matter (DM) intake increased for all the PL treatments compared to the control (p < .01). In the second experiment, black locust (BL) leaves were treated by various methods in an attempt to counter the effect of tannins. Rabbits were fed diets containing 50% alfalfa (control), 25% alfalfa and 25% black locust meal (BLM) (BLM control), BLM + 1% polyethylene glycol (PEG), BLM + 1% phytase, and BLM + 0.3% L-methionine and 0.3% choline chloride. In general, nutrient utilization and ADG were better for the control than for the BLM treatments. The addition of PEG increased CP digestibility (p < .01) and ADF (p < .03) compared to the BLM control, partially alleviating the reduced nutrient availability. The addition of L-methionine and choline chloride increased ADF digestibility (p < .02). In the third trial, black locust (BL) bark and other tree products were used to study the possible toxic effects of lectins in BL bark. Rabbits were fed diets containing 25% BL bark, oak sawdust, red alder bark, or red alder sawdust (all diets also included 25% alfalfa). A 50% alfalfa diet served as a control. In general, nutrient digestibilities and ADG were higher for the control than the treatments and, also, higher for the BL bark diet than the alder bark diet. The ADG with the BL bark diet was lower than for the alder bark diet (p < .01), which indicated a possible toxic effect of the BL bark. The fourth trial examined the feeding value of poplar leaves for sheep. Sheep were fed diets containing 50% PL or 50% alfalfa. Nutrient digestibilities were lower for the PL diet (p < .01). In the fifth experiment, BL leaves were fed to sheep and goats in order to determine if goats, being browsers instead of grazers like the sheep, are better equipped to tolerate the anti-nutritive effects from BL forage. Sheep and goats were fed diets composed solely of BL leaves or alfalfa (control). Overall, the nutrient digestibilities were higher for alfalfa than for BL leaves, and there was no difference in terms of digestibility between species. Although the leaves of black locust and poplar contain anti-nutritive factors, it was concluded that the trees have potential as multipurpose trees from which the leaves could be harvested as animal fodder, particularly in temperate areas of the developing world. Title: Evaluation of tree forage as a nontraditional feedstuff for small livestock Author: Ayers, Anne Christine Five experiments were conducted to evaluate tree forage as a feedstuff for small livestock, using the foliage of black locust (Robinia pseudoacacia) and hybrid poplar (Populus spp.). In the first trial, rabbits were fed diets containing 40% alfalfa (control), and 10%, 20% and 40% poplar leaves (PL) from untrimmed or uncoppiced growth, and 10% and 20% PL from trimmed or coppiced growth. At the 20% level, crude protein (CP) was better digested for the coppiced PL than for the uncoppiced (p < .05). No significant difference was evident between treatments in the average daily gain (ADG) or feed efficiency, but dry matter (DM) intake increased for all the PL treatments compared to the control (p < .01). In the second experiment, black locust (BL) leaves were treated by various methods in an attempt to counter the effect of tannins. Rabbits were fed diets containing 50% alfalfa (control), 25% alfalfa and 25% black locust meal (BLM) (BLM control), BLM + 1% polyethylene glycol (PEG), BLM + 1% phytase, and BLM + 0.3% L-methionine and 0.3% choline chloride. In general, nutrient utilization and ADG were better for the control than for the BLM treatments. The addition of PEG increased CP digestibility (p < .01) and ADF (p < .03) compared to the BLM control, partially alleviating the reduced nutrient availability. The addition of L-methionine and choline chloride increased ADF digestibility (p < .02). In the third trial, black locust (BL) bark and other tree products were used to study the possible toxic effects of lectins in BL bark. Rabbits were fed diets containing 25% BL bark, oak sawdust, red alder bark, or red alder sawdust (all diets also included 25% alfalfa). A 50% alfalfa diet served as a control. In general, nutrient digestibilities and ADG were higher for the control than the treatments and, also, higher for the BL bark diet than the alder bark diet. The ADG with the BL bark diet was lower than for the alder bark diet (p < .01), which indicated a possible toxic effect of the BL bark. The fourth trial examined the feeding value of poplar leaves for sheep. Sheep were fed diets containing 50% PL or 50% alfalfa. Nutrient digestibilities were lower for the PL diet (p < .01). In the fifth experiment, BL leaves were fed to sheep and goats in order to determine if goats, being browsers instead of grazers like the sheep, are better equipped to tolerate the anti-nutritive effects from BL forage. Sheep and goats were fed diets composed solely of BL leaves or alfalfa (control). Overall, the nutrient digestibilities were higher for alfalfa than for BL leaves, and there was no difference in terms of digestibility between species. Although the leaves of black locust and poplar contain anti-nutritive factors, it was concluded that the trees have potential as multipurpose trees from which the leaves could be harvested as animal fodder, particularly in temperate areas of the developing world. Close

• 1825. [Article] Influence of Norbak, Dacagin, and Vistik on spray drift, volatility, adherence, and efficacy of several herbicides

  Norbak, Dacagin, and Vistik, when mixed with a spray solution, each have the unique property of increasing the viscosity of that solution. This property has been used commercially for the reduction of ...

  Citation × Citation Citation Abstract Copy Title: Influence of Norbak, Dacagin, and Vistik on spray drift, volatility, adherence, and efficacy of several herbicides Author: Ekins, Walter Leo Norbak, Dacagin, and Vistik, when mixed with a spray solution, each have the unique property of increasing the viscosity of that solution. This property has been used commercially for the reduction of spray drift. Studies were made of the drift control adjuvants to determine the following: (1) the effect of the adjuvants on the phytotoxicity of selected herbicides to several crops, (2) the effect of the adjuvants on the herbicidal efficacy of paraquat, (3) the effectiveness of the adjuvants in reducing spray drift under field conditions, (4) the effect of the adjuvants in preventing amitrole-T from being washed off plants with simulated rainfall, and (5) the ability of the adjuvants to reduce vapor loss of 2,4-D ethyl ester when applied in combination to plant surfaces. Field experiments in which adjuvants were sprayed in combination with 2,4-D amine on wheat and corn, dicamba on barley, and MCPA on red clover, indicated that only in the case of Vistik applied with MCPA at rates of 1.0 and 1.5 lbs./A. was there a reduction in herbicidal selectivity. This reduction was very slight. The adjuvants were each very effective in reducing spray drift in paraquat field studies. Injury to test plants 50 feet from the spray swath was less than five percent for the paraquat solution containing an adjuvant as compared to 20 percent for the solution without an adjuvant. Studies were conducted to determine whether the adjuvants would substitute for the wetting agent X-77 in paraquat applications under field conditions. Thirty-two plant species were sprayed in each plot and visually evaluated several weeks later for injury. Results showed that the adjuvants were not effective substitutes for X-77. On the other hand, the addition of Dacagin or Vistik to the paraquat solution did not decrease the herbicidal efficacy when X-77 was used. Norbak decreased the herbicidal efficacy of paraquat with or without the addition of X-77. A study to determine the effectiveness of the adjuvants in preventing amitrole-T from being washed off plant surfaces was conducted. Tomato plants were sprayed with an amitrole-T solution containing adjuvant and washed with simulated rainfall at various time intervals following the spraying. The adjuvants proved ineffective in preventing the amitrole-T from being washed off the plants. In another experiment bean plants were sprayed with a 2,4-D ethyl ester solution in which adjuvant was mixed. These plants were placed in a plastic bag enclosure with untreated bean plants to study the effectiveness of these adjuvants in reducing vapor loss of 2,4-D from the treated beans. Results suggested that only Dacagin had properties that reduced vapor loss, and this reduction was slight. Throughout the above experiments Norbak noticeably decreased the efficacy of the herbicides. This decrease is attributed to the reduction in the number of spray droplets per unit area in the spray swath. Title: Influence of Norbak, Dacagin, and Vistik on spray drift, volatility, adherence, and efficacy of several herbicides Author: Ekins, Walter Leo Norbak, Dacagin, and Vistik, when mixed with a spray solution, each have the unique property of increasing the viscosity of that solution. This property has been used commercially for the reduction of spray drift. Studies were made of the drift control adjuvants to determine the following: (1) the effect of the adjuvants on the phytotoxicity of selected herbicides to several crops, (2) the effect of the adjuvants on the herbicidal efficacy of paraquat, (3) the effectiveness of the adjuvants in reducing spray drift under field conditions, (4) the effect of the adjuvants in preventing amitrole-T from being washed off plants with simulated rainfall, and (5) the ability of the adjuvants to reduce vapor loss of 2,4-D ethyl ester when applied in combination to plant surfaces. Field experiments in which adjuvants were sprayed in combination with 2,4-D amine on wheat and corn, dicamba on barley, and MCPA on red clover, indicated that only in the case of Vistik applied with MCPA at rates of 1.0 and 1.5 lbs./A. was there a reduction in herbicidal selectivity. This reduction was very slight. The adjuvants were each very effective in reducing spray drift in paraquat field studies. Injury to test plants 50 feet from the spray swath was less than five percent for the paraquat solution containing an adjuvant as compared to 20 percent for the solution without an adjuvant. Studies were conducted to determine whether the adjuvants would substitute for the wetting agent X-77 in paraquat applications under field conditions. Thirty-two plant species were sprayed in each plot and visually evaluated several weeks later for injury. Results showed that the adjuvants were not effective substitutes for X-77. On the other hand, the addition of Dacagin or Vistik to the paraquat solution did not decrease the herbicidal efficacy when X-77 was used. Norbak decreased the herbicidal efficacy of paraquat with or without the addition of X-77. A study to determine the effectiveness of the adjuvants in preventing amitrole-T from being washed off plant surfaces was conducted. Tomato plants were sprayed with an amitrole-T solution containing adjuvant and washed with simulated rainfall at various time intervals following the spraying. The adjuvants proved ineffective in preventing the amitrole-T from being washed off the plants. In another experiment bean plants were sprayed with a 2,4-D ethyl ester solution in which adjuvant was mixed. These plants were placed in a plastic bag enclosure with untreated bean plants to study the effectiveness of these adjuvants in reducing vapor loss of 2,4-D from the treated beans. Results suggested that only Dacagin had properties that reduced vapor loss, and this reduction was slight. Throughout the above experiments Norbak noticeably decreased the efficacy of the herbicides. This decrease is attributed to the reduction in the number of spray droplets per unit area in the spray swath. Close

• 1826. [Article] Lodging control and yield enhancement in Morex spring barley with paclobutrazol treatment

  Lodging in cereals can cause significant decreases in yield. It is both a problem in susceptible cereal cultivars with a tall-stemmed, weak-strawed growing habit and in lodging-resistant cereal cultivars ...

  Citation × Citation Citation Abstract Copy Title: Lodging control and yield enhancement in Morex spring barley with paclobutrazol treatment Author: Morrison, Laura A. Lodging in cereals can cause significant decreases in yield. It is both a problem in susceptible cereal cultivars with a tall-stemmed, weak-strawed growing habit and in lodging-resistant cereal cultivars when they are grown under high-nitrogen, high-moisture regimes. Plant growth regulators (PGR's) are chemical growth retardants that offer a method of lodging control. For the susceptible cultivars that are not amenable to genetic shortening through plant breeding, PGR's accomplish on a seasonal basis what has not been possible through gene manipulation. For cultivars that become susceptible in the high-intensive systems of modern agriculture, PGR's can be integrated into the chemical regime to control the lodging-promoting conditions created by yield-promotion practices. Morex spring barley is a lodging-susceptible cultivar that is tall-stemmed and weak-strawed. This growth habit aggravates the lodging problem when Morex is grown under intensive yield-promoting conditions. In greenhouse and field experiments, chemical control of the Morex lodging tendency was tested with an experimental chemical, Paclobutrazol. Paclobutrazol acts on the endogenous gibberellin hormone system in the plant by inhibiting its synthesis. The chemical's effect on the cereal plant is reported to occur in the internodes which Paclobutrazol shortens by decreasing longitudinal growth and strengthens by increasing transverse growth. Lodging control is realized through height reduction which lessens the torque effect created by the weather conditions that actually cause the event of lodging to occur. Paclobutrazol caused significant shortening of the basal internodes in the greenhouse and field experiments. Uncharacteristic of the expected effect, the PGR did not strengthen the shortened internodes. Specific stem weight and breaking strength values for the treated plants were significantly lower than the corresponding control values. In the field, Paclobutrazol delayed lodging until after the critical lodging period that occurs from approximately 15 days before anthesis to 15 days after anthesis. Lodging control was reflected in yield increases. Treated plots yielded significantly higher than did the control plots. The two high treatments of 800 and 1000 g/ha also yielded significantly higher than did the low treatments of 400 and 600 g/ha. Yield increases in the treated plots can be attributed to improved seed filling given the fact that lodging in the control plots occurred during the period when yield losses are caused by poor seed development. Unfortunately, the data did not give any clear indication of other possible sources of yield enhancement. Beneficial effects of Paclobutrazol on the tillering and inflorescence development that several researchers have reported for the PGR, Chlormequat, were not evident. The experiments showed that Paclobutrazol is effective on Morex spring barley as a chemical lodging control agent and yield enhancer. A clear association of reduced height with lodging control and concomitantly with yield increases was shown by the data. The absence of improved stem strength raised questions concerning the mechanism of Paclobutrazol's effect on the barley species and the possible mechanism of its effect in combination with nitrogen fertility. Title: Lodging control and yield enhancement in Morex spring barley with paclobutrazol treatment Author: Morrison, Laura A. Lodging in cereals can cause significant decreases in yield. It is both a problem in susceptible cereal cultivars with a tall-stemmed, weak-strawed growing habit and in lodging-resistant cereal cultivars when they are grown under high-nitrogen, high-moisture regimes. Plant growth regulators (PGR's) are chemical growth retardants that offer a method of lodging control. For the susceptible cultivars that are not amenable to genetic shortening through plant breeding, PGR's accomplish on a seasonal basis what has not been possible through gene manipulation. For cultivars that become susceptible in the high-intensive systems of modern agriculture, PGR's can be integrated into the chemical regime to control the lodging-promoting conditions created by yield-promotion practices. Morex spring barley is a lodging-susceptible cultivar that is tall-stemmed and weak-strawed. This growth habit aggravates the lodging problem when Morex is grown under intensive yield-promoting conditions. In greenhouse and field experiments, chemical control of the Morex lodging tendency was tested with an experimental chemical, Paclobutrazol. Paclobutrazol acts on the endogenous gibberellin hormone system in the plant by inhibiting its synthesis. The chemical's effect on the cereal plant is reported to occur in the internodes which Paclobutrazol shortens by decreasing longitudinal growth and strengthens by increasing transverse growth. Lodging control is realized through height reduction which lessens the torque effect created by the weather conditions that actually cause the event of lodging to occur. Paclobutrazol caused significant shortening of the basal internodes in the greenhouse and field experiments. Uncharacteristic of the expected effect, the PGR did not strengthen the shortened internodes. Specific stem weight and breaking strength values for the treated plants were significantly lower than the corresponding control values. In the field, Paclobutrazol delayed lodging until after the critical lodging period that occurs from approximately 15 days before anthesis to 15 days after anthesis. Lodging control was reflected in yield increases. Treated plots yielded significantly higher than did the control plots. The two high treatments of 800 and 1000 g/ha also yielded significantly higher than did the low treatments of 400 and 600 g/ha. Yield increases in the treated plots can be attributed to improved seed filling given the fact that lodging in the control plots occurred during the period when yield losses are caused by poor seed development. Unfortunately, the data did not give any clear indication of other possible sources of yield enhancement. Beneficial effects of Paclobutrazol on the tillering and inflorescence development that several researchers have reported for the PGR, Chlormequat, were not evident. The experiments showed that Paclobutrazol is effective on Morex spring barley as a chemical lodging control agent and yield enhancer. A clear association of reduced height with lodging control and concomitantly with yield increases was shown by the data. The absence of improved stem strength raised questions concerning the mechanism of Paclobutrazol's effect on the barley species and the possible mechanism of its effect in combination with nitrogen fertility. Close

• 1827. [Article] Preparation, evaluation, and use of lyophilized, concentrated dairy starter cultures in cheese and yogurt manufacture

  Cultures of Streptococcus lactis and Streptococcus cremoris were grown in sterile 11% nonfat milk (NFM) at 32 C for 17 hr with the pH maintained at 6. 3 with sodium carbonate. The cells were harvested ...

  Citation × Citation Citation Abstract Copy Title: Preparation, evaluation, and use of lyophilized, concentrated dairy starter cultures in cheese and yogurt manufacture Author: Speckman, Calvin Albert Cultures of Streptococcus lactis and Streptococcus cremoris were grown in sterile 11% nonfat milk (NFM) at 32 C for 17 hr with the pH maintained at 6. 3 with sodium carbonate. The cells were harvested and resuspended in a medium of 5% gelatin, 5% sodium citrate, 2% monosodium glutamate and 10% sucrose (GCGS) to 1/20th the original culture volume. Suspensions were then frozen in a dryice- acetone bath and lyophilized to a residual moisture of 2%. The lyophilized culture produced was approximately 1/600th the weight of a conventional culture containing the same amount of cells. Vials containing the dry concentrate were sealed under vacuum and stored at -22° and +22° for periodic examination for cell viability and acidproducing activity. Rehydration was accomplished by the addition of a sterile solution of 20% lactose containing 1% protein hydrolysate (rehydration medium RM) which permitted maximum activity of the culture. Culture activity was assayed by simulating Cottage cheese and Cheddar cheese making procedures and measuring the final pH obtained. Appropriate dilutions of the lyophilized concentrate were made so a comparison could be made on a per cell basis with an actively-growing conventional culture. The final pH obtained for S. lactis C10 was 5.3 for both the dry and the conventional culture; this activity resulted in a period of 5 1/4 hr from milk inoculation to milling in Cheddar cheese making. Several cultures maintained activity values similar to the conventional culture for periods of up to 3 months. Cheddar and Cottage cheese were made in 800 lb vats with lyophilized concentrates and conventional cultures with results similar to ghat projected by the activity tests. This procedure was also applied to cultures commercially available as frozen concentrates with good activity retained in the lyophilized concentrate. Modifications of the above methods required for the production of lyophilized concentrates of the yogurt starter cultures included supplementation of the growth medium with 0. 1% Tween 80, growth at 37 C for 14 hr, and the use of 6% malt extract as a cryoprotective agent. With these modifications and proper culture strain selection, approximately 10% survival was observed with Lactobacillus bulgaricus and 25% for Streptococcus thermophilus. Low (30 C for 16 hr) and high temperature (42 C for 5.5 hr) yogurt manufacturing conditions were simulated for evaluation of culture activity. The activity test consisted of inoculating 100 ml of steamed (30 min) 13% NFM with equal volumes (0.25 ml of culture dried from 2. 0 -ml volume and rehydrated in 10.0 ml RM) of L. bulgaricus and S. thermophilus and measuring the final pH attained after 5.5 or 16 hr at the appropriate temperature. Lyophilized concentrates provided pH values almost as low (4. 4 to 4. 7) as those achieved with conventional yogurt cultures (4.4 to 4. 6), and required only an additional 15 to 30 min of manufacturing time. Lyophilized concentrates of flavor-producing cultures which included S. diacetilactis, Leuconostoc and Propioniibacterium retained a high level of viability (90 to 100%) with GCGS as the suspending medium. The Propioniibacterium could be grown either in milk or non-milk media without reduction of viability while Leuconostoc and S. diacetilactis required growth in milk, which in case of S. diacetilactis had to be supplemented with yeast extract. All lyophilized cultures had reduced viability when vacuum was lost during storage indicating a deleterious effect of oxygen. Rehydration medium was important in the reduction of osmoticallyinduced cell injury during rehydration and to provide peptides for required nitrogen metabolism. The cryoprotective requirements were not the same for all species studied and varied within strains. Title: Preparation, evaluation, and use of lyophilized, concentrated dairy starter cultures in cheese and yogurt manufacture Author: Speckman, Calvin Albert Cultures of Streptococcus lactis and Streptococcus cremoris were grown in sterile 11% nonfat milk (NFM) at 32 C for 17 hr with the pH maintained at 6. 3 with sodium carbonate. The cells were harvested and resuspended in a medium of 5% gelatin, 5% sodium citrate, 2% monosodium glutamate and 10% sucrose (GCGS) to 1/20th the original culture volume. Suspensions were then frozen in a dryice- acetone bath and lyophilized to a residual moisture of 2%. The lyophilized culture produced was approximately 1/600th the weight of a conventional culture containing the same amount of cells. Vials containing the dry concentrate were sealed under vacuum and stored at -22° and +22° for periodic examination for cell viability and acidproducing activity. Rehydration was accomplished by the addition of a sterile solution of 20% lactose containing 1% protein hydrolysate (rehydration medium RM) which permitted maximum activity of the culture. Culture activity was assayed by simulating Cottage cheese and Cheddar cheese making procedures and measuring the final pH obtained. Appropriate dilutions of the lyophilized concentrate were made so a comparison could be made on a per cell basis with an actively-growing conventional culture. The final pH obtained for S. lactis C10 was 5.3 for both the dry and the conventional culture; this activity resulted in a period of 5 1/4 hr from milk inoculation to milling in Cheddar cheese making. Several cultures maintained activity values similar to the conventional culture for periods of up to 3 months. Cheddar and Cottage cheese were made in 800 lb vats with lyophilized concentrates and conventional cultures with results similar to ghat projected by the activity tests. This procedure was also applied to cultures commercially available as frozen concentrates with good activity retained in the lyophilized concentrate. Modifications of the above methods required for the production of lyophilized concentrates of the yogurt starter cultures included supplementation of the growth medium with 0. 1% Tween 80, growth at 37 C for 14 hr, and the use of 6% malt extract as a cryoprotective agent. With these modifications and proper culture strain selection, approximately 10% survival was observed with Lactobacillus bulgaricus and 25% for Streptococcus thermophilus. Low (30 C for 16 hr) and high temperature (42 C for 5.5 hr) yogurt manufacturing conditions were simulated for evaluation of culture activity. The activity test consisted of inoculating 100 ml of steamed (30 min) 13% NFM with equal volumes (0.25 ml of culture dried from 2. 0 -ml volume and rehydrated in 10.0 ml RM) of L. bulgaricus and S. thermophilus and measuring the final pH attained after 5.5 or 16 hr at the appropriate temperature. Lyophilized concentrates provided pH values almost as low (4. 4 to 4. 7) as those achieved with conventional yogurt cultures (4.4 to 4. 6), and required only an additional 15 to 30 min of manufacturing time. Lyophilized concentrates of flavor-producing cultures which included S. diacetilactis, Leuconostoc and Propioniibacterium retained a high level of viability (90 to 100%) with GCGS as the suspending medium. The Propioniibacterium could be grown either in milk or non-milk media without reduction of viability while Leuconostoc and S. diacetilactis required growth in milk, which in case of S. diacetilactis had to be supplemented with yeast extract. All lyophilized cultures had reduced viability when vacuum was lost during storage indicating a deleterious effect of oxygen. Rehydration medium was important in the reduction of osmoticallyinduced cell injury during rehydration and to provide peptides for required nitrogen metabolism. The cryoprotective requirements were not the same for all species studied and varied within strains. Close

• 1828. [Article] Influence of post-harvest management practices on plant growth and seed yield of cool season grasses

  Field and controlled environment chamber studies were carried out to evaluate modes of action of post-harvest treatments on the development and seed yield of cool season grasses. Red fescue (Festuca rubra L.) ...

  Citation × Citation Citation Abstract Copy Title: Influence of post-harvest management practices on plant growth and seed yield of cool season grasses Author: Stanwood, Phillip Charles Field and controlled environment chamber studies were carried out to evaluate modes of action of post-harvest treatments on the development and seed yield of cool season grasses. Red fescue (Festuca rubra L.) was used as the primary test species. There was no difference in total biomass production of red fescue as influenced by either burning or mechanical removal of post-harvest residue. Burning did cause a shift in biomass distribution resulting in a 168% increase in seed yield. Variation in the number of fertile tillers per unit area accounted for 69% of the seed yield variation. Burned plots produced 582 fertile tillers m⁻² while mechanically removed plots produced 392 fertile tillers m⁻². Statistical analysis indicated that most of the differences in seed yield due to treatment were accounted for by the number of fertile tillers per unit area. Mechanical removal of residue resulted in the development of one axillary tiller per 10 primary tillers of red fescue by December. Burning significantly increased the rate of 16 axillary tillers per 10 primary tillers by the same date. This clearly suggests an increased availability of substrates for fall plant development. This in turn may have contributed to a greater number of fertile tillers in the spring. The overall effect was higher seed yield. Linn perennial ryegrass (Lolium perenne), Merion bluegrass (Poa pratensis), Highland bentgrass (Agrostis tenuis), and Alta tall fescue (Festuca arundinacea) all showed a significant increase in the number of axillary tillers developed by November as a result of burning postharvest residue as opposed to mechanical removal. Light energy received by the individual tiller appears to be a major factor influencing early tiller development in red fescue. This factor can be strongly influenced by tiller density. Controlled environment studies suggest that at a tiller (seedling) density of 2 per 100 cm², 47 axillary tillers per 10 primary tillers are produced. When the density is increased to 100 per 100 cm², only 8 axillary tillers per 10 primary tillers are produced. Parallel experiments with light energy showed that at 1800 μwatts cm⁻² and 2 seedlings per 100 cm², 48 axillary tillers were produced per 10 primary tillers. At 900 μwatts cm⁻² under the same conditions only 25 axillary tillers per 10 primary tillers were produced. A reduction in the day temperature from 19 C to 9 C and night temperature from 14 C to 6 C did not affect this light energy-axillary tiller production relationship. Title: Influence of post-harvest management practices on plant growth and seed yield of cool season grasses Author: Stanwood, Phillip Charles Field and controlled environment chamber studies were carried out to evaluate modes of action of post-harvest treatments on the development and seed yield of cool season grasses. Red fescue (Festuca rubra L.) was used as the primary test species. There was no difference in total biomass production of red fescue as influenced by either burning or mechanical removal of post-harvest residue. Burning did cause a shift in biomass distribution resulting in a 168% increase in seed yield. Variation in the number of fertile tillers per unit area accounted for 69% of the seed yield variation. Burned plots produced 582 fertile tillers m⁻² while mechanically removed plots produced 392 fertile tillers m⁻². Statistical analysis indicated that most of the differences in seed yield due to treatment were accounted for by the number of fertile tillers per unit area. Mechanical removal of residue resulted in the development of one axillary tiller per 10 primary tillers of red fescue by December. Burning significantly increased the rate of 16 axillary tillers per 10 primary tillers by the same date. This clearly suggests an increased availability of substrates for fall plant development. This in turn may have contributed to a greater number of fertile tillers in the spring. The overall effect was higher seed yield. Linn perennial ryegrass (Lolium perenne), Merion bluegrass (Poa pratensis), Highland bentgrass (Agrostis tenuis), and Alta tall fescue (Festuca arundinacea) all showed a significant increase in the number of axillary tillers developed by November as a result of burning postharvest residue as opposed to mechanical removal. Light energy received by the individual tiller appears to be a major factor influencing early tiller development in red fescue. This factor can be strongly influenced by tiller density. Controlled environment studies suggest that at a tiller (seedling) density of 2 per 100 cm², 47 axillary tillers per 10 primary tillers are produced. When the density is increased to 100 per 100 cm², only 8 axillary tillers per 10 primary tillers are produced. Parallel experiments with light energy showed that at 1800 μwatts cm⁻² and 2 seedlings per 100 cm², 48 axillary tillers were produced per 10 primary tillers. At 900 μwatts cm⁻² under the same conditions only 25 axillary tillers per 10 primary tillers were produced. A reduction in the day temperature from 19 C to 9 C and night temperature from 14 C to 6 C did not affect this light energy-axillary tiller production relationship. Close

• 1829. [Article] Development and application of a resource selection model for pygmy rabbits

  Pygmy rabbits (Brachylagus idahoensis) in Oregon and Washington are a sagebrush (Artemisia tridentata spp.) obligate species of concern because of declining populations and extirpation from much of their ...

  Citation × Citation Citation Abstract Copy Title: Development and application of a resource selection model for pygmy rabbits Author: Meisel, Jennifer K. Pygmy rabbits (Brachylagus idahoensis) in Oregon and Washington are a sagebrush (Artemisia tridentata spp.) obligate species of concern because of declining populations and extirpation from much of their range. Efforts are underway to establish a captive bred population of the Columbia Basin pygmy rabbit in Washington state for reintroduction into the wild. We developed a resource selection model based on soil and vegetation characteristics of occupied pygmy rabbit habitat at Hart Mountain National Antelope Refuge in Oregon. Data collected in Oregon were used to quantify relationships of pygmy rabbits with their habitat. Using logistic regression and Akaike’s Information Criterion (AICc) to identify the best model, we determined that big sagebrush height and soil percent sand content were the two habitat characteristics most predictive of occupied pygmy rabbit burrow locations. The model indicated that the odds ratio of an occupied pygmy rabbit burrow occurrence increased with an increase in percent sand content of soils and big sagebrush height. We then applied the resource selection model using a two-step approach. We first used a Geographic Information System (GIS) to determine broad scale areas of suitable habitat for the potential reintroduction of pygmy rabbits at Hanford Reach National Monument in Washington, and then collected data on the ground to determine the best suitable habitat. Using GIS procedures, we found approximately 8500 ha of potential habitat at Hanford Reach National Monument. Field data collected within the potential habitat were used to further define 3035 ha as the most suitable habitat for pygmy rabbits. Lands that currently support pygmy rabbits, or areas identified as potential habitat in Washington, can be used to prioritize management or restoration efforts for pygmy rabbits and their habitats. Title: Development and application of a resource selection model for pygmy rabbits Author: Meisel, Jennifer K. Pygmy rabbits (Brachylagus idahoensis) in Oregon and Washington are a sagebrush (Artemisia tridentata spp.) obligate species of concern because of declining populations and extirpation from much of their range. Efforts are underway to establish a captive bred population of the Columbia Basin pygmy rabbit in Washington state for reintroduction into the wild. We developed a resource selection model based on soil and vegetation characteristics of occupied pygmy rabbit habitat at Hart Mountain National Antelope Refuge in Oregon. Data collected in Oregon were used to quantify relationships of pygmy rabbits with their habitat. Using logistic regression and Akaike’s Information Criterion (AICc) to identify the best model, we determined that big sagebrush height and soil percent sand content were the two habitat characteristics most predictive of occupied pygmy rabbit burrow locations. The model indicated that the odds ratio of an occupied pygmy rabbit burrow occurrence increased with an increase in percent sand content of soils and big sagebrush height. We then applied the resource selection model using a two-step approach. We first used a Geographic Information System (GIS) to determine broad scale areas of suitable habitat for the potential reintroduction of pygmy rabbits at Hanford Reach National Monument in Washington, and then collected data on the ground to determine the best suitable habitat. Using GIS procedures, we found approximately 8500 ha of potential habitat at Hanford Reach National Monument. Field data collected within the potential habitat were used to further define 3035 ha as the most suitable habitat for pygmy rabbits. Lands that currently support pygmy rabbits, or areas identified as potential habitat in Washington, can be used to prioritize management or restoration efforts for pygmy rabbits and their habitats. Close

• 1830. [Article] The significance of glutathione conjugation for aflatoxin B₁ metabolism in rainbow trout and coho salmon

  In rodent models as well as in fish models there are significant species differences in the susceptibility toward aflatoxin B₁ (AFB₁) carcinogenesis. Mouse is less susceptible toward AFB₁ carcinogenesis than ...

  Citation × Citation Citation Abstract Copy Title: The significance of glutathione conjugation for aflatoxin B₁ metabolism in rainbow trout and coho salmon Author: Valsta, Liisa M. In rodent models as well as in fish models there are significant species differences in the susceptibility toward aflatoxin B₁ (AFB₁) carcinogenesis. Mouse is less susceptible toward AFB₁ carcinogenesis than rat. Researchers have come to the conclusion that the lower susceptibility of mice is not a result of less effective activation of AFB₁, but rather of more effective inactivation of the toxic intermediate AFB₁-2,3-epoxide, and especially inactivation through the glutathione (GSH) conjugation of the epoxide. Rainbow trout fed Oregon Test Diet are more sensitive toward AFB₁ hepatocarcinogenesis than coho salmon, or, than trout fed the inhibitors β-naphthoflavone (BNF), 1ndole-3-carbinol (I3C), or Aroclor 1254 (PCB). This study examined the role of AFB1-glutathione (AFB₁-SG) conjugation In these differences. A tritiated AFB₁-glutathione conjugate standard (³H-AFB₁-S6) was produced in vitro using mouse liver S-9 fraction as a source of GSH transferase. It was purified by reverse phase HPLC, and its structure verified by amino acid analysis and mass spectrometry. Coho salmon and rainbow trout fed the various diets were injected i.p. with ³H-AFB₁ (49μCi, 50 μg/ kg fish); bile, liver and kidney were collected at 24 h. Recovery of total aflatoxin radioactivity was determined for all three tissues, and the hepatic AFB₁-DNA binding was also determined. Bile metabolites were quantitated by reverse phase HPLC using the mouse ³H-AFB₁-SG as a standard. The resistance of coho salmon toward AFB₁ carcinogenicity was supported by a 20-fold lower hepatic AFB₁-DNA binding compared to control trout. AFB₁-SG was detected in bile only in control, BNF, and I3C fed trout, at < 1% of total recovered metabolites, and at < 0.2% of the original dose, being highest in control trout. The major conjugates were glucuronides of aflatoxicol (AFL) and aflatoxicol-M₁ (AFL-M₁) (80-902 of the total recovered metabolites). In vitro metabolism studies using isolated liver cell fractions supported the in vivo metabolism results. Less than 0.531 of the original AFB₁ dose was converted to AFB₁-SG conjugate in salmon and trout samples. In contrast, with isolated mouse liver cell fractions approximately 25% of the original AFB₁ dose was conjugated with GSH. The GSH concentration of control trout liver was 2.9 mmol/ kg. Coho salmon had GSH concentration 70% of that found in control trout. In BNF pre-fed trout liver GSH concentration was enhanced by 25% compared to controls. Liver GSH transferase activity using l-chloro-2,4- dlnitrobenzene as substrate was 1.15 μmol/min/mg protein in control trout. This enzyme activity In salmon was only 26% of that found in control trout. A 62% elevation In GSH transferase activity compared to controls was detected in trout fed BNF diet. There is no apparent correlation between liver GSH or GSH transferase activities among the various groups, and their relative sensitivities to AFB₁ carcinogenesis. This study indicates that AFB₁-SG conjugation is not a significant pathway in salmon and trout fed control diets, or trout fed various inhibitors, and cannot account for the variation In AFB₁ sensitivity. Title: The significance of glutathione conjugation for aflatoxin B₁ metabolism in rainbow trout and coho salmon Author: Valsta, Liisa M. In rodent models as well as in fish models there are significant species differences in the susceptibility toward aflatoxin B₁ (AFB₁) carcinogenesis. Mouse is less susceptible toward AFB₁ carcinogenesis than rat. Researchers have come to the conclusion that the lower susceptibility of mice is not a result of less effective activation of AFB₁, but rather of more effective inactivation of the toxic intermediate AFB₁-2,3-epoxide, and especially inactivation through the glutathione (GSH) conjugation of the epoxide. Rainbow trout fed Oregon Test Diet are more sensitive toward AFB₁ hepatocarcinogenesis than coho salmon, or, than trout fed the inhibitors β-naphthoflavone (BNF), 1ndole-3-carbinol (I3C), or Aroclor 1254 (PCB). This study examined the role of AFB1-glutathione (AFB₁-SG) conjugation In these differences. A tritiated AFB₁-glutathione conjugate standard (³H-AFB₁-S6) was produced in vitro using mouse liver S-9 fraction as a source of GSH transferase. It was purified by reverse phase HPLC, and its structure verified by amino acid analysis and mass spectrometry. Coho salmon and rainbow trout fed the various diets were injected i.p. with ³H-AFB₁ (49μCi, 50 μg/ kg fish); bile, liver and kidney were collected at 24 h. Recovery of total aflatoxin radioactivity was determined for all three tissues, and the hepatic AFB₁-DNA binding was also determined. Bile metabolites were quantitated by reverse phase HPLC using the mouse ³H-AFB₁-SG as a standard. The resistance of coho salmon toward AFB₁ carcinogenicity was supported by a 20-fold lower hepatic AFB₁-DNA binding compared to control trout. AFB₁-SG was detected in bile only in control, BNF, and I3C fed trout, at < 1% of total recovered metabolites, and at < 0.2% of the original dose, being highest in control trout. The major conjugates were glucuronides of aflatoxicol (AFL) and aflatoxicol-M₁ (AFL-M₁) (80-902 of the total recovered metabolites). In vitro metabolism studies using isolated liver cell fractions supported the in vivo metabolism results. Less than 0.531 of the original AFB₁ dose was converted to AFB₁-SG conjugate in salmon and trout samples. In contrast, with isolated mouse liver cell fractions approximately 25% of the original AFB₁ dose was conjugated with GSH. The GSH concentration of control trout liver was 2.9 mmol/ kg. Coho salmon had GSH concentration 70% of that found in control trout. In BNF pre-fed trout liver GSH concentration was enhanced by 25% compared to controls. Liver GSH transferase activity using l-chloro-2,4- dlnitrobenzene as substrate was 1.15 μmol/min/mg protein in control trout. This enzyme activity In salmon was only 26% of that found in control trout. A 62% elevation In GSH transferase activity compared to controls was detected in trout fed BNF diet. There is no apparent correlation between liver GSH or GSH transferase activities among the various groups, and their relative sensitivities to AFB₁ carcinogenesis. This study indicates that AFB₁-SG conjugation is not a significant pathway in salmon and trout fed control diets, or trout fed various inhibitors, and cannot account for the variation In AFB₁ sensitivity. Close

• 1831. [Article] Influence of abiotic and biotic factors on developmental parameters of Drosophila suzukii (Diptera: Drosophilidae)

  Drosophila suzukii (Diptera: Drosophilidae), a pest of thin-skinned fruits, has been detected worldwide recently, with new locations of establishment determined annually since it first became a concern ...

  Citation × Citation Citation Abstract Copy Title: Influence of abiotic and biotic factors on developmental parameters of Drosophila suzukii (Diptera: Drosophilidae) Author: Tochen, Samantha Drosophila suzukii (Diptera: Drosophilidae), a pest of thin-skinned fruits, has been detected worldwide recently, with new locations of establishment determined annually since it first became a concern on continental North America in 2008. Drosophila suzukii females are different from most other drosophilids as being one of two known species capable of economic injury in fruit. This is achieved via a serrated ovipositor that pierces the skin of ripening susceptible fruit, depositing eggs that will then hatch into larvae, utilizing the fruit as a food source. Current control methods involve the application of pesticides on a weekly basis upon the coloring of fruit, ending when harvest is complete. To shift back towards IPM, knowledge of D. suzukii development under different environmental factors is necessary to improve upon current management options. The first objective of this research project was to determine the developmental period, longevity, and fecundity of D. suzukii when exposed to seven constant temperatures and separately, five constant relative humidities (RHs) at 22 ± 2 ºC. Temperature had an influence on these parameters, with decreasing developmental periods as temperatures increased from 10 to 28ºC. Developmental period increased above 28ºC. The highest net reproductive rate and intrinsic rate of population increase was 22 ºC. Estimations using linear and nonlinear fit for the minimum, optimal and maximum were 7.2, 28.1, and 42.1 ºC, respectively. The minimal, optimal, and maximal temperatures for intrinsic rate of population increase were 13.4, 21.0, and 29.0 ºC . Relative humidity also had a significant influence on these parameters. The estimated minimum, optimal and maximum development thresholds for RH were 27, 79, and 100% RH, respectively. Fecundity appeared to increase with RH, with a maximum observed at 93%, however ovary dissections indicated that no differences in ovary maturation occurred between 78 and 93% RH. The second objective of this research was conducted to determine the effect of floral resource feeding on nutrient levels in female D. suzukii when provided cherry or blueberry blossoms as well as lifespan over an observed feeding period. When adults were provided cherry blossoms, they had significantly longer lifespans than their water-fed counterparts over a 41-day observation period. Adults provided blueberry blossoms exhibited longer lifespans, however, this observation could not be statistically compared with the cherry and water treatments due to availability of blossoms and a staggered start date. A nutritional assay showed higher levels of glycogen and sugar levels amongst female flies provided either blossom type or sucrose over water-fed flies. Lipid levels tended to be the same across treatments. Overall, this research discovered new information about D. suzukii biology that can be incorporated into future management strategies. The temperature-related development and fecundity study contributed to the development of a population prediction model. The humidity work will be incorporated into the D. suzukii model to refine estimates across different locations. The model will provide a tool for growers to determine management timing. The nutritional work may aide in the development of a bait spray and timing of bait spray application. Title: Influence of abiotic and biotic factors on developmental parameters of Drosophila suzukii (Diptera: Drosophilidae) Author: Tochen, Samantha Drosophila suzukii (Diptera: Drosophilidae), a pest of thin-skinned fruits, has been detected worldwide recently, with new locations of establishment determined annually since it first became a concern on continental North America in 2008. Drosophila suzukii females are different from most other drosophilids as being one of two known species capable of economic injury in fruit. This is achieved via a serrated ovipositor that pierces the skin of ripening susceptible fruit, depositing eggs that will then hatch into larvae, utilizing the fruit as a food source. Current control methods involve the application of pesticides on a weekly basis upon the coloring of fruit, ending when harvest is complete. To shift back towards IPM, knowledge of D. suzukii development under different environmental factors is necessary to improve upon current management options. The first objective of this research project was to determine the developmental period, longevity, and fecundity of D. suzukii when exposed to seven constant temperatures and separately, five constant relative humidities (RHs) at 22 ± 2 ºC. Temperature had an influence on these parameters, with decreasing developmental periods as temperatures increased from 10 to 28ºC. Developmental period increased above 28ºC. The highest net reproductive rate and intrinsic rate of population increase was 22 ºC. Estimations using linear and nonlinear fit for the minimum, optimal and maximum were 7.2, 28.1, and 42.1 ºC, respectively. The minimal, optimal, and maximal temperatures for intrinsic rate of population increase were 13.4, 21.0, and 29.0 ºC . Relative humidity also had a significant influence on these parameters. The estimated minimum, optimal and maximum development thresholds for RH were 27, 79, and 100% RH, respectively. Fecundity appeared to increase with RH, with a maximum observed at 93%, however ovary dissections indicated that no differences in ovary maturation occurred between 78 and 93% RH. The second objective of this research was conducted to determine the effect of floral resource feeding on nutrient levels in female D. suzukii when provided cherry or blueberry blossoms as well as lifespan over an observed feeding period. When adults were provided cherry blossoms, they had significantly longer lifespans than their water-fed counterparts over a 41-day observation period. Adults provided blueberry blossoms exhibited longer lifespans, however, this observation could not be statistically compared with the cherry and water treatments due to availability of blossoms and a staggered start date. A nutritional assay showed higher levels of glycogen and sugar levels amongst female flies provided either blossom type or sucrose over water-fed flies. Lipid levels tended to be the same across treatments. Overall, this research discovered new information about D. suzukii biology that can be incorporated into future management strategies. The temperature-related development and fecundity study contributed to the development of a population prediction model. The humidity work will be incorporated into the D. suzukii model to refine estimates across different locations. The model will provide a tool for growers to determine management timing. The nutritional work may aide in the development of a bait spray and timing of bait spray application. Close

• 1832. [Article] Nesting season ecology of marbled murrelets at a remote mainland fjord in southeast Alaska

  This thesis focuses on the nesting ecology and marine space use of Marbled Murrelets (Brachyramphus marmoratus) during the 2007 and 2008 nesting seasons in and around Port Snettisham, a remote mainland ...

  Citation × Citation Citation Abstract Copy Title: Nesting season ecology of marbled murrelets at a remote mainland fjord in southeast Alaska Author: Barbaree, Blake A. This thesis focuses on the nesting ecology and marine space use of Marbled Murrelets (Brachyramphus marmoratus) during the 2007 and 2008 nesting seasons in and around Port Snettisham, a remote mainland fjord in Southeast Alaska. Marbled Murrelets (murrelets) are a declining species throughout most of their range, and their conservation is a challenging endeavor because they rely on relatively large expanses of terrestrial habitat for nesting and marine habitat for food. Murrelets are especially difficult to study because they place their nests at variable and often considerable distance from the sea in largely inaccessible locations; consequently, we know relatively little about their breeding ecology and overall life history compared to other seabirds. I used radio-telemetry to gather data on reproduction, behavior, and at-sea locations of murrelets. Herein, I describe individual and population-level marine space use, identify nesting habitat, estimate reproductive success, and characterize patterns of nest visits. Mean marine home range size for adult murrelets was significantly larger in 2008 (158.6 ± 103.7 km²) than 2007 (97.8 ± 59.4 km²), suggesting that foraging conditions were relatively poor in 2008. Similarly, mean commuting distance from at-sea location to nest sites was significantly longer in 2008 (20.0 ± 2.0 km) than 2007 (12.0 ± 0.9 km), and murrelets nesting further from the coast likely reduced their foraging ranges in 2008. Central foraging hot spots were identified throughout Port Snettisham and near Holkham Bay and Tracy Arm to the south. Boundaries of these hot spots can be used to guide management of commercial fishing and tourism, and designation of marine protected areas. I located 33 active nests in mostly inaccessible sites within forest and non-forest habitat, including visually confirmed nest sites on the branches of large conifer trees and on ledges of steep cliffs near water (e.g., waterfall, lake, river, or glacier). Widespread use of rock cliff and subalpine nesting habitats (≥ 48.5% of located nests) indicated that nesting habitat models in Southeast Alaska should include these types of habitats. Nests were located further inland (range 1.0 - 52.0 km) and at higher elevations (range 42 - 1100 m) than previously documented in Alaska, including two nest sites > 15 km east of the USA/Canada border in British Columbia, Canada. The nesting season was ca. 113 days long (25 May - 16 September), and four late-season re-nesting attempts were documented. Apparent fledge success, derived by inference from behavior of radio-tagged adults, was 17.6% (n = 6 of 34). The low reproductive success at Port Snettisham was similar to estimates from south of Alaska, and unexpected because the area has relatively high densities of murrelets and seemingly ideal conditions for nesting. This information is noteworthy to future conservation planning because it provides evidence that murrelet reproduction may be low even when conditions for nesting are relatively good. Despite an adaptation to high adult survival, murrelet populations cannot sustain themselves with similarly low levels of reproduction. Based on my results future research should focus on monitoring regional population trends, identifying causes of nest failure, estimating adult survival rates, and identifying sources of adult mortality. Title: Nesting season ecology of marbled murrelets at a remote mainland fjord in southeast Alaska Author: Barbaree, Blake A. This thesis focuses on the nesting ecology and marine space use of Marbled Murrelets (Brachyramphus marmoratus) during the 2007 and 2008 nesting seasons in and around Port Snettisham, a remote mainland fjord in Southeast Alaska. Marbled Murrelets (murrelets) are a declining species throughout most of their range, and their conservation is a challenging endeavor because they rely on relatively large expanses of terrestrial habitat for nesting and marine habitat for food. Murrelets are especially difficult to study because they place their nests at variable and often considerable distance from the sea in largely inaccessible locations; consequently, we know relatively little about their breeding ecology and overall life history compared to other seabirds. I used radio-telemetry to gather data on reproduction, behavior, and at-sea locations of murrelets. Herein, I describe individual and population-level marine space use, identify nesting habitat, estimate reproductive success, and characterize patterns of nest visits. Mean marine home range size for adult murrelets was significantly larger in 2008 (158.6 ± 103.7 km²) than 2007 (97.8 ± 59.4 km²), suggesting that foraging conditions were relatively poor in 2008. Similarly, mean commuting distance from at-sea location to nest sites was significantly longer in 2008 (20.0 ± 2.0 km) than 2007 (12.0 ± 0.9 km), and murrelets nesting further from the coast likely reduced their foraging ranges in 2008. Central foraging hot spots were identified throughout Port Snettisham and near Holkham Bay and Tracy Arm to the south. Boundaries of these hot spots can be used to guide management of commercial fishing and tourism, and designation of marine protected areas. I located 33 active nests in mostly inaccessible sites within forest and non-forest habitat, including visually confirmed nest sites on the branches of large conifer trees and on ledges of steep cliffs near water (e.g., waterfall, lake, river, or glacier). Widespread use of rock cliff and subalpine nesting habitats (≥ 48.5% of located nests) indicated that nesting habitat models in Southeast Alaska should include these types of habitats. Nests were located further inland (range 1.0 - 52.0 km) and at higher elevations (range 42 - 1100 m) than previously documented in Alaska, including two nest sites > 15 km east of the USA/Canada border in British Columbia, Canada. The nesting season was ca. 113 days long (25 May - 16 September), and four late-season re-nesting attempts were documented. Apparent fledge success, derived by inference from behavior of radio-tagged adults, was 17.6% (n = 6 of 34). The low reproductive success at Port Snettisham was similar to estimates from south of Alaska, and unexpected because the area has relatively high densities of murrelets and seemingly ideal conditions for nesting. This information is noteworthy to future conservation planning because it provides evidence that murrelet reproduction may be low even when conditions for nesting are relatively good. Despite an adaptation to high adult survival, murrelet populations cannot sustain themselves with similarly low levels of reproduction. Based on my results future research should focus on monitoring regional population trends, identifying causes of nest failure, estimating adult survival rates, and identifying sources of adult mortality. Close

• 1833. [Article] Forest Successional and Disturbance Dynamics in the Southern Blue Mountains of Eastern Oregon

  The application of modern land management practices beginning at the turn of the 20th century is widely believed to have dramatically transformed forest landscapes of the inland Pacific Northwest. Restoring ...

  Citation × Citation Citation Abstract Copy Title: Forest Successional and Disturbance Dynamics in the Southern Blue Mountains of Eastern Oregon Author: Johnston, James D. (James Daniel) The application of modern land management practices beginning at the turn of the 20th century is widely believed to have dramatically transformed forest landscapes of the inland Pacific Northwest. Restoring historical conditions to make forests resilient to future climate and disturbance regimes is a major goal of federal forest managers. However, information about historical relationships between forest structure, forest composition, topography, climate, and disturbance sufficient to parameterize managers' decision-making is often lacking. This study uses dendroecological methods to reconstruct historical (1650-1900 CE) forest structure, composition, and fire disturbance, and to describe change over time across a wide range of forest types in the southern Blue Mountains of eastern Oregon. Results indicate that both fire frequency and climate controls on fire occurrence were similar across a broad range of forest types. Southern Blue Mountains forests are markedly different with respect to inherent site productivity and species composition, but frequent fire tended to equalize stand densities across the landscape prior to the exclusion of fire in the late 1800s. In the absence of fire, more productive mixed conifer sites have generally experienced the same or greater successional change as drier pine dominated sites. If restoring historical conditions is a goal, treatments appropriate to restore dry ponderosa pine forests are also appropriate for moister mixed conifer forest types. Title: Forest Successional and Disturbance Dynamics in the Southern Blue Mountains of Eastern Oregon Author: Johnston, James D. (James Daniel) The application of modern land management practices beginning at the turn of the 20th century is widely believed to have dramatically transformed forest landscapes of the inland Pacific Northwest. Restoring historical conditions to make forests resilient to future climate and disturbance regimes is a major goal of federal forest managers. However, information about historical relationships between forest structure, forest composition, topography, climate, and disturbance sufficient to parameterize managers' decision-making is often lacking. This study uses dendroecological methods to reconstruct historical (1650-1900 CE) forest structure, composition, and fire disturbance, and to describe change over time across a wide range of forest types in the southern Blue Mountains of eastern Oregon. Results indicate that both fire frequency and climate controls on fire occurrence were similar across a broad range of forest types. Southern Blue Mountains forests are markedly different with respect to inherent site productivity and species composition, but frequent fire tended to equalize stand densities across the landscape prior to the exclusion of fire in the late 1800s. In the absence of fire, more productive mixed conifer sites have generally experienced the same or greater successional change as drier pine dominated sites. If restoring historical conditions is a goal, treatments appropriate to restore dry ponderosa pine forests are also appropriate for moister mixed conifer forest types. Close

• 1834. [Article] A pharmacognostic study of the root of Heracleum mantegazzianum Somier et Levier

  A pharmacognostic study was made of the root of Heracleum mantegazzianum, an umbelliferous species which is of value as a source of natural coumarins. Three groups of seeds were tested to determine the ...

  Citation × Citation Citation Abstract Copy Title: A pharmacognostic study of the root of Heracleum mantegazzianum Somier et Levier Author: Lee, Eugene Carlton A pharmacognostic study was made of the root of Heracleum mantegazzianum, an umbelliferous species which is of value as a source of natural coumarins. Three groups of seeds were tested to determine the presence of a germination requirement for moist cold and the possible value of gibberellic acid in obviating this requirement. The first group of seeds was cold-treated for 74 days at a range of from 2 to 5°C. The second group of seeds was soaked for 20 hours in a solution containing 100 parts per million of gibberellic acid. The third group of seeds, used as controls, was soaked in water. When planted and maintained under greenhouse conditions only the cold-treated seeds germinated. The germination rate was 10.3%. Both seeds treated with gibberellic acid and the controls failed to germinate, showing that a cold requirement does exist and that treatment with gibber-ellic acid will not substitute for the cold requirement. A fourth group of seeds, cold- treated for 294 days, germinated at a rate of approximately 55%, showing that germination is proportional to total days of cold treatment. Sequential selective solvent extraction with a series of increasing polarity gave the following fractions as average percentages of dry weight: petroleum ether, 2.4; ether, anhydrous, 2.5; ether U.S.P., 2.0 alcohol 95%, 8.5; water, 19.4. Copious foaming of the aqueous fraction showed the possible presence of saponins. The description and histology of the whole root as well as the character of the powdered root was recorded. Among diagnostic characters of the powdered root are its blue coloration when moistened with iodine water, a slight yellow fluorescence under ultraviolet light turning to luminescence for several seconds following extinction of the light, and the presence of numerous clustered starch grains which gelatinize rapidly in chloral hydrate solution. Thin-layer chromatography of the ether extract of the air-dried root on Silica Gel G showed seven principal spots fluorescing under ultraviolet light. R[subscript f] values and colors corresponded to those of six standard coumarins. The following coumarins are presumed to be present: isobergapten, pimpinellin, bergapten, isopimpinellin, sphondin and umbelliferone. The seventh spot was not identified. The R[subscript f] values in two solvent systems and the fluorescent colors under ultraviolet light are reported for the extract spots as well as for six coumarins. Studies were also made to determine the relative stability of coumarins to heat. Six standard coumarins as well as the extract of the air-dried root were spotted individually on Silica Gel G plates and developed two-dimensionally. Following development in the first direction and prior to development in the second direction the plates were exposed to a temperature of 65°C. for 30 minutes in an oven. With the exception of sphondin the chromatograms of the individual coumarins showed from one to two additional spots. This indicates that coumarins as a group are subject to modification at a temperature of 65°C. Regular two-dimensional chromatography of the ether extract of the root material which had been dried at 38°C. gave spots for only five coumarins. It is concluded that the roots should be dried only at the normal air temperatures. Title: A pharmacognostic study of the root of Heracleum mantegazzianum Somier et Levier Author: Lee, Eugene Carlton A pharmacognostic study was made of the root of Heracleum mantegazzianum, an umbelliferous species which is of value as a source of natural coumarins. Three groups of seeds were tested to determine the presence of a germination requirement for moist cold and the possible value of gibberellic acid in obviating this requirement. The first group of seeds was cold-treated for 74 days at a range of from 2 to 5°C. The second group of seeds was soaked for 20 hours in a solution containing 100 parts per million of gibberellic acid. The third group of seeds, used as controls, was soaked in water. When planted and maintained under greenhouse conditions only the cold-treated seeds germinated. The germination rate was 10.3%. Both seeds treated with gibberellic acid and the controls failed to germinate, showing that a cold requirement does exist and that treatment with gibber-ellic acid will not substitute for the cold requirement. A fourth group of seeds, cold- treated for 294 days, germinated at a rate of approximately 55%, showing that germination is proportional to total days of cold treatment. Sequential selective solvent extraction with a series of increasing polarity gave the following fractions as average percentages of dry weight: petroleum ether, 2.4; ether, anhydrous, 2.5; ether U.S.P., 2.0 alcohol 95%, 8.5; water, 19.4. Copious foaming of the aqueous fraction showed the possible presence of saponins. The description and histology of the whole root as well as the character of the powdered root was recorded. Among diagnostic characters of the powdered root are its blue coloration when moistened with iodine water, a slight yellow fluorescence under ultraviolet light turning to luminescence for several seconds following extinction of the light, and the presence of numerous clustered starch grains which gelatinize rapidly in chloral hydrate solution. Thin-layer chromatography of the ether extract of the air-dried root on Silica Gel G showed seven principal spots fluorescing under ultraviolet light. R[subscript f] values and colors corresponded to those of six standard coumarins. The following coumarins are presumed to be present: isobergapten, pimpinellin, bergapten, isopimpinellin, sphondin and umbelliferone. The seventh spot was not identified. The R[subscript f] values in two solvent systems and the fluorescent colors under ultraviolet light are reported for the extract spots as well as for six coumarins. Studies were also made to determine the relative stability of coumarins to heat. Six standard coumarins as well as the extract of the air-dried root were spotted individually on Silica Gel G plates and developed two-dimensionally. Following development in the first direction and prior to development in the second direction the plates were exposed to a temperature of 65°C. for 30 minutes in an oven. With the exception of sphondin the chromatograms of the individual coumarins showed from one to two additional spots. This indicates that coumarins as a group are subject to modification at a temperature of 65°C. Regular two-dimensional chromatography of the ether extract of the root material which had been dried at 38°C. gave spots for only five coumarins. It is concluded that the roots should be dried only at the normal air temperatures. Close

• 1835. [Article] A study of the quantity and distribution of bark debris resulting from log rafting

  A study was conducted to determine the quantity and distribution of bark debris resulting from log rafting. Three distinct problems were studied: (I) the quantity of bark dislodged from the logs while ...

  Citation × Citation Citation Abstract Copy Title: A study of the quantity and distribution of bark debris resulting from log rafting Author: Williamson, Kenneth J. A study was conducted to determine the quantity and distribution of bark debris resulting from log rafting. Three distinct problems were studied: (I) the quantity of bark dislodged from the logs while being placed in the rivers and during transport in log rafts; (2) the percentage of the bark that sinks as a function of time; and (3) the amount of bark and debris in existing benthic deposits. Two major areas were studied covering both fresh and salt water: the Klamath River in South-Central Oregon and the Yaquina River estuary near Newport in Western Oregon. The logs stored in the Klamath River consisted primarily of ponderosa pine, and those in the Yaquina estuary were primarily Douglas fir. Studies by several authors listed high chemical oxygen demands and low dissolved oxygen contents in waters used for the storage of logs. Fish kills have been noted from bark deposits in lakes and streams. Photographic measurements of logs were used to determine the percentage of bark dislodged. For Douglas fir logs approximately 17 percent of the bark is dislodged during unloading and 5 percent during raft transport, for a total of 22 percent. Comparatively, the total for ponderosa pine was only 6 percent. Flotation studies showed a total of 10 percent sinkage in water within one day and 75 percent in two months, regardless of the species. The pine bark sank at a faster rate as compared to the fir bark; primarily due to the smaller size of the pine bark. Core samples were taken in areas free of log rafting, in areas of log raft storage and in areas of log dumping to determine the extent of bark debris in the benthic deposits. Samples consisting of primarily deposited bark had a volatile solids content of about 15 pounds per cubic foot. The average increase in volatile solids content in the log storage areas as compared to the control samples was approximately two pounds of volatile solids per cubic foot. For the log dumping areas this average increase ranged from 0. 5 to 15 pounds of volatile solids per cubic foot. The results of this study indicate clearly that large amounts of bark are added to the water courses used for log storage and that large amounts of bark debris presently exist in the benthic deposits of these water courses. Title: A study of the quantity and distribution of bark debris resulting from log rafting Author: Williamson, Kenneth J. A study was conducted to determine the quantity and distribution of bark debris resulting from log rafting. Three distinct problems were studied: (I) the quantity of bark dislodged from the logs while being placed in the rivers and during transport in log rafts; (2) the percentage of the bark that sinks as a function of time; and (3) the amount of bark and debris in existing benthic deposits. Two major areas were studied covering both fresh and salt water: the Klamath River in South-Central Oregon and the Yaquina River estuary near Newport in Western Oregon. The logs stored in the Klamath River consisted primarily of ponderosa pine, and those in the Yaquina estuary were primarily Douglas fir. Studies by several authors listed high chemical oxygen demands and low dissolved oxygen contents in waters used for the storage of logs. Fish kills have been noted from bark deposits in lakes and streams. Photographic measurements of logs were used to determine the percentage of bark dislodged. For Douglas fir logs approximately 17 percent of the bark is dislodged during unloading and 5 percent during raft transport, for a total of 22 percent. Comparatively, the total for ponderosa pine was only 6 percent. Flotation studies showed a total of 10 percent sinkage in water within one day and 75 percent in two months, regardless of the species. The pine bark sank at a faster rate as compared to the fir bark; primarily due to the smaller size of the pine bark. Core samples were taken in areas free of log rafting, in areas of log raft storage and in areas of log dumping to determine the extent of bark debris in the benthic deposits. Samples consisting of primarily deposited bark had a volatile solids content of about 15 pounds per cubic foot. The average increase in volatile solids content in the log storage areas as compared to the control samples was approximately two pounds of volatile solids per cubic foot. For the log dumping areas this average increase ranged from 0. 5 to 15 pounds of volatile solids per cubic foot. The results of this study indicate clearly that large amounts of bark are added to the water courses used for log storage and that large amounts of bark debris presently exist in the benthic deposits of these water courses. Close

• 1836. [Article] Assessing disease impacts of hatcheries on downstream salmonids in the Willamette River Basin, Oregon

  Hatcheries are often perceived as a source of pathogen amplification, potentially increasing disease risk to free-ranging populations; at the same time, free-ranging fishes may introduce pathogens into ...

  Citation × Citation Citation Abstract Copy Title: Assessing disease impacts of hatcheries on downstream salmonids in the Willamette River Basin, Oregon Author: Jakaitis, Michelle Hatcheries are often perceived as a source of pathogen amplification, potentially increasing disease risk to free-ranging populations; at the same time, free-ranging fishes may introduce pathogens into hatcheries through untreated water sources. Many pathogens exist naturally within the environment (with the exception of introduced pathogens) and the presence of a pathogen does not guarantee infection or disease (Naish, Taylor III, Levin, Quinn, Winton, Huppert & Hilborn 2007). Infections can be acute, chronic, or asymptomatic, fish may die, recover, or become carriers (Naish et al. 2007), and pathogens may be shed from any of these stages (Scottish Executive 2002). Most salmon and trout hatcheries along the Willamette River Basin, Oregon, USA, utilize an untreated river water supply for their rearing ponds and release this water, untreated, back into the river. This creates a potential for waterborne pathogens present in free-ranging hosts to be transmitted through the water supply to hatchery populations. Moreover, any hatchery epizootic can amplify pathogens and release these into the water, which could have a direct impact on free-ranging populations exposed to those pathogens in hatchery effluent. The goal of this thesis was to assess transmission of the pathogens Flavobacterium columnare, F. psychrophilum, Aeromonas salmonicida, Renibacterium salmonicida, and Infectious Hematopoietic Necrosis Virus (IHNV), at selected hatcheries in the Willamette River Basin. To accomplish this, I considered historical data and hatchery-specific and pathogen-specific factors involved in transmission and disease. Additionally, I conducted sentinel fishes exposures (Oncorhynchus mykiss and O. tshawytscha) at hatcheries during both epizootics and non-epizootic periods. Naïve sentinel fish were placed in hatchery influents and effluents to determine transmission direction and pathogen prevalence associated with hatcheries. I found that sentinel fishes developed infections downstream of hatcheries that were undergoing specific bacterial epizootics, or had low levels of pathogen prevalence within the hatchery, but not at any other time. Infections and mortality were due to the same pathogens responsible for hatchery epizootics, indicating the hatchery as a potential source. This may be a limited effect dependent on distance, dilution, and pathogen. The presence of large numbers of returning, congregating adult fishes may also contribute pathogens to the river in hatchery areas. Sentinel fishes held in hatchery influents did not, at any point, become infected with target pathogens, even during hatchery epizootics. Although I was unable to identify the pathogen entry point leading to hatchery epizootics, I determined that pathogen transmission appeared to be dependent on the pathogen, species, and location where sentinel fish were held. This thesis identifies routes and risks of pathogen transmission at selected Oregon hatcheries, with applications to inform state-wide fish health management. Title: Assessing disease impacts of hatcheries on downstream salmonids in the Willamette River Basin, Oregon Author: Jakaitis, Michelle Hatcheries are often perceived as a source of pathogen amplification, potentially increasing disease risk to free-ranging populations; at the same time, free-ranging fishes may introduce pathogens into hatcheries through untreated water sources. Many pathogens exist naturally within the environment (with the exception of introduced pathogens) and the presence of a pathogen does not guarantee infection or disease (Naish, Taylor III, Levin, Quinn, Winton, Huppert & Hilborn 2007). Infections can be acute, chronic, or asymptomatic, fish may die, recover, or become carriers (Naish et al. 2007), and pathogens may be shed from any of these stages (Scottish Executive 2002). Most salmon and trout hatcheries along the Willamette River Basin, Oregon, USA, utilize an untreated river water supply for their rearing ponds and release this water, untreated, back into the river. This creates a potential for waterborne pathogens present in free-ranging hosts to be transmitted through the water supply to hatchery populations. Moreover, any hatchery epizootic can amplify pathogens and release these into the water, which could have a direct impact on free-ranging populations exposed to those pathogens in hatchery effluent. The goal of this thesis was to assess transmission of the pathogens Flavobacterium columnare, F. psychrophilum, Aeromonas salmonicida, Renibacterium salmonicida, and Infectious Hematopoietic Necrosis Virus (IHNV), at selected hatcheries in the Willamette River Basin. To accomplish this, I considered historical data and hatchery-specific and pathogen-specific factors involved in transmission and disease. Additionally, I conducted sentinel fishes exposures (Oncorhynchus mykiss and O. tshawytscha) at hatcheries during both epizootics and non-epizootic periods. Naïve sentinel fish were placed in hatchery influents and effluents to determine transmission direction and pathogen prevalence associated with hatcheries. I found that sentinel fishes developed infections downstream of hatcheries that were undergoing specific bacterial epizootics, or had low levels of pathogen prevalence within the hatchery, but not at any other time. Infections and mortality were due to the same pathogens responsible for hatchery epizootics, indicating the hatchery as a potential source. This may be a limited effect dependent on distance, dilution, and pathogen. The presence of large numbers of returning, congregating adult fishes may also contribute pathogens to the river in hatchery areas. Sentinel fishes held in hatchery influents did not, at any point, become infected with target pathogens, even during hatchery epizootics. Although I was unable to identify the pathogen entry point leading to hatchery epizootics, I determined that pathogen transmission appeared to be dependent on the pathogen, species, and location where sentinel fish were held. This thesis identifies routes and risks of pathogen transmission at selected Oregon hatcheries, with applications to inform state-wide fish health management. Close

• 1837. [Article] Development of an enzyme-linked immunosorbent assay to detect antibodies against Pasteurella multocida in infected rabbits

  Enzyme-linked immunosorbent assays (ELISA) were developed to detect rabbit antibodies against Pasteurella multocida. Antigens for ELISA were prepared from 2.5% saline extracts of P. multocida by chromatographic ...

  Citation × Citation Citation Abstract Copy Title: Development of an enzyme-linked immunosorbent assay to detect antibodies against Pasteurella multocida in infected rabbits Author: Hwang, Eun Ju Enzyme-linked immunosorbent assays (ELISA) were developed to detect rabbit antibodies against Pasteurella multocida. Antigens for ELISA were prepared from 2.5% saline extracts of P. multocida by chromatographic methods. From a crude saline extract of a type 3, 4 isolate designated as R11146, two protein peaks were obtained by gel filtration with Sephadex G-200. The first peak produced a single precipitin line with rabbit anti-whole cell or anti-purified type 3 antigen sera. The first peak was further purified by DEAE-cellulose chromatography. Four protein peaks were obtained, and all of them contained a single identical antigen. The purified antigen contained two protein species of molecular weights of 44,000 and 25,500. The purified antigen was attached to 96 well microtiter plates, and an ELISA was developed by the use of alka-line phosphatase-conjugated sheep anti-rabbit IgG to detect anti bodies. Six Pasteurella-free rabbits were intranasally infected with R11146 isolate and antibody responses were measured by the ELISA. High titers ranging from 1:10³ to 1:10⁴ persisted for longer than 96 days after the infection, while the titers of all the preinoculation sera were lower than 1:10. A similar surface antigen was also purified from a type 12 isolate, R040. Three protein peaks were obtained from crude extract by gel filtration with Sephadex G-200. The first peak contained a major antigen. In some instances, crude extract was concentrated by ultracentrifugation prior to the gel filtration. A major protein component of molecular weights 42,000 and minor ones of 25,000 and 110,000 were present in t the first peak fraction. The antigen purified from a type 12 isolate showed antigenic cross-reaction with the purified antigen from a type 3, 4 isolate. An ELISA was developed with the purified type 12 antigen, and used for detecting antibodies in rabbits intranasally infected with the type 12 strain. Titers of ELISA ranging from 1:10⁴ to 1:10⁵ were obtained for longer than 77 days post inoculation. The preinoculation sera showed titers of less than 1:50. The results indicate that the purified antigen is useful to detect antibodies against P. multocida in rabbits infected with type 3 or type 12 strains. Title: Development of an enzyme-linked immunosorbent assay to detect antibodies against Pasteurella multocida in infected rabbits Author: Hwang, Eun Ju Enzyme-linked immunosorbent assays (ELISA) were developed to detect rabbit antibodies against Pasteurella multocida. Antigens for ELISA were prepared from 2.5% saline extracts of P. multocida by chromatographic methods. From a crude saline extract of a type 3, 4 isolate designated as R11146, two protein peaks were obtained by gel filtration with Sephadex G-200. The first peak produced a single precipitin line with rabbit anti-whole cell or anti-purified type 3 antigen sera. The first peak was further purified by DEAE-cellulose chromatography. Four protein peaks were obtained, and all of them contained a single identical antigen. The purified antigen contained two protein species of molecular weights of 44,000 and 25,500. The purified antigen was attached to 96 well microtiter plates, and an ELISA was developed by the use of alka-line phosphatase-conjugated sheep anti-rabbit IgG to detect anti bodies. Six Pasteurella-free rabbits were intranasally infected with R11146 isolate and antibody responses were measured by the ELISA. High titers ranging from 1:10³ to 1:10⁴ persisted for longer than 96 days after the infection, while the titers of all the preinoculation sera were lower than 1:10. A similar surface antigen was also purified from a type 12 isolate, R040. Three protein peaks were obtained from crude extract by gel filtration with Sephadex G-200. The first peak contained a major antigen. In some instances, crude extract was concentrated by ultracentrifugation prior to the gel filtration. A major protein component of molecular weights 42,000 and minor ones of 25,000 and 110,000 were present in t the first peak fraction. The antigen purified from a type 12 isolate showed antigenic cross-reaction with the purified antigen from a type 3, 4 isolate. An ELISA was developed with the purified type 12 antigen, and used for detecting antibodies in rabbits intranasally infected with the type 12 strain. Titers of ELISA ranging from 1:10⁴ to 1:10⁵ were obtained for longer than 77 days post inoculation. The preinoculation sera showed titers of less than 1:50. The results indicate that the purified antigen is useful to detect antibodies against P. multocida in rabbits infected with type 3 or type 12 strains. Close

• 1838. [Article] A comparison of the hydraulic efficiency of a palm species (Iriartea deltoidea) with other wood types

  This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Oxford University Press and can be found at: http://treephys.oxfordjournals.org...

  Citation × Citation Citation Abstract Copy Title: A comparison of the hydraulic efficiency of a palm species (Iriartea deltoidea) with other wood types Author: Renninger, Heidi J., Phillips, Nathan, McCulloh, Katherine A. This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Oxford University Press and can be found at: http://treephys.oxfordjournals.org/. Title: A comparison of the hydraulic efficiency of a palm species (Iriartea deltoidea) with other wood types Author: Renninger, Heidi J., Phillips, Nathan, McCulloh, Katherine A. This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Oxford University Press and can be found at: http://treephys.oxfordjournals.org/. Close

• 1839. [Article] Ecological relationships between cervid herbivory and understory vegetation in old-growth Sitka spruce-western hemlock forests in western Washington

  The relationships between black-tailed deer (Odocoileus hemionus columbianus) and Roosevelt elk (Cervus elaphus roosevelti) herbivory and understory vegetation in unmanaged forests in Olympic National ...

  Citation × Citation Citation Abstract Copy Title: Ecological relationships between cervid herbivory and understory vegetation in old-growth Sitka spruce-western hemlock forests in western Washington Author: Happe, Patricia Jenkins The relationships between black-tailed deer (Odocoileus hemionus columbianus) and Roosevelt elk (Cervus elaphus roosevelti) herbivory and understory vegetation in unmanaged forests in Olympic National Park were studied from 1985 - 1989. From 1985 to 1986 I studied the impact of cervid exclusion on shrub, fern, and forb forage quality, tannin content, tannin astringency, shrub morphology, and shrub standing crop biomass, in old-growth and seral forests. Long-term protection from cervid herbivory had little effect on forage quality, tannin content, or tannin astringency. However, herbivory reduced leaf area, leaf weight, and plant standing crop biomass. From March 1987 through March 1989 I measured the amount of cervid herbivory in the understory of old-growth forests, and the effects of that herbivory on herb, fern, and shrub biomass, production, and nutrient content. The amount, timing, and impacts of cervid herbivory varied among understory plant communities, plant species, and years. Forage biomass, production, herbivory, and the influence of herbivory, were greatest in areas with grass-dominated understories. In those sites, production was either stimulated or not affected by herbivory, and herbivory altered plant structure and nutrient content such that foraging efficiency was improved during both summer and late winter. In sites with a forb-moss herb layer, biomass, production, and herbivory were less. Although herbivory either stimulated or had no effect on production in forb sites, it had no effect on forage nutrient content or structure, and thus did not impact foraging efficiency. The effects of long-term exclusion of ungulates in the study area indicated that soon after exclusion, grass-dominated understories disappear. Thus, cervid herbivory was found to influence understories in old-growth forest on several spacial and temporal scales. In the short-term, cervid herbivory improved forage structure and nutrient concentration in grass dominated understories. In the long term, cervid herbivory maintained grass dominated patches within the system. On both temporal and spatial scales, the net result of cervid herbivory was the creation of a more favorable foraging environment for both deer and elk. Title: Ecological relationships between cervid herbivory and understory vegetation in old-growth Sitka spruce-western hemlock forests in western Washington Author: Happe, Patricia Jenkins The relationships between black-tailed deer (Odocoileus hemionus columbianus) and Roosevelt elk (Cervus elaphus roosevelti) herbivory and understory vegetation in unmanaged forests in Olympic National Park were studied from 1985 - 1989. From 1985 to 1986 I studied the impact of cervid exclusion on shrub, fern, and forb forage quality, tannin content, tannin astringency, shrub morphology, and shrub standing crop biomass, in old-growth and seral forests. Long-term protection from cervid herbivory had little effect on forage quality, tannin content, or tannin astringency. However, herbivory reduced leaf area, leaf weight, and plant standing crop biomass. From March 1987 through March 1989 I measured the amount of cervid herbivory in the understory of old-growth forests, and the effects of that herbivory on herb, fern, and shrub biomass, production, and nutrient content. The amount, timing, and impacts of cervid herbivory varied among understory plant communities, plant species, and years. Forage biomass, production, herbivory, and the influence of herbivory, were greatest in areas with grass-dominated understories. In those sites, production was either stimulated or not affected by herbivory, and herbivory altered plant structure and nutrient content such that foraging efficiency was improved during both summer and late winter. In sites with a forb-moss herb layer, biomass, production, and herbivory were less. Although herbivory either stimulated or had no effect on production in forb sites, it had no effect on forage nutrient content or structure, and thus did not impact foraging efficiency. The effects of long-term exclusion of ungulates in the study area indicated that soon after exclusion, grass-dominated understories disappear. Thus, cervid herbivory was found to influence understories in old-growth forest on several spacial and temporal scales. In the short-term, cervid herbivory improved forage structure and nutrient concentration in grass dominated understories. In the long term, cervid herbivory maintained grass dominated patches within the system. On both temporal and spatial scales, the net result of cervid herbivory was the creation of a more favorable foraging environment for both deer and elk. Close

• 1840. [Article] Escapement and Productivity of Summer Steelhead and Spring Chinook Salmon in the John Day River; Annual Report 2017

  Abstract -- The John Day River, located in northeastern Oregon, supports five wild populations of summer steelhead (Oncorhynchus mykiss) and three populations of wild spring chinook (Oncorhynchus tschawytscha) ...

  Citation × Citation Citation Abstract Copy Title: Escapement and Productivity of Summer Steelhead and Spring Chinook Salmon in the John Day River; Annual Report 2017 Abstract -- The John Day River, located in northeastern Oregon, supports five wild populations of summer steelhead (Oncorhynchus mykiss) and three populations of wild spring chinook (Oncorhynchus tschawytscha) with no hatchery supplementation. However, these populations remain depressed relative to historic levels. In 1999, the National Marine Fisheries Service (NMFS) listed the Middle Columbia River summer steelhead Distinct Population Segment (DPS), which includes the John Day River Major Population Group (MPG), as threatened under the Endangered Species Act (ESA). Although numerous habitat protection and rehabilitation projects have been implemented within the John Day River basin to improve steelhead and other salmonid freshwater production and survival, it has been difficult to estimate the effectiveness of these projects without a systematic program in place to collect information on the status, trends, and distribution of spawning activity, juvenile salmonids, and aquatic habitat conditions within the basin. Prior to the inception of this project, population and environmental monitoring of steelhead in the basin consisted of a combination of index spawning surveys and periodic monitoring of some status and trend indicators. While index spawning data is useful for drawing inference about long-term trends in adult steelhead abundance, they are limited for determining the status of steelhead escapement or distribution at the population or MPG scale because survey sites are not randomly selected and are likely biased towards streams with higher fish abundance. A broader approach to the monitoring and evaluation of status and trends in anadromous and resident salmonid populations and their habitats was needed to provide data to effectively support restoration efforts and guide alternative future management actions in the basin. The Independent Scientific Review Panel (ISRP) recommended that the region move away from index surveys and embrace probabilistic sampling for most population and habitat monitoring. To meet the ISRP recommendation, the structure and methods employed by the Oregon Plan for Salmon and Watersheds Monitoring Program were extended to the John Day basin. This approach incorporates the sampling strategy of the United States Environmental Protection Agency’s (EPA) Environmental Monitoring and Assessment Program (EMAP). This research effort employs a statistically based and spatially explicit sampling design to answer key monitoring questions, integrate on-going sampling efforts, and improve agency coordination. The current program seeks to integrate project objectives focused on summer steelhead spawning metrics, juvenile salmonid metrics, and aquatic habitat conditions. Title: Escapement and Productivity of Summer Steelhead and Spring Chinook Salmon in the John Day River; Annual Report 2017 Abstract -- The John Day River, located in northeastern Oregon, supports five wild populations of summer steelhead (Oncorhynchus mykiss) and three populations of wild spring chinook (Oncorhynchus tschawytscha) with no hatchery supplementation. However, these populations remain depressed relative to historic levels. In 1999, the National Marine Fisheries Service (NMFS) listed the Middle Columbia River summer steelhead Distinct Population Segment (DPS), which includes the John Day River Major Population Group (MPG), as threatened under the Endangered Species Act (ESA). Although numerous habitat protection and rehabilitation projects have been implemented within the John Day River basin to improve steelhead and other salmonid freshwater production and survival, it has been difficult to estimate the effectiveness of these projects without a systematic program in place to collect information on the status, trends, and distribution of spawning activity, juvenile salmonids, and aquatic habitat conditions within the basin. Prior to the inception of this project, population and environmental monitoring of steelhead in the basin consisted of a combination of index spawning surveys and periodic monitoring of some status and trend indicators. While index spawning data is useful for drawing inference about long-term trends in adult steelhead abundance, they are limited for determining the status of steelhead escapement or distribution at the population or MPG scale because survey sites are not randomly selected and are likely biased towards streams with higher fish abundance. A broader approach to the monitoring and evaluation of status and trends in anadromous and resident salmonid populations and their habitats was needed to provide data to effectively support restoration efforts and guide alternative future management actions in the basin. The Independent Scientific Review Panel (ISRP) recommended that the region move away from index surveys and embrace probabilistic sampling for most population and habitat monitoring. To meet the ISRP recommendation, the structure and methods employed by the Oregon Plan for Salmon and Watersheds Monitoring Program were extended to the John Day basin. This approach incorporates the sampling strategy of the United States Environmental Protection Agency’s (EPA) Environmental Monitoring and Assessment Program (EMAP). This research effort employs a statistically based and spatially explicit sampling design to answer key monitoring questions, integrate on-going sampling efforts, and improve agency coordination. The current program seeks to integrate project objectives focused on summer steelhead spawning metrics, juvenile salmonid metrics, and aquatic habitat conditions. Close

• 1841. [Image] Lower Klamath River instream flow study : scoping evaluation for the Yurok Indian Reservation

  	ABSTRACT The U.S. Fish and Wildlife Service, Lower Columbia River Fishery Resource Office was funded by Bureau of Indian Affairs to conduct an instream flow assessment for the lower Klamath River within ...
  	Citation × Citation Citation Abstract Copy Title: Lower Klamath River instream flow study : scoping evaluation for the Yurok Indian Reservation Author: Anglin, Donald R Year: 1994, 2007, 2006 ABSTRACT The U.S. Fish and Wildlife Service, Lower Columbia River Fishery Resource Office was funded by Bureau of Indian Affairs to conduct an instream flow assessment for the lower Klamath River within the Yurok Indian Reservation in northern California using the Instream Flow Incremental Methodology (IFIM). Specific study tasks consisted of developing an explicit statement of purpose, definition of the study area and target species, assembly and evaluation of hydrologic, water quality, and physical data as well as biological and fish habitat information. A reconnaissance survey of the proposed study area was also conducted. The purpose for conducting the proposed flow study was the Yurok Tribe's desire to protect the Klamath basin water supply for the production of anadromous fish. The ultimate goal was to protect, restore, and enhance the anadromous fishery resources on the Reservation and in the basin as a whole. The study area was defined as the lower Klamath River and tributaries from the confluence with the Trinity River downstream to the area of tidal influence. Although the mainstem Klamath only was proposed for flow studies, the tributaries were included in the study area as a result of their hydrologic and biological relevance. Target species were identified as chinook salmon {Oncorhynchus tshawytscha), coho salmon (0. kisutch), steelhead trout (0. mykiss) , green sturgeon {Acipenser medirostris) , eulachon (Thaleichthys pacificus) , and Pacific lamprey (Lampetra tridentata) . Assembly and evaluation of relevant information was accomplished from results of a public scoping meeting and the review of a large volume of both published and file reports as well as numerous personal communications. Hydrology of the lower Klamath River is affected by U.S. Bureau of Reclamation projects in both the upper Klamath and upper Trinity subbasins. Several hydroelectric projects in the upper Klamath subbasin affect flow patterns, and agricultural activities in the upper Klamath subbasin and tributaries and the Central Valley Project in the upper Trinity subbasin have reduced water yield from the basin. Water quality concerns were identified as elevated water temperatures and nutrient levels resulting from land use activities throughout the basin. Hydrologic and water quality impacts are partially mitigated in the lower Klamath by tributary inflow throughout the basin. The physical environment in the basin has been altered by land use practices and several major flood events. Alterations include loss of riparian vegetation and stream channel stability, loss of soil moisture storage capacity and infiltration potential, debris slides and logjams resulting in migration barriers, reduced supply of large woody debris for recruitment into the stream channel, and sedimentation of spawning and rearing habitat. Fish habitat in most lower Klamath tributaries has been surveyed and deficiencies as well as good quality habitat have been described. Significant production potential exists in most tributaries, however much restoration work needs to be completed to realize the potential. Habitat characteristics for the mainstem Klamath have not been described. Life history and production data are presented for target species and a brief review of sources for suitability criteria is presented. Harvest management and escapement for naturally spawning fall chinook salmon were reviewed from 1978 through 1993. Escapement has varied over the years but a general downward trend in naturally spawning fall chinook can be observed, particularly in recent years. Escapement goals for the Klamath basin varied from 115,000 in 1978 to an "emergency" floor of 27,000 in 1992. Actual escapement of naturally spawning adult fall chinook varied from a high of 113,000 in 1986 to a low of 11,600 in 1991. Escapement in 1978 totalled 58,500 and preliminary estimates of escapement in 1993 were 21,000 naturally spawning adults. Factors affecting production and subsequent stock size and escapement included variable ocean survival, degraded freshwater habitat conditions, the recent six-year drought, releases of large numbers of hatchery juveniles, and harvest management methodologies that have failed to adequately match harvest to predicted stock size. Differential harvest rates for Klamath and Trinity subbasin fall chinook have also complicated attempts to structure the harvest. Field reconnaisance surveys were conducted in spring and summer 1993 for the proposed mainstem Klamath study area. Two distinct river segments were identified based on macrohabitat characteristics. Microhabitat was classified within each river segment and mapped on USGS quadrangle maps. Cross section identification was postponed pending the decision to move forward with the flow study. Following the scoping tasks described above, conclusions and recommendations were developed. No information was reviewed that indicated the need for an instream flow study in the lower Klamath River. The two basic problems affecting anadromous fish production are degraded freshwater habitat and chronic underescapement. Coordination and planning for instream flow studies on a basin-wide scale was recommended. Biological data gaps were identified which need to be addressed before an instream flow study can be completed for the lower Klamath. Suitability criteria for habitat analysis also need to be identified. Habitat restoration and protection and proper management of anadromous fishery resources were identified as the highest priorities to begin restoration of anadromous stocks. Specific recommendations for habitat restoration included watershed and riparian zone restoration, barrier removal, instream habitat inventory, restoration, and monitoring, estuary studies, and description of streamflow characteristics for lower Klamath tributaries. Recommended fishery resource studies included collection of basic life history data, monitoring for adult escapement and juvenile production, description of estuary usage, effects of hatchery programs on both adult and juvenile wild fish, evaluation of the accelerated stocking program, and refinement of harvest management methodologies to achieve appropriate escapement of naturally spawning stocks into all subbasins. Title: Lower Klamath River instream flow study : scoping evaluation for the Yurok Indian Reservation Author: Anglin, Donald R Year: 1994, 2007, 2006 ABSTRACT The U.S. Fish and Wildlife Service, Lower Columbia River Fishery Resource Office was funded by Bureau of Indian Affairs to conduct an instream flow assessment for the lower Klamath River within the Yurok Indian Reservation in northern California using the Instream Flow Incremental Methodology (IFIM). Specific study tasks consisted of developing an explicit statement of purpose, definition of the study area and target species, assembly and evaluation of hydrologic, water quality, and physical data as well as biological and fish habitat information. A reconnaissance survey of the proposed study area was also conducted. The purpose for conducting the proposed flow study was the Yurok Tribe's desire to protect the Klamath basin water supply for the production of anadromous fish. The ultimate goal was to protect, restore, and enhance the anadromous fishery resources on the Reservation and in the basin as a whole. The study area was defined as the lower Klamath River and tributaries from the confluence with the Trinity River downstream to the area of tidal influence. Although the mainstem Klamath only was proposed for flow studies, the tributaries were included in the study area as a result of their hydrologic and biological relevance. Target species were identified as chinook salmon {Oncorhynchus tshawytscha), coho salmon (0. kisutch), steelhead trout (0. mykiss) , green sturgeon {Acipenser medirostris) , eulachon (Thaleichthys pacificus) , and Pacific lamprey (Lampetra tridentata) . Assembly and evaluation of relevant information was accomplished from results of a public scoping meeting and the review of a large volume of both published and file reports as well as numerous personal communications. Hydrology of the lower Klamath River is affected by U.S. Bureau of Reclamation projects in both the upper Klamath and upper Trinity subbasins. Several hydroelectric projects in the upper Klamath subbasin affect flow patterns, and agricultural activities in the upper Klamath subbasin and tributaries and the Central Valley Project in the upper Trinity subbasin have reduced water yield from the basin. Water quality concerns were identified as elevated water temperatures and nutrient levels resulting from land use activities throughout the basin. Hydrologic and water quality impacts are partially mitigated in the lower Klamath by tributary inflow throughout the basin. The physical environment in the basin has been altered by land use practices and several major flood events. Alterations include loss of riparian vegetation and stream channel stability, loss of soil moisture storage capacity and infiltration potential, debris slides and logjams resulting in migration barriers, reduced supply of large woody debris for recruitment into the stream channel, and sedimentation of spawning and rearing habitat. Fish habitat in most lower Klamath tributaries has been surveyed and deficiencies as well as good quality habitat have been described. Significant production potential exists in most tributaries, however much restoration work needs to be completed to realize the potential. Habitat characteristics for the mainstem Klamath have not been described. Life history and production data are presented for target species and a brief review of sources for suitability criteria is presented. Harvest management and escapement for naturally spawning fall chinook salmon were reviewed from 1978 through 1993. Escapement has varied over the years but a general downward trend in naturally spawning fall chinook can be observed, particularly in recent years. Escapement goals for the Klamath basin varied from 115,000 in 1978 to an "emergency" floor of 27,000 in 1992. Actual escapement of naturally spawning adult fall chinook varied from a high of 113,000 in 1986 to a low of 11,600 in 1991. Escapement in 1978 totalled 58,500 and preliminary estimates of escapement in 1993 were 21,000 naturally spawning adults. Factors affecting production and subsequent stock size and escapement included variable ocean survival, degraded freshwater habitat conditions, the recent six-year drought, releases of large numbers of hatchery juveniles, and harvest management methodologies that have failed to adequately match harvest to predicted stock size. Differential harvest rates for Klamath and Trinity subbasin fall chinook have also complicated attempts to structure the harvest. Field reconnaisance surveys were conducted in spring and summer 1993 for the proposed mainstem Klamath study area. Two distinct river segments were identified based on macrohabitat characteristics. Microhabitat was classified within each river segment and mapped on USGS quadrangle maps. Cross section identification was postponed pending the decision to move forward with the flow study. Following the scoping tasks described above, conclusions and recommendations were developed. No information was reviewed that indicated the need for an instream flow study in the lower Klamath River. The two basic problems affecting anadromous fish production are degraded freshwater habitat and chronic underescapement. Coordination and planning for instream flow studies on a basin-wide scale was recommended. Biological data gaps were identified which need to be addressed before an instream flow study can be completed for the lower Klamath. Suitability criteria for habitat analysis also need to be identified. Habitat restoration and protection and proper management of anadromous fishery resources were identified as the highest priorities to begin restoration of anadromous stocks. Specific recommendations for habitat restoration included watershed and riparian zone restoration, barrier removal, instream habitat inventory, restoration, and monitoring, estuary studies, and description of streamflow characteristics for lower Klamath tributaries. Recommended fishery resource studies included collection of basic life history data, monitoring for adult escapement and juvenile production, description of estuary usage, effects of hatchery programs on both adult and juvenile wild fish, evaluation of the accelerated stocking program, and refinement of harvest management methodologies to achieve appropriate escapement of naturally spawning stocks into all subbasins. Close

• 1842. [Image] A report on Crater Lake water quality: Crater Lake National Park, Oregon, 1984-1985

  	ill., maps; Report title; Includes appendices: Crater Lake Liminological Studies 1984 and 1985; Includes bibliographical references; "Robert E. Benton, Superintendent Crater Lake National Park." - T.p....
  	Citation × Citation Citation Abstract Copy Title: A report on Crater Lake water quality: Crater Lake National Park, Oregon, 1984-1985 Author: Benton, Robert E. Year: 1986, 2008 ill., maps; Report title; Includes appendices: Crater Lake Liminological Studies 1984 and 1985; Includes bibliographical references; "Robert E. Benton, Superintendent Crater Lake National Park." - T.p. Title: A report on Crater Lake water quality: Crater Lake National Park, Oregon, 1984-1985 Author: Benton, Robert E. Year: 1986, 2008 ill., maps; Report title; Includes appendices: Crater Lake Liminological Studies 1984 and 1985; Includes bibliographical references; "Robert E. Benton, Superintendent Crater Lake National Park." - T.p. Close

• 1843. [Image] Draft upper Klamath River management plan environmental impact statement and resource management plan amendments. Volume 2 - Appendices

  	"BLM/OR/WA/PL-02/038+1792"--P. [2] of cover; Cover title; Includes bibliographical references (v. 2, p. 219-228) and index
  	Citation × Citation Citation Abstract Copy Title: Draft upper Klamath River management plan environmental impact statement and resource management plan amendments. Volume 2 - Appendices Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office Year: 2003, 2004 "BLM/OR/WA/PL-02/038+1792"--P. [2] of cover; Cover title; Includes bibliographical references (v. 2, p. 219-228) and index Title: Draft upper Klamath River management plan environmental impact statement and resource management plan amendments. Volume 2 - Appendices Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office Year: 2003, 2004 "BLM/OR/WA/PL-02/038+1792"--P. [2] of cover; Cover title; Includes bibliographical references (v. 2, p. 219-228) and index Close

• 1844. [Image] Annual program summary 2004

  	Annual Program Summary and Monitoring Report - FY2004 Table of Contents ANNUAL PROGRAM SUMMARY 1.0 Introduction 3 2.0 Summary of Accomplishments 3 3.0 Budget and Employment 6 4.0 Land ...
  	Citation × Citation Citation Abstract Copy Title: Annual program summary 2004 Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office District Year: 2005 Annual Program Summary and Monitoring Report - FY2004 Table of Contents ANNUAL PROGRAM SUMMARY 1.0 Introduction 3 2.0 Summary of Accomplishments 3 3.0 Budget and Employment 6 4.0 Land Use Allocations within the Klamath Falls Resource Area 6 Late-Successional Reserves and Assessments 8 Matrix 8 5.0 Aquatic Conservation Strategy 9 Riparian Reserves 9 Watershed Analysis and Key Watersheds 9 Watershed Restoration 10 Roads 10 Riparian Habitat Enhancement 10 Stream Restoration 11 6.0 Air Quality 11 7.0 Water and Soils 11 Water - Project Implementation 11 Soils - Project Implementation 12 Water - Inventory and Monitoring 12 Soils -Inventory and Monitoring 13 State-listed Clean Water Act 303d Streams 13 RMP Best Management Practices 13 8.0 Terrestrial Species and Habitat Management 14 Survey and Manage Species 14 Threatened/Endangered Species 14 Northern Spotted Owl 14 Bald Eagle 14 Special Status Species-Animals 15 Peregrine Falcon 15 Yellow Rails 15 Bats 15 Northern Goshawk 15 Oregon Spotted Frog 15 Sage Grouse 16 vii Klamath Falls Resource Area Mollusks 16 Great Gray Owl 16 Special Status Species - Plants 16 Other Species of Concern 17 Neotropical Migratory Landbirds 17 Terrestrial Habitat Management 17 Nest Sites, Activity Centers, and Rookeries 17 Big Game Habitat 19 9.0 Aquatic Species and Habitat Management 19 Threatened/Endangered Species 19 Lost River and Shortnose Suckers 19 Bull Trout 20 Endangered Species Act Consultation 20 Aquatic Habitat Restoration 20 Klamath River Hydroelectric Facility Relicensing 21 10.0 Pathogen, Disease, and Pest Management 21 11.0 Weed Management 22 Inventories 22 Control 22 12.0 Special Areas/Management 23 Wild and Scenic Rivers 23 Wilderness 23 Areas of Critical Environmental Concern 23 Tunnel Creek Special Botanical Area 24 Klamath Canyon ACEC 24 Old Baldy Research Natural Area 24 Wood River Wetland ACEC 24 Environmental Education Areas 25 13.0 Cultural Resources 26 14.0 Visual Resources 26 15.0 Rural Interface Areas 26 16.0 Socioeconomic Conditions 27 Jobs-in-the-Woods 28 17.0 Environmental Justice 30 18.0 Recreation 30 Recreation Pipeline Restoration Funds 30 Recreation Projects 31 viii Annual Program Summary and Monitoring Report - FY2004 Recreation Fee Demonstration Project 31 Status of Recreation Plans 32 Volunteer Activities 32 Tourism 33 19.0 Forest Management and Timber Resources 33 Silvicultural Prescriptions 33 Timber Sale Planning 34 FY 2004 Timber Sale Accomplishments 34 Status of Sold & Awarded Klamath Falls RMP Timber Sales 35 Forest Development Activities 39 Stewardship Contracting 42 20.0 Special Forest Products 42 21.0 Energy and Minerals 43 22.0 Land Tenure Adjustments 44 23.0 Access and Rights-of-Way 45 24.0 Transportation and Roads 45 25.0 Hazardous Materials 46 26.0 Wildfire/Fuels Management 46 27.0 Law Enforcement 47 28.0 Rangeland Resources / Grazing Management 48 Fiscal Year 2004 Summary 49 Fiscal Years 1996-2004 Summary 50 Wild Horse Management 51 29.0 Cadastral Survey 52 30.0 Education and Outreach 52 31.0 Research 56 32.0 Coordination and Consultation 58 Federal Agencies 58 State of Oregon 58 Counties 59 Cities 59 Tribes 59 IX Klamath Falls Resource Area Watershed Councils 59 Chartered Advisory Groups 60 Other Local Coordination and Cooperation 61 33.0 National Environmental Policy Act Analysis and Documentation 63 NEPA documentation 63 Klamath Falls Resource Area Environmental Documentation 63 Protests and Appeals 63 34.0 Plan Evaluations 64 Third Year Evaluation 64 Eighth Year Evaluation 64 35.0 Plan Maintenance 65 36.0 Plan Amendments 72 Plan Revision 76 MONITORING REPORT Introduction 79 All Land Use Allocations 83 Late-Successional Reserves 86 Matrix 88 Riparian Reserves 92 Air Quality 95 Water and Soils 96 Terrestrial Species Habitat 101 Special Status and SEIS Special Attention Species Habitat 106 Aquatic Species Habitat 110 Noxious Weeds 112 Special Areas 113 Wild and Scenic Rivers 115 Cultural Resources Including American Indian Values 116 Visual Resources 118 Rural Interface Areas 119 Socioeconomic Conditions 120 Recreation 121 Forest Management and Timber Resources 121 Special Forest/Natural Products 122 Wildfire / Fuels Management 124 Rangeland Resources / Grazing Management 124 GLOSSARY/ACRONYMS 129 Annual Program Summary and Monitoring Report - FY2004 List of Tables Table 2.1 - Summary of Resource Management Actions, Directions, and Accomplishments 4 Table 2.1 - Summary of Resource Management Actions, Directions, and Accomplishments (Cont.).5 Table 3.1 - Resource Area Budget Fiscal Year 2004 6 Table 4.1 - Land Use Allocation 8 Table 5.1 - Watershed Analysis Schedule 10 Table 5.2-Watershed Analysis Status Fiscal Year 2004 10 Table 6.1 -Air Quality Management Fiscal Year 2004 11 Table 7.1 - Watershed Activity Fiscal Year 2004 12 Table 7.2 - KFRA Clean Water Act 303(d) Water Bodies 13 Table 8.1a - BLM /KFRA Special Status Species Designations Summary -Animals 18 Table 8.1b - BLM (KFRA) Special Status Species Designations Summary - Plants 18 Table 8.2 - Terrestrial Habitat Monitoring Fiscal Year 2004 18 Table 8.3 - Monitoring for Nest Sites, Activity Centers, Rookeries, Special Habitats 18 Table 9.1 -Aquatic Habitat/ Fish Passage Management Fiscal Year 2004 19 Table 11.1 - Managed Weed Species 20 Table 12.1 - Special Management Areas 25 Table 13.1 - Cultural Resources Management Fiscal Year 2004 26 Table 16.1 - Total Payments in Lieu of Taxes and Acres by County for FY 2004 28 Table 16.2 - O&C Payments To Counties FY 2004 29 Table 16.3 - Jobs in the Woods Program Fiscal Year 2004 29 Table 18.1 - Recreation Statistics Fiscal Year 2004 30 Table 18.2 - Recreation Fee Demonstration Project Fiscal Year 2004 32 Table 19.1 - Klamath Falls Timber Sale Volume (MBF) and Acres FY 2004 35 Table 19.2-Timber Volume Sold in FY 2004 36 Table 19.3 - Harvest Activity for FY 2004 36 Table 19.4 - Planned Timber Sales (FY 2005 & 2006) 36 Table 19.5 - Status of Sold and Awarded Timber Sales 37 Table 19.6 - Summary of Volume Sold 38 Table 19.7 -Volume and Acres Sold by Allocations 38 Table 19.8 - Timber Sales Sold by Harvest Types 38 Table 19.9 - Timber Sale Acres Sold by Age Class 39 Table 19.10 - Forest Development Activities 41 Table 20.1 - Special Forest Products Fiscal Year 2004 43 Table 21.1 - Energy and Minerals Management Fiscal Year 2004 44 Table 22.1 - Land Use Tenure Adjustments Fiscal Year 2004 45 Table 24.1 - Roads and Transportation Management Fiscal Year 2004 45 Table 25.1 - Hazardous Materials Management Fiscal Year 2004 46 Table 26.1 - Fire and Fuels Management Fiscal Year 2004 46 Table 27.1 - Law Enforcement Fiscal Year 2004 47 Table 28.1 - Range Resources Management Fiscal Year 2004 48 Table 29.1 -Cadastral Survey Summary Fiscal Year 2004 52 Table 30.1 - Environmental Education/Outreach Program Summary FY2004 54 Table 30.2 - Environmental Education/Outreach Special Events FY2004 55 Table 30.3 - Environmental Education/Outreach Programs & Tours FY 2004 56 Table 32.1 - Challenge Cost Share Fiscal Year 2004 62 XI Klamath Falls Resource Area Table 33.1 - NEPA Analyses and Documentation Fiscal Year 2004 64 Table 36.1 - Redefined Survey and Manage Categories 74 Table M.I - Projects Monitored FY 2004 80 Table M-2 - FY 2004 Implementation Monitoring Selection Categories 81 Table M-3 - Comparison of Projected vs. Actual Harvest Volume (MMBF)/Acres to Date 82 Table M-4 - Timber Sale Volume and Acres Offered (Entire Resource Area) 83 Table M-5 - Timber Sale Monitoring Summary 89 Table M-6 - Post Treatment Stand Characteristics for West Grenada Timber Sale - FY 2004 90 Table M-7 - Status of Watershed Analysis 98 List of Figures Figure 1 - General Location Map 2 Figure 2 - KFRA Land Allocations 7 Xll Title: Annual program summary 2004 Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office District Year: 2005 Annual Program Summary and Monitoring Report - FY2004 Table of Contents ANNUAL PROGRAM SUMMARY 1.0 Introduction 3 2.0 Summary of Accomplishments 3 3.0 Budget and Employment 6 4.0 Land Use Allocations within the Klamath Falls Resource Area 6 Late-Successional Reserves and Assessments 8 Matrix 8 5.0 Aquatic Conservation Strategy 9 Riparian Reserves 9 Watershed Analysis and Key Watersheds 9 Watershed Restoration 10 Roads 10 Riparian Habitat Enhancement 10 Stream Restoration 11 6.0 Air Quality 11 7.0 Water and Soils 11 Water - Project Implementation 11 Soils - Project Implementation 12 Water - Inventory and Monitoring 12 Soils -Inventory and Monitoring 13 State-listed Clean Water Act 303d Streams 13 RMP Best Management Practices 13 8.0 Terrestrial Species and Habitat Management 14 Survey and Manage Species 14 Threatened/Endangered Species 14 Northern Spotted Owl 14 Bald Eagle 14 Special Status Species-Animals 15 Peregrine Falcon 15 Yellow Rails 15 Bats 15 Northern Goshawk 15 Oregon Spotted Frog 15 Sage Grouse 16 vii Klamath Falls Resource Area Mollusks 16 Great Gray Owl 16 Special Status Species - Plants 16 Other Species of Concern 17 Neotropical Migratory Landbirds 17 Terrestrial Habitat Management 17 Nest Sites, Activity Centers, and Rookeries 17 Big Game Habitat 19 9.0 Aquatic Species and Habitat Management 19 Threatened/Endangered Species 19 Lost River and Shortnose Suckers 19 Bull Trout 20 Endangered Species Act Consultation 20 Aquatic Habitat Restoration 20 Klamath River Hydroelectric Facility Relicensing 21 10.0 Pathogen, Disease, and Pest Management 21 11.0 Weed Management 22 Inventories 22 Control 22 12.0 Special Areas/Management 23 Wild and Scenic Rivers 23 Wilderness 23 Areas of Critical Environmental Concern 23 Tunnel Creek Special Botanical Area 24 Klamath Canyon ACEC 24 Old Baldy Research Natural Area 24 Wood River Wetland ACEC 24 Environmental Education Areas 25 13.0 Cultural Resources 26 14.0 Visual Resources 26 15.0 Rural Interface Areas 26 16.0 Socioeconomic Conditions 27 Jobs-in-the-Woods 28 17.0 Environmental Justice 30 18.0 Recreation 30 Recreation Pipeline Restoration Funds 30 Recreation Projects 31 viii Annual Program Summary and Monitoring Report - FY2004 Recreation Fee Demonstration Project 31 Status of Recreation Plans 32 Volunteer Activities 32 Tourism 33 19.0 Forest Management and Timber Resources 33 Silvicultural Prescriptions 33 Timber Sale Planning 34 FY 2004 Timber Sale Accomplishments 34 Status of Sold & Awarded Klamath Falls RMP Timber Sales 35 Forest Development Activities 39 Stewardship Contracting 42 20.0 Special Forest Products 42 21.0 Energy and Minerals 43 22.0 Land Tenure Adjustments 44 23.0 Access and Rights-of-Way 45 24.0 Transportation and Roads 45 25.0 Hazardous Materials 46 26.0 Wildfire/Fuels Management 46 27.0 Law Enforcement 47 28.0 Rangeland Resources / Grazing Management 48 Fiscal Year 2004 Summary 49 Fiscal Years 1996-2004 Summary 50 Wild Horse Management 51 29.0 Cadastral Survey 52 30.0 Education and Outreach 52 31.0 Research 56 32.0 Coordination and Consultation 58 Federal Agencies 58 State of Oregon 58 Counties 59 Cities 59 Tribes 59 IX Klamath Falls Resource Area Watershed Councils 59 Chartered Advisory Groups 60 Other Local Coordination and Cooperation 61 33.0 National Environmental Policy Act Analysis and Documentation 63 NEPA documentation 63 Klamath Falls Resource Area Environmental Documentation 63 Protests and Appeals 63 34.0 Plan Evaluations 64 Third Year Evaluation 64 Eighth Year Evaluation 64 35.0 Plan Maintenance 65 36.0 Plan Amendments 72 Plan Revision 76 MONITORING REPORT Introduction 79 All Land Use Allocations 83 Late-Successional Reserves 86 Matrix 88 Riparian Reserves 92 Air Quality 95 Water and Soils 96 Terrestrial Species Habitat 101 Special Status and SEIS Special Attention Species Habitat 106 Aquatic Species Habitat 110 Noxious Weeds 112 Special Areas 113 Wild and Scenic Rivers 115 Cultural Resources Including American Indian Values 116 Visual Resources 118 Rural Interface Areas 119 Socioeconomic Conditions 120 Recreation 121 Forest Management and Timber Resources 121 Special Forest/Natural Products 122 Wildfire / Fuels Management 124 Rangeland Resources / Grazing Management 124 GLOSSARY/ACRONYMS 129 Annual Program Summary and Monitoring Report - FY2004 List of Tables Table 2.1 - Summary of Resource Management Actions, Directions, and Accomplishments 4 Table 2.1 - Summary of Resource Management Actions, Directions, and Accomplishments (Cont.).5 Table 3.1 - Resource Area Budget Fiscal Year 2004 6 Table 4.1 - Land Use Allocation 8 Table 5.1 - Watershed Analysis Schedule 10 Table 5.2-Watershed Analysis Status Fiscal Year 2004 10 Table 6.1 -Air Quality Management Fiscal Year 2004 11 Table 7.1 - Watershed Activity Fiscal Year 2004 12 Table 7.2 - KFRA Clean Water Act 303(d) Water Bodies 13 Table 8.1a - BLM /KFRA Special Status Species Designations Summary -Animals 18 Table 8.1b - BLM (KFRA) Special Status Species Designations Summary - Plants 18 Table 8.2 - Terrestrial Habitat Monitoring Fiscal Year 2004 18 Table 8.3 - Monitoring for Nest Sites, Activity Centers, Rookeries, Special Habitats 18 Table 9.1 -Aquatic Habitat/ Fish Passage Management Fiscal Year 2004 19 Table 11.1 - Managed Weed Species 20 Table 12.1 - Special Management Areas 25 Table 13.1 - Cultural Resources Management Fiscal Year 2004 26 Table 16.1 - Total Payments in Lieu of Taxes and Acres by County for FY 2004 28 Table 16.2 - O&C Payments To Counties FY 2004 29 Table 16.3 - Jobs in the Woods Program Fiscal Year 2004 29 Table 18.1 - Recreation Statistics Fiscal Year 2004 30 Table 18.2 - Recreation Fee Demonstration Project Fiscal Year 2004 32 Table 19.1 - Klamath Falls Timber Sale Volume (MBF) and Acres FY 2004 35 Table 19.2-Timber Volume Sold in FY 2004 36 Table 19.3 - Harvest Activity for FY 2004 36 Table 19.4 - Planned Timber Sales (FY 2005 & 2006) 36 Table 19.5 - Status of Sold and Awarded Timber Sales 37 Table 19.6 - Summary of Volume Sold 38 Table 19.7 -Volume and Acres Sold by Allocations 38 Table 19.8 - Timber Sales Sold by Harvest Types 38 Table 19.9 - Timber Sale Acres Sold by Age Class 39 Table 19.10 - Forest Development Activities 41 Table 20.1 - Special Forest Products Fiscal Year 2004 43 Table 21.1 - Energy and Minerals Management Fiscal Year 2004 44 Table 22.1 - Land Use Tenure Adjustments Fiscal Year 2004 45 Table 24.1 - Roads and Transportation Management Fiscal Year 2004 45 Table 25.1 - Hazardous Materials Management Fiscal Year 2004 46 Table 26.1 - Fire and Fuels Management Fiscal Year 2004 46 Table 27.1 - Law Enforcement Fiscal Year 2004 47 Table 28.1 - Range Resources Management Fiscal Year 2004 48 Table 29.1 -Cadastral Survey Summary Fiscal Year 2004 52 Table 30.1 - Environmental Education/Outreach Program Summary FY2004 54 Table 30.2 - Environmental Education/Outreach Special Events FY2004 55 Table 30.3 - Environmental Education/Outreach Programs & Tours FY 2004 56 Table 32.1 - Challenge Cost Share Fiscal Year 2004 62 XI Klamath Falls Resource Area Table 33.1 - NEPA Analyses and Documentation Fiscal Year 2004 64 Table 36.1 - Redefined Survey and Manage Categories 74 Table M.I - Projects Monitored FY 2004 80 Table M-2 - FY 2004 Implementation Monitoring Selection Categories 81 Table M-3 - Comparison of Projected vs. Actual Harvest Volume (MMBF)/Acres to Date 82 Table M-4 - Timber Sale Volume and Acres Offered (Entire Resource Area) 83 Table M-5 - Timber Sale Monitoring Summary 89 Table M-6 - Post Treatment Stand Characteristics for West Grenada Timber Sale - FY 2004 90 Table M-7 - Status of Watershed Analysis 98 List of Figures Figure 1 - General Location Map 2 Figure 2 - KFRA Land Allocations 7 Xll Close

• 1845. [Image] A framework for ecosystem management in the interior Columbia Basin and portions of the Klamath and Great Basins

  	Haynes, Richard W.; Graham, Russell T.; Quigley, Thomas M., tech. eds. 1996. A framework for ecosystem management in the Interior Columbia Basin including portions of the Klamath and Great Basins. Gen. ...
  	Citation × Citation Citation Abstract Copy Title: A framework for ecosystem management in the interior Columbia Basin and portions of the Klamath and Great Basins Year: 1996, 2005 Haynes, Richard W.; Graham, Russell T.; Quigley, Thomas M., tech. eds. 1996. A framework for ecosystem management in the Interior Columbia Basin including portions of the Klamath and Great Basins. Gen. Tech. Rep. PNW-GTR-374. Portland, OR; U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 66 p. A framework for ecosystem management is proposed. This framework assumes the purpose of ecosystem management is to maintain the integrity of ecosystems over time and space. It is based on four ecosystem principles: ecosystems are dynamic, can be viewed as hierarchies with temporal and spatial dimensions, have limits, and are relatively unpredictable. This approach recognizes that people are part of ecosystems and that stewardship must be able to resolve tough challenges including how to meet multiple demands with finite resources. The framework describes a general planning model for ecosystem management that has four iterative steps: monitoring, assessment, decision-making, and implementation. Since ecosystems cross jurisdictional lines, the implementation of the framework depends on partnerships among land managers, the scientific community, and stakeholders. It proposes that decision-making be based on information provided by the best available science and the most appropriate technologies for land management. Keywords: Ecosystem assessment, ecosystem principles, ecosystem management, planning models, management goals, risk analysis. Title: A framework for ecosystem management in the interior Columbia Basin and portions of the Klamath and Great Basins Year: 1996, 2005 Haynes, Richard W.; Graham, Russell T.; Quigley, Thomas M., tech. eds. 1996. A framework for ecosystem management in the Interior Columbia Basin including portions of the Klamath and Great Basins. Gen. Tech. Rep. PNW-GTR-374. Portland, OR; U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 66 p. A framework for ecosystem management is proposed. This framework assumes the purpose of ecosystem management is to maintain the integrity of ecosystems over time and space. It is based on four ecosystem principles: ecosystems are dynamic, can be viewed as hierarchies with temporal and spatial dimensions, have limits, and are relatively unpredictable. This approach recognizes that people are part of ecosystems and that stewardship must be able to resolve tough challenges including how to meet multiple demands with finite resources. The framework describes a general planning model for ecosystem management that has four iterative steps: monitoring, assessment, decision-making, and implementation. Since ecosystems cross jurisdictional lines, the implementation of the framework depends on partnerships among land managers, the scientific community, and stakeholders. It proposes that decision-making be based on information provided by the best available science and the most appropriate technologies for land management. Keywords: Ecosystem assessment, ecosystem principles, ecosystem management, planning models, management goals, risk analysis. Close

• 1846. [Image] An examination of the Klamath Basin crisis : restructuring the discourse within an identity-based framework

  	Thesis (B.A.) -- Whitman College, 2002; Includes bibliographical references (leaves 79-83)
  	Citation × Citation Citation Abstract Copy Title: An examination of the Klamath Basin crisis : restructuring the discourse within an identity-based framework Author: Dornsife, Alison M. Year: 2002, 2005, 2004 Thesis (B.A.) -- Whitman College, 2002; Includes bibliographical references (leaves 79-83) Title: An examination of the Klamath Basin crisis : restructuring the discourse within an identity-based framework Author: Dornsife, Alison M. Year: 2002, 2005, 2004 Thesis (B.A.) -- Whitman College, 2002; Includes bibliographical references (leaves 79-83) Close

• 1847. [Article] The effects of habitat, climate, and Barred Owls on long-term demography of Northern Spotted Owls

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by Cooper Ornithological ...

  Citation × Citation Citation Abstract Copy Title: The effects of habitat, climate, and Barred Owls on long-term demography of Northern Spotted Owls Author: Franklin, Alan B., Diller, Lowell V., Horn, Rob B., Schwarz, Carl J., McCafferty, Christopher, Gremel, Scott A., Biswell, Brian L., Clark, Darren A., Herter, Dale R., Doherty, Paul F. Jr, Hines, James E., McDonnell, Kevin, Bailey, Larissa, Higley, J. Mark, Yackulic, Charles B., Hobson, Jeremy, Burnham, Kenneth P., Dugger, Katie M., Carlson, Peter C., Clement, Matthew J., Davis, Raymond J., Rockweit, Jeremy, Huyvaert, Kathryn P., Andrews, Lawrence S., Forsman, Eric D., Augustine, Benjamin, Saenz, Jessica, Glenn, Elizabeth M., Blakesley, Jennifer, Olson, Gail S., Ackers, Steven H., McDonald, Trent, Nichols, James D., Green, Adam, Ruiz, Viviana, Sovern, Stan G., White, Gary C., Reid, Janice A. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by Cooper Ornithological Society and published by Central Ornithology Publication Office. It can be found at: http://www.aoucospubs.org/loi/cond Title: The effects of habitat, climate, and Barred Owls on long-term demography of Northern Spotted Owls Author: Franklin, Alan B., Diller, Lowell V., Horn, Rob B., Schwarz, Carl J., McCafferty, Christopher, Gremel, Scott A., Biswell, Brian L., Clark, Darren A., Herter, Dale R., Doherty, Paul F. Jr, Hines, James E., McDonnell, Kevin, Bailey, Larissa, Higley, J. Mark, Yackulic, Charles B., Hobson, Jeremy, Burnham, Kenneth P., Dugger, Katie M., Carlson, Peter C., Clement, Matthew J., Davis, Raymond J., Rockweit, Jeremy, Huyvaert, Kathryn P., Andrews, Lawrence S., Forsman, Eric D., Augustine, Benjamin, Saenz, Jessica, Glenn, Elizabeth M., Blakesley, Jennifer, Olson, Gail S., Ackers, Steven H., McDonald, Trent, Nichols, James D., Green, Adam, Ruiz, Viviana, Sovern, Stan G., White, Gary C., Reid, Janice A. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by Cooper Ornithological Society and published by Central Ornithology Publication Office. It can be found at: http://www.aoucospubs.org/loi/cond Close

• 1848. [Article] Evaluating tools used to estimate and manage browse available to wintering moose on the Copper River Delta, Alaska

  Ungulates comprise some of the most well researched and intensely managed wildlife populations on earth. As such, they are recognized as ideal study subjects for developing and modifying management tools ...

  Citation × Citation Citation Abstract Copy Title: Evaluating tools used to estimate and manage browse available to wintering moose on the Copper River Delta, Alaska Author: Smythe, Sharon E. Ungulates comprise some of the most well researched and intensely managed wildlife populations on earth. As such, they are recognized as ideal study subjects for developing and modifying management tools or theories (Danell et al. 1994, Shipley 2010). An introduced moose (Alces alces gigas) population on the Copper River Delta (CRD; Delta) of south-central Alaska functions as a valuable resource for the residents of Cordova and an isolated research population on which to test managerial techniques. Since its introduction (1949-1958), the founding population of 23 moose has grown to over 830 in 2013, divided into two sub-populations. However, in 1964, the largest earthquake recorded in U.S. history (9.2 magnitude) uplifted the Delta by 1.0-4.0 m, initiating delta-wide changes in hydrology, vegetation distributions, and successional processes. The proportion of stands dominated by woody species, especially alder (Alnus viridis sinuata) and spruce (Picea sitchensis), increased visibly. Furthermore, previous research (1987-89) observed that 90% of the moose on the western region of the Delta wintered within 9-24% of the total land area, possibly restricting their available winter browse. Because moose diets on the CRD are dominated by willows (Salix spp.), managers were concerned that the combined effects of a restricted winter range and earthquake-initiated vegetation changes would negatively influence the population. Managers have responded to this concern by 1) supporting work to estimate the nutritional carrying capacity (NCC; i.e., the forage available to a population within a specified area and time) of the Delta, and 2) by exploring the feasibility of mechanical treatment as a means of stimulating browse production for the moose. Thus, the objectives of this thesis were to 1) explore the factors influencing NCC for moose on the west CRD while combining updated digital and field-collected data to estimate NCC, and 2) to assess the effects of mechanical treatment on the production of moose browse across stand types and over time. We collected field data and evaluated differences in the past (1988-89) and present (2012-13) biomass-predicting regression equations for two willow species (Barclay's and Hooker's willow, Salix barclayi and hookeriana) used within NCC models to determine 1) whether past and present models of Barclay's willow predicted similarly and 2) whether Hooker’s and Barclay's willow differed in average available biomass, nutritional quality, and utilization by moose. The linear coefficients for the current (2013) Barclay’s willow, Hooker's willow, and combined equations were 2.2x, 1.6x, and 1.9x larger, respectively, than that derived from the 1988 model for Barclay’s willow (which possibly included Hooker's willow data). Thus, willows on the CRD may now be supporting more biomass per stem than predicted by prior models. Hooker's and Barclay's willow did not differ in mean available biomass, nutritional values, or utilization rates. These results suggest a need to evaluate the accuracy of older allometric regressions, though separate identification of the visually-similar Barclay's and Hooker's willow may be unnecessary for future biomass-estimating efforts on the CRD. To further explore the factors influencing the biomass available to moose and their associated NCC estimates, we compared 5 NCC model types across 4 winter ranges and under 3 winter-severity scenarios for the western CRD moose population. We conducted a sensitivity analysis (Sx) of our final model to determine the relative influence of factors affecting NCC estimates. Lastly, we compared current (2012-13) browse available biomass, stand type areas (2011), and NCC results to those obtained by past research (1987-89, MacCracken et al. 1997 and 1959/1986, Stephenson et al. 2006) to determine changes over time, while evaluating the effects of models incorporating satellite-based estimates of stand areas and forage nutritional values on NCC estimates. Because recent aerial survey observations suggest expansion of the moose winter range, our final model estimated NCC between 2,198-3,471 moose depending on winter severity within a winter range encompassing the entire west Delta. These results suggest the current western moose population (approximately 600 in 2013) is below NCC. Model components with the largest and smallest Sx were snow depth and tannin- and lignin-caused reductions in forage nutritional quality, respectively. Changes from 1987-2013 in available biomass of forage species ranged from -66-493%, while changes from 1959-2011 in stand type areas ranged from -60-661%. Overall, NCC estimates only declined by 2% from 1959-2013, however inclusion of forage nutritional quality in models reduced NCC estimates by 60%. Lastly, we assessed the use of hydraulic-axing (i.e., hydro-axing) as tool for increasing the available willow biomass. We evaluated treatment effects on biomass, height, nutritional quality (crude protein, lignin, and tannin levels), utilization, and snow burial of the winter forage species within 3 winter-severity scenarios. Sites were treated in 4 winters (1990-92, 2008, 2010, and 2012) within 5 stand types in 20 locations varying from 0.86-63.40 ha in size. Results indicate few significant differences relative to controls, though treatment significantly increased the ratio of willow to alder. Our results may be limited by sample sizes (n = 1-9 per stand type or treatment year) as visual comparison suggests treatment via hydraulic-axing may be an effective method for increasing willow biomass without influencing nutritional quality. However, willows 20-23 years post-treatment are still significantly shorter than untreated willows (P = 0.03). Thus, treatment may result in decreased forage available to moose in severe winters. Management concerns regarding continued earthquake-initiated changes in vegetation distributions and successional processes prompted our investigation. However, studies on the vegetation dynamics of the CRD suggest the vegetation distribution of the Delta may be relatively stable (Boggs 2000, Thilenius 2008). If so, our current estimates of NCC suggest the west Delta can support a larger moose population than is currently present. Hydro-axing may not be necessary to ensure the future of the moose population, though it could be used to counter increases in alder (Alnus viridis sinuata) which are likely within certain successional sequences. However, together with earthquakes, the processes determining the future forage available on the CRD include complex, interactive forces such as glaciers, the Copper River, oceanic tides, and zoological- and human-caused influences. These forces and their effects on the vegetation create a dynamic ecosystem for the moose population, are difficult to predict, and may be further complicated by climate change. As a result, application of any managerial tool may be temporary and often difficult. However, this guarantees a constant need for further revision and redevelopment of the tools used to manage the moose population, ensuring that the moose of the CRD will remain an important resource for researching and refining ungulate management worldwide. Title: Evaluating tools used to estimate and manage browse available to wintering moose on the Copper River Delta, Alaska Author: Smythe, Sharon E. Ungulates comprise some of the most well researched and intensely managed wildlife populations on earth. As such, they are recognized as ideal study subjects for developing and modifying management tools or theories (Danell et al. 1994, Shipley 2010). An introduced moose (Alces alces gigas) population on the Copper River Delta (CRD; Delta) of south-central Alaska functions as a valuable resource for the residents of Cordova and an isolated research population on which to test managerial techniques. Since its introduction (1949-1958), the founding population of 23 moose has grown to over 830 in 2013, divided into two sub-populations. However, in 1964, the largest earthquake recorded in U.S. history (9.2 magnitude) uplifted the Delta by 1.0-4.0 m, initiating delta-wide changes in hydrology, vegetation distributions, and successional processes. The proportion of stands dominated by woody species, especially alder (Alnus viridis sinuata) and spruce (Picea sitchensis), increased visibly. Furthermore, previous research (1987-89) observed that 90% of the moose on the western region of the Delta wintered within 9-24% of the total land area, possibly restricting their available winter browse. Because moose diets on the CRD are dominated by willows (Salix spp.), managers were concerned that the combined effects of a restricted winter range and earthquake-initiated vegetation changes would negatively influence the population. Managers have responded to this concern by 1) supporting work to estimate the nutritional carrying capacity (NCC; i.e., the forage available to a population within a specified area and time) of the Delta, and 2) by exploring the feasibility of mechanical treatment as a means of stimulating browse production for the moose. Thus, the objectives of this thesis were to 1) explore the factors influencing NCC for moose on the west CRD while combining updated digital and field-collected data to estimate NCC, and 2) to assess the effects of mechanical treatment on the production of moose browse across stand types and over time. We collected field data and evaluated differences in the past (1988-89) and present (2012-13) biomass-predicting regression equations for two willow species (Barclay's and Hooker's willow, Salix barclayi and hookeriana) used within NCC models to determine 1) whether past and present models of Barclay's willow predicted similarly and 2) whether Hooker’s and Barclay's willow differed in average available biomass, nutritional quality, and utilization by moose. The linear coefficients for the current (2013) Barclay’s willow, Hooker's willow, and combined equations were 2.2x, 1.6x, and 1.9x larger, respectively, than that derived from the 1988 model for Barclay’s willow (which possibly included Hooker's willow data). Thus, willows on the CRD may now be supporting more biomass per stem than predicted by prior models. Hooker's and Barclay's willow did not differ in mean available biomass, nutritional values, or utilization rates. These results suggest a need to evaluate the accuracy of older allometric regressions, though separate identification of the visually-similar Barclay's and Hooker's willow may be unnecessary for future biomass-estimating efforts on the CRD. To further explore the factors influencing the biomass available to moose and their associated NCC estimates, we compared 5 NCC model types across 4 winter ranges and under 3 winter-severity scenarios for the western CRD moose population. We conducted a sensitivity analysis (Sx) of our final model to determine the relative influence of factors affecting NCC estimates. Lastly, we compared current (2012-13) browse available biomass, stand type areas (2011), and NCC results to those obtained by past research (1987-89, MacCracken et al. 1997 and 1959/1986, Stephenson et al. 2006) to determine changes over time, while evaluating the effects of models incorporating satellite-based estimates of stand areas and forage nutritional values on NCC estimates. Because recent aerial survey observations suggest expansion of the moose winter range, our final model estimated NCC between 2,198-3,471 moose depending on winter severity within a winter range encompassing the entire west Delta. These results suggest the current western moose population (approximately 600 in 2013) is below NCC. Model components with the largest and smallest Sx were snow depth and tannin- and lignin-caused reductions in forage nutritional quality, respectively. Changes from 1987-2013 in available biomass of forage species ranged from -66-493%, while changes from 1959-2011 in stand type areas ranged from -60-661%. Overall, NCC estimates only declined by 2% from 1959-2013, however inclusion of forage nutritional quality in models reduced NCC estimates by 60%. Lastly, we assessed the use of hydraulic-axing (i.e., hydro-axing) as tool for increasing the available willow biomass. We evaluated treatment effects on biomass, height, nutritional quality (crude protein, lignin, and tannin levels), utilization, and snow burial of the winter forage species within 3 winter-severity scenarios. Sites were treated in 4 winters (1990-92, 2008, 2010, and 2012) within 5 stand types in 20 locations varying from 0.86-63.40 ha in size. Results indicate few significant differences relative to controls, though treatment significantly increased the ratio of willow to alder. Our results may be limited by sample sizes (n = 1-9 per stand type or treatment year) as visual comparison suggests treatment via hydraulic-axing may be an effective method for increasing willow biomass without influencing nutritional quality. However, willows 20-23 years post-treatment are still significantly shorter than untreated willows (P = 0.03). Thus, treatment may result in decreased forage available to moose in severe winters. Management concerns regarding continued earthquake-initiated changes in vegetation distributions and successional processes prompted our investigation. However, studies on the vegetation dynamics of the CRD suggest the vegetation distribution of the Delta may be relatively stable (Boggs 2000, Thilenius 2008). If so, our current estimates of NCC suggest the west Delta can support a larger moose population than is currently present. Hydro-axing may not be necessary to ensure the future of the moose population, though it could be used to counter increases in alder (Alnus viridis sinuata) which are likely within certain successional sequences. However, together with earthquakes, the processes determining the future forage available on the CRD include complex, interactive forces such as glaciers, the Copper River, oceanic tides, and zoological- and human-caused influences. These forces and their effects on the vegetation create a dynamic ecosystem for the moose population, are difficult to predict, and may be further complicated by climate change. As a result, application of any managerial tool may be temporary and often difficult. However, this guarantees a constant need for further revision and redevelopment of the tools used to manage the moose population, ensuring that the moose of the CRD will remain an important resource for researching and refining ungulate management worldwide. Close

• 1849. [Image] Summary of the analysis of the management situation: Klamath Falls Resource Area resource management plan

  	"December 1990"
  	Citation × Citation Citation Abstract Copy Title: Summary of the analysis of the management situation: Klamath Falls Resource Area resource management plan Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office. Year: 1990, 2005, 2004 "December 1990" Title: Summary of the analysis of the management situation: Klamath Falls Resource Area resource management plan Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office. Year: 1990, 2005, 2004 "December 1990" Close

• 1850. [Image] Freshwater supply : states' views of how federal agencies could help them meet the challenges of expected shortages : report to Congressional Requesters

  	"July 2003."; "GAO-03-514."
  	Citation × Citation Citation Abstract Copy Title: Freshwater supply : states' views of how federal agencies could help them meet the challenges of expected shortages : report to Congressional Requesters Author: United States. General Accounting Office Year: 2003, 2005 "July 2003."; "GAO-03-514." Title: Freshwater supply : states' views of how federal agencies could help them meet the challenges of expected shortages : report to Congressional Requesters Author: United States. General Accounting Office Year: 2003, 2005 "July 2003."; "GAO-03-514." Close

• 1851. [Image] A conservation strategy for the northern spotted owl

  	ill., maps; Shipping list no.: 90-263-P; "May 1990."; Includes bibliographical references
  	Citation × Citation Citation Abstract Copy Title: A conservation strategy for the northern spotted owl Author: Thomas, Jack Ward Year: 1990, 2010 ill., maps; Shipping list no.: 90-263-P; "May 1990."; Includes bibliographical references Title: A conservation strategy for the northern spotted owl Author: Thomas, Jack Ward Year: 1990, 2010 ill., maps; Shipping list no.: 90-263-P; "May 1990."; Includes bibliographical references Close

• 1852. [Image] Forest conditions in the Cascade Range Forest Reserve, Oregon

  	Subject series H. Forestry 6
  	Citation × Citation Citation Abstract Copy Title: Forest conditions in the Cascade Range Forest Reserve, Oregon Author: Geological Survey (U.S.) Year: 1903, 2007 Subject series H. Forestry 6 Title: Forest conditions in the Cascade Range Forest Reserve, Oregon Author: Geological Survey (U.S.) Year: 1903, 2007 Subject series H. Forestry 6 Close

• 1853. [Image] Final winter use plan and environmental assessment: Crater Lake National Park, Oregon

  	ill., maps; "August, 1994"; Includes appendices; "Jones/Winter use 08/22/94e."
  	Citation × Citation Citation Abstract Copy Title: Final winter use plan and environmental assessment: Crater Lake National Park, Oregon Author: United States; National Park Service; Denver Service Center Year: 1994, 2009, 2010 ill., maps; "August, 1994"; Includes appendices; "Jones/Winter use 08/22/94e." Title: Final winter use plan and environmental assessment: Crater Lake National Park, Oregon Author: United States; National Park Service; Denver Service Center Year: 1994, 2009, 2010 ill., maps; "August, 1994"; Includes appendices; "Jones/Winter use 08/22/94e." Close

• 1854. [Image] Genetic analysis of Klamath River green sturgeon (acipensar [i.e. acipenser] medirostris)

  	Abstract The utility of using isozyme analysis to study the stock structure among West Coast populations of green sturgeon (Acipenser medirostris) was assessed. Isozyme analysis was not determined ...
  	Citation × Citation Citation Abstract Copy Title: Genetic analysis of Klamath River green sturgeon (acipensar [i.e. acipenser] medirostris) Author: Mulligan, Helen Year: 2000, 2005 Abstract The utility of using isozyme analysis to study the stock structure among West Coast populations of green sturgeon (Acipenser medirostris) was assessed. Isozyme analysis was not determined to be an adequate method for assessing stock structure in green sturgeon for the following reasons: 1) the complex nature of isozyme expression 2) the relatively poor resolution of enzyme systems for our samples 3) the invasive nature of collecting tissue samples for isozyme analysis, which necessitates sacrificing the fish, precludes collection of samples from some rivers. The stomach contents of 23 green sturgeon collected from fish harvested in the Klamath River were analyzed. Only four stomachs contained identifiable food items, with the others containing food far too digested for identification, gravel, or no contents. Two stomachs contained the small gastropod, Olivellapyna, one stomach contained the carapace remains of a female Dungeness crab, Cancer magister, and one stomach contained the posterior portions of three ammocoetes, Lampetra tridentata. Preliminary analysis was conducted using mtDNA to assess the potential of using this technique for assessing the stock structure of green sturgeon. Although the Klamath River Fishery Restoration Program did not fund this analysis, the results are presented because this work was designed to yield complementary information to the isozyme study. No diagnostic differences were detected between samples collected from the Klamath River and the Columbia River estuary using Restriction Fragment Length Polymorphism analysis. Study results indicated that microsateliite DNA analyst might be the most appropriate current genetic technique for assessing the population structure of green sturgeon. Title: Genetic analysis of Klamath River green sturgeon (acipensar [i.e. acipenser] medirostris) Author: Mulligan, Helen Year: 2000, 2005 Abstract The utility of using isozyme analysis to study the stock structure among West Coast populations of green sturgeon (Acipenser medirostris) was assessed. Isozyme analysis was not determined to be an adequate method for assessing stock structure in green sturgeon for the following reasons: 1) the complex nature of isozyme expression 2) the relatively poor resolution of enzyme systems for our samples 3) the invasive nature of collecting tissue samples for isozyme analysis, which necessitates sacrificing the fish, precludes collection of samples from some rivers. The stomach contents of 23 green sturgeon collected from fish harvested in the Klamath River were analyzed. Only four stomachs contained identifiable food items, with the others containing food far too digested for identification, gravel, or no contents. Two stomachs contained the small gastropod, Olivellapyna, one stomach contained the carapace remains of a female Dungeness crab, Cancer magister, and one stomach contained the posterior portions of three ammocoetes, Lampetra tridentata. Preliminary analysis was conducted using mtDNA to assess the potential of using this technique for assessing the stock structure of green sturgeon. Although the Klamath River Fishery Restoration Program did not fund this analysis, the results are presented because this work was designed to yield complementary information to the isozyme study. No diagnostic differences were detected between samples collected from the Klamath River and the Columbia River estuary using Restriction Fragment Length Polymorphism analysis. Study results indicated that microsateliite DNA analyst might be the most appropriate current genetic technique for assessing the population structure of green sturgeon. Close

• 1855. [Image] Pinniped and seabird predation : implications for recovery of threatened stocks of salmonids in Oregon under the Oregon Plan for Salmon and Watersheds

  	"December 22, 1998."
  	Citation × Citation Citation Abstract Copy Title: Pinniped and seabird predation : implications for recovery of threatened stocks of salmonids in Oregon under the Oregon Plan for Salmon and Watersheds Author: Independent Multidisciplinary Science Team (Or.) Year: 1998, 2005 "December 22, 1998." Title: Pinniped and seabird predation : implications for recovery of threatened stocks of salmonids in Oregon under the Oregon Plan for Salmon and Watersheds Author: Independent Multidisciplinary Science Team (Or.) Year: 1998, 2005 "December 22, 1998." Close

• 1856. [Image] Klamath Falls Resource Area resource management plan and environmental impact statement : final : Volume 1

  	Proposed resource management plan/final environmental impact statement for the Klamath Falls Resource Area
  	Citation × Citation Citation Abstract Copy Title: Klamath Falls Resource Area resource management plan and environmental impact statement : final : Volume 1 Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office Year: 1994, 2005, 2004 Proposed resource management plan/final environmental impact statement for the Klamath Falls Resource Area Title: Klamath Falls Resource Area resource management plan and environmental impact statement : final : Volume 1 Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office Year: 1994, 2005, 2004 Proposed resource management plan/final environmental impact statement for the Klamath Falls Resource Area Close

• 1857. [Image] Draft resource management plan/environmental impact statement for the Upper Klamath Basin

  	"March 1994."
  	Citation × Citation Citation Abstract Copy Title: Draft resource management plan/environmental impact statement for the Upper Klamath Basin Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office Year: 1994, 2005 "March 1994." Title: Draft resource management plan/environmental impact statement for the Upper Klamath Basin Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office Year: 1994, 2005 "March 1994." Close

• 1858. [Image] Integrated land management on Tule Lake Wildlife Refuge: an alternative management strategy developed by the Integrated Land Management Working Group: promoting productive wetland habitats and sustainable agriculture on Tule Lake National Wildlife Refuge

  	EXECUTIVE SUMMARY This document describes the rationale for and implementation of an Integrated Land Management (ILM) Plan for the Tule Lake National Wildlife Refuge (NWR). The proposal is the recommendation ...
  	Citation × Citation Citation Abstract Copy Title: Integrated land management on Tule Lake Wildlife Refuge: an alternative management strategy developed by the Integrated Land Management Working Group: promoting productive wetland habitats and sustainable agriculture on Tule Lake National Wildlife Refuge Author: Integrated Land Management Working Group (Tule Lake National Wildlife Refuge, Calif.) Year: 2000, 2006, 2005 EXECUTIVE SUMMARY This document describes the rationale for and implementation of an Integrated Land Management (ILM) Plan for the Tule Lake National Wildlife Refuge (NWR). The proposal is the recommendation of 5 representative stakeholders in the Tule Lake area. During the 1950fs, 1960fs, and early 1970's, Tule Lake NWR was considered the single most important waterfowl refuge in North America when peak populations exceeded 2.5 million ducks and 1.0 million geese. The Kuchel Act of 1964 was enacted to preserve these waterfowl values as well as the local agricultural economy dependent on Refuge lands. However, restrictive management of wetlands and water levels under the Kuchel Act has eliminated the ecological processes critical to the Refuge's sustained wetland diversity and productivity. Currently, Tule Lake NWR supports a fraction of its past waterfowl use, species diversity has declined, and its value to endangered species has diminished. Agricultural sustainability is also thre Title: Integrated land management on Tule Lake Wildlife Refuge: an alternative management strategy developed by the Integrated Land Management Working Group: promoting productive wetland habitats and sustainable agriculture on Tule Lake National Wildlife Refuge Author: Integrated Land Management Working Group (Tule Lake National Wildlife Refuge, Calif.) Year: 2000, 2006, 2005 EXECUTIVE SUMMARY This document describes the rationale for and implementation of an Integrated Land Management (ILM) Plan for the Tule Lake National Wildlife Refuge (NWR). The proposal is the recommendation of 5 representative stakeholders in the Tule Lake area. During the 1950fs, 1960fs, and early 1970's, Tule Lake NWR was considered the single most important waterfowl refuge in North America when peak populations exceeded 2.5 million ducks and 1.0 million geese. The Kuchel Act of 1964 was enacted to preserve these waterfowl values as well as the local agricultural economy dependent on Refuge lands. However, restrictive management of wetlands and water levels under the Kuchel Act has eliminated the ecological processes critical to the Refuge's sustained wetland diversity and productivity. Currently, Tule Lake NWR supports a fraction of its past waterfowl use, species diversity has declined, and its value to endangered species has diminished. Agricultural sustainability is also thre Close

• 1859. [Image] Natural history and ecology of larval Lost River suckers and larval shortnose suckers in the Williamson River-Upper Klamath Lake System

  	We monitored larval Lost River and shortnose suckers from natal beds in the Williamson and Sprague rivers to nursery grounds in Upper Klamath Lake. Downstream movements occurred at night, in the middle ...
  	Citation × Citation Citation Abstract Copy Title: Natural history and ecology of larval Lost River suckers and larval shortnose suckers in the Williamson River-Upper Klamath Lake System Author: Cooperman, Michael S. Year: 2004, 2005 We monitored larval Lost River and shortnose suckers from natal beds in the Williamson and Sprague rivers to nursery grounds in Upper Klamath Lake. Downstream movements occurred at night, in the middle of the channel, and on the falling limb of the hydrograph. Ages, sizes, and developmental stages of larvae from spawning beds and the river mouth were similar, while larvae collected contemporaneously from the lake tended to be larger and better fed. Our results indicate in-river rearing was rare, that a rapid outmigration to the lake was favorable for larval survival, and that modification of the lower Williamson River does not appear to have prohibited rapid entry or preclude access to Upper Klamath Lake. Within the Williamson River and Upper Klamath Lake, emergent macrophytes supported significantly higher abundance, larger mean sizes, and better fed larvae than submerged macrophytes, woody vegetation, or open water areas. Analysis of seven years of larval sucker production and survival corroborated the habitat analysis by identifying a positive relationship with emergent macrophyte availability as well as a positive relationship with air temperature and a negative relationship with high wind. These findings illustrate the importance of fast growth, appropriate habitat and calm hydrological conditions for larvae, and are highly consistent with other larval fish studies. Title: Natural history and ecology of larval Lost River suckers and larval shortnose suckers in the Williamson River-Upper Klamath Lake System Author: Cooperman, Michael S. Year: 2004, 2005 We monitored larval Lost River and shortnose suckers from natal beds in the Williamson and Sprague rivers to nursery grounds in Upper Klamath Lake. Downstream movements occurred at night, in the middle of the channel, and on the falling limb of the hydrograph. Ages, sizes, and developmental stages of larvae from spawning beds and the river mouth were similar, while larvae collected contemporaneously from the lake tended to be larger and better fed. Our results indicate in-river rearing was rare, that a rapid outmigration to the lake was favorable for larval survival, and that modification of the lower Williamson River does not appear to have prohibited rapid entry or preclude access to Upper Klamath Lake. Within the Williamson River and Upper Klamath Lake, emergent macrophytes supported significantly higher abundance, larger mean sizes, and better fed larvae than submerged macrophytes, woody vegetation, or open water areas. Analysis of seven years of larval sucker production and survival corroborated the habitat analysis by identifying a positive relationship with emergent macrophyte availability as well as a positive relationship with air temperature and a negative relationship with high wind. These findings illustrate the importance of fast growth, appropriate habitat and calm hydrological conditions for larvae, and are highly consistent with other larval fish studies. Close

• 1860. [Article] Potential for dispersal of the non-native parasite Myxobolus cerebralis : qualitative risk assessments for the state of Alaska and the Willamette River Basin, Oregon

  First introduced to the USA in 1958, Myxobolus cerebralis, the parasite responsible for whirling disease in salmonids, has since spread across the country causing severe declines in wild trout populations ...

  Citation × Citation Citation Abstract Copy Title: Potential for dispersal of the non-native parasite Myxobolus cerebralis : qualitative risk assessments for the state of Alaska and the Willamette River Basin, Oregon Author: Arsan, E. Leyla First introduced to the USA in 1958, Myxobolus cerebralis, the parasite responsible for whirling disease in salmonids, has since spread across the country causing severe declines in wild trout populations in the intermountain west. Recent development of risk assessment models used to assess the likelihood and consequences of exotic parasite introduction, have strengthened the process of science-based decision-making in aquatic animal health. In the case of M. cerebralis, it is necessary to use a risk assessment model with two unique segments that clearly address the distinct life stages and respective hosts of the parasite separately. The studies described examine the probability of M. cerebralis introduction and establishment for two regions: the state of Alaska, and the Willamette River basin, Oregon. The Alaska risk assessment was based on the assumption that the parasite did not already occur in the state. However, in the process of validating this assumption, we documented the first polymerase chain reaction (PCR) detection of the parasite in the state. The pathogen was identified in hatchery rainbow trout (Oncorhynchus mykiss) from the Anchorage area. Although this is the first detection of the parasite in Alaska, clinical whirling disease has never been documented in the state. To qualitatively assess the risk of further spread of M. cerebralis in Alaska, four potential routes of dissemination were examined: movement of fish by humans, natural dispersal (via migratory birds and stray anadromous salmon), recreational activities, and commercial seafood processing. This research indicates the most likely pathway for M. cerebralis transport in Alaska is human movement of fish. In the Willamette River basin, Oregon, introduction of M. cerebralis has already occurred, though establishment appears limited to a single private hatchery. Introduction in this region was considered the most likely to occur as a result of human movements of fish. Straying anadromous salmonids were also assessed and were present in higher numbers than predicted. However, they were not infected with the parasite, and thus the probability for introduction by this route is low. The probability of introduction of the parasite varies throughout the Willamette River basin. Areas with the highest probability for M. cerebralis introduction were identified as the Clackamas and Santiam River subbasins. The Clackamas River has already experienced an introduction of the parasite, has the largest concentration of hatcheries (state, federal, and private), has a popular sport fishery, and is the closest major tributary to the enormous piscivorous bird-populations in the Columbia River estuary. The Santiam subbasin has a popular sport fishery, received the highest number of stray fish in the Willamette River basin, and has the second largest concentration of hatcheries in the Willamette River basin. Unique from introduction, establishment of the parasite is dependent upon several environmental and biological factors including: water temperatures, spatial/temporal overlap of hosts, and the distribution and genetic composition of the parasite’s invertebrate host, Tubifex tubifex. The distribution, genetic composition and susceptibility of T. tubifex, were considered the most important factor in the ability of M. cerebralis to establish in both systems. Surveys of oligochaete populations were conducted in both study regions. In Alaska, T. tubifex was not detected from the southeast region and the apparent lack of appropriate tubificid hosts may prevent establishment in that part of the state. However, 4 lineages (I, III, IV, and VI) of the species were identified from southcentral Alaska. Lineage IV has not been previously been described in North America and its susceptibility to M. cerebralis was unknown. When lineage IV T. tubifex and 3 mixed-lineage (I, III, IV and VI) groups were exposed to M. cerebralis, only lineage III became infected under our experimental conditions. Thus, if the parasite were dispersed, conditions are appropriate for establishment and propagation of the parasite life cycle in southcentral Alaska, although detrimental effects on fish populations may be reduced as a result of the presence of non-susceptible lineages of T. tubifex. The probability of further establishment in this area is greatest in Ship Creek, where the abundance of susceptible T. tubifex, the presence of susceptible rainbow trout (Oncorhynchus mykiss), and the proximity to the known area of infection make conditions particularly appropriate. Similar to findings in Alaska, the Willamette River basin, Oregon also supports populations of susceptible T. tubifex. If the pathogen were introduced, probability of establishment is high in certain areas of the basin as all conditions are appropriate for propagation of the parasite life cycle. Tributaries to the mainstem Willamette River have the highest probability of establishment as these areas have the greatest numbers of susceptible T. tubifex. However, the abundance of resistant strains of T. tubifex could mitigate the effects of M. cerebralis if introduced. Management recommendations to reduce the likelihood of parasite dissemination are similar for Oregon and Alaska since human movement of fish and angler activities were considered the most likely routes of introduction for both regions. Based on this research, steps should also be taken to limit human movement of fish, whether by restricting carcass planting for stream enrichment in Oregon, or by prohibiting use of fish heads as bait in southcentral Alaska. The states should also allot resources to angler education and awareness of the effects of angler activity and recreation on dispersal of M. cerebralis. This could be done using a combination of brochures and signage at boat ramps describing how to prevent spread of aquatic nuisance species. Title: Potential for dispersal of the non-native parasite Myxobolus cerebralis : qualitative risk assessments for the state of Alaska and the Willamette River Basin, Oregon Author: Arsan, E. Leyla First introduced to the USA in 1958, Myxobolus cerebralis, the parasite responsible for whirling disease in salmonids, has since spread across the country causing severe declines in wild trout populations in the intermountain west. Recent development of risk assessment models used to assess the likelihood and consequences of exotic parasite introduction, have strengthened the process of science-based decision-making in aquatic animal health. In the case of M. cerebralis, it is necessary to use a risk assessment model with two unique segments that clearly address the distinct life stages and respective hosts of the parasite separately. The studies described examine the probability of M. cerebralis introduction and establishment for two regions: the state of Alaska, and the Willamette River basin, Oregon. The Alaska risk assessment was based on the assumption that the parasite did not already occur in the state. However, in the process of validating this assumption, we documented the first polymerase chain reaction (PCR) detection of the parasite in the state. The pathogen was identified in hatchery rainbow trout (Oncorhynchus mykiss) from the Anchorage area. Although this is the first detection of the parasite in Alaska, clinical whirling disease has never been documented in the state. To qualitatively assess the risk of further spread of M. cerebralis in Alaska, four potential routes of dissemination were examined: movement of fish by humans, natural dispersal (via migratory birds and stray anadromous salmon), recreational activities, and commercial seafood processing. This research indicates the most likely pathway for M. cerebralis transport in Alaska is human movement of fish. In the Willamette River basin, Oregon, introduction of M. cerebralis has already occurred, though establishment appears limited to a single private hatchery. Introduction in this region was considered the most likely to occur as a result of human movements of fish. Straying anadromous salmonids were also assessed and were present in higher numbers than predicted. However, they were not infected with the parasite, and thus the probability for introduction by this route is low. The probability of introduction of the parasite varies throughout the Willamette River basin. Areas with the highest probability for M. cerebralis introduction were identified as the Clackamas and Santiam River subbasins. The Clackamas River has already experienced an introduction of the parasite, has the largest concentration of hatcheries (state, federal, and private), has a popular sport fishery, and is the closest major tributary to the enormous piscivorous bird-populations in the Columbia River estuary. The Santiam subbasin has a popular sport fishery, received the highest number of stray fish in the Willamette River basin, and has the second largest concentration of hatcheries in the Willamette River basin. Unique from introduction, establishment of the parasite is dependent upon several environmental and biological factors including: water temperatures, spatial/temporal overlap of hosts, and the distribution and genetic composition of the parasite’s invertebrate host, Tubifex tubifex. The distribution, genetic composition and susceptibility of T. tubifex, were considered the most important factor in the ability of M. cerebralis to establish in both systems. Surveys of oligochaete populations were conducted in both study regions. In Alaska, T. tubifex was not detected from the southeast region and the apparent lack of appropriate tubificid hosts may prevent establishment in that part of the state. However, 4 lineages (I, III, IV, and VI) of the species were identified from southcentral Alaska. Lineage IV has not been previously been described in North America and its susceptibility to M. cerebralis was unknown. When lineage IV T. tubifex and 3 mixed-lineage (I, III, IV and VI) groups were exposed to M. cerebralis, only lineage III became infected under our experimental conditions. Thus, if the parasite were dispersed, conditions are appropriate for establishment and propagation of the parasite life cycle in southcentral Alaska, although detrimental effects on fish populations may be reduced as a result of the presence of non-susceptible lineages of T. tubifex. The probability of further establishment in this area is greatest in Ship Creek, where the abundance of susceptible T. tubifex, the presence of susceptible rainbow trout (Oncorhynchus mykiss), and the proximity to the known area of infection make conditions particularly appropriate. Similar to findings in Alaska, the Willamette River basin, Oregon also supports populations of susceptible T. tubifex. If the pathogen were introduced, probability of establishment is high in certain areas of the basin as all conditions are appropriate for propagation of the parasite life cycle. Tributaries to the mainstem Willamette River have the highest probability of establishment as these areas have the greatest numbers of susceptible T. tubifex. However, the abundance of resistant strains of T. tubifex could mitigate the effects of M. cerebralis if introduced. Management recommendations to reduce the likelihood of parasite dissemination are similar for Oregon and Alaska since human movement of fish and angler activities were considered the most likely routes of introduction for both regions. Based on this research, steps should also be taken to limit human movement of fish, whether by restricting carcass planting for stream enrichment in Oregon, or by prohibiting use of fish heads as bait in southcentral Alaska. The states should also allot resources to angler education and awareness of the effects of angler activity and recreation on dispersal of M. cerebralis. This could be done using a combination of brochures and signage at boat ramps describing how to prevent spread of aquatic nuisance species. Close

• 1861. [Article] The biochemical oxygen demand of Douglas-fir needles and twigs, western hemlock needles and red alder leaves in stream water

  Field studies indicate that accumulation of finely divided organic debris in the channels of mountain streams after clearcutting may be responsible for subsequent reduction in the dissolved oxygen concentration. The ...

  Citation × Citation Citation Abstract Copy Title: The biochemical oxygen demand of Douglas-fir needles and twigs, western hemlock needles and red alder leaves in stream water Author: Ponce, Stanley L. Field studies indicate that accumulation of finely divided organic debris in the channels of mountain streams after clearcutting may be responsible for subsequent reduction in the dissolved oxygen concentration. The purpose of this study was to quantify the biochemical oxygen demand (BOD) of Douglas-fir needles and twigs, western hemlock needles and red alder leaves, ascertain the chemical characteristics of the leachate from these materials, and determine if such materials are toxic to fish. Long- and short-term BOD and BOD rate constants were determined for the different types of vegetation. A standard temperature BOD test was run 90 days for the leaf material and 45 days for the Douglas-fir twigs. Four replications were run for the leaves and three run for the twigs. Half the leaf samples were fixed with a nitrification inhibitor. However, later analyses proved nitrification did not occur. As a result, all the replications within a species were combined and one curve was fitted through each group of data. A BOD curve was constructed by least squares fit through the 90 days of leaf data and through 45 days of the twig data and extended to 90 days. The 90 day K1 and the B0D90 were calculated from this curve and were: 0. 125 and 110 mg 02/gm (dry weight) for Douglas-fir needles, 0.056 and 110 mg 02/gm (dry weight) for Douglas-fir twigs, 0.064 and 166 mg 02/gm (dry weight) for western hemlock needles, and 0. 046 and 286 mg 02/gm (dry weight) for red alder leaves. Further tests showed that these 90 day values could be accurately estimated by tests of shorter duration; 20 days for Douglas-fir and western hemlock, and 60 days for red alder. The 20-day western hemlock values may, in fact, yield a more precise estimate of the actual 90-day values than the composite fit. The 20-day western hemlock projections were 0.049 for K1 and 200 mg O2Igm (dry weight) for the B0D90. Leachates of the test materials were analyzed with respect to composition, concentration, and rate of nutrient release. This information was to be used in the explanation of the 90 day BOD values obtained. Half the samples were poisoned with 2. 7 mg/l mercuric chloride to inhibit microorganism growth while the rest of the samples remained untreated to show the effect of the microorganisms. These data were of limited use due to fungal growths appearing after 20 days and failure of half the twig samples to be adequately poisoned. The test was terminated after 20 days. Simple sugars and phenolic compounds were found in all the samples. Simple sugars present were arabinose, xylose, galactose, mannose, and glucose. Mean maximum sugar concentrations released in poisoned leaf samples varied from 21.5 mg glucose equivalent/gm (fresh weight) to 15. 0 mg/gm (fresh weight) for Douglas-fir and red alder. The mean maximum sugar concentrations in the non-poisoned samples were much less: 6. 0, 5. 0, and 8. 0 mg glucose equivalent/ gm (fresh weight) respectively for Douglas-fir, western hemlock, and red alder. The rate of sugar release was rapid for Douglas-fir needles, slow for red alder, and intermediate for western hemlock. The different types of phenolic compounds were not identified. The mean maximum concentration of phenolics in the poisoned samples were 0.72, 0.46, and 0.55 mg gallic acid/gm (fresh weight) respectively for Douglas-fir, western hemlock, and red alder leaves. There was little difference between mean concentrations of the poisoned and non-poisoned samples until day 10, at which time mean phenolic concentrations of the non-poisoned samples began to drop. The Douglas-fir twigs had a slow initial sugar release, followed by an increase in the rate; the maximum concentration reached was 10. 0 mg glucose equivalent/gm (fresh weight). The pattern of phenolic release was the same with a maximum concentration of about 1. 0 mg gallic acid/gm (fresh weight). The five-day BOD of leaf material was determined under conditions of fluctuating temperature (12. 8 to 35.00 C) similar to that observed in streams exposed by clearcutting. The BOD5 values were: 202 mg 02/gm (dry weight) for Douglas-fir, 109 mg 02/gm (dry weight) for western hemlock, and 249 mg 02/gm (dry weight) for red alder leaves. The BOD5 of samples incubated at standard temperature was much lower than those exposed to conditions of fluctuating temperature; it was 25, 42, and 24 percent of the temperature fluctuated BOD5 for Douglas-fir, western hemlock, and red alder leaves respectively. The toxicity of leachate extracted from 50 grams (fresh weight) per liter of water of each species was determined on guppies and steelhead fry. The 96-hr. LC5O to guppies from leachate of Douglas-fir, western hemlock, and red alder was 35, 65, and 18 percent of the original concentration as opposed to 26, 7. 5 and 25 percent of the original concentration for the steelhead fry. These are extremely low levels of toxicity to such a concentrated sample and pose no threat to the fish. Title: The biochemical oxygen demand of Douglas-fir needles and twigs, western hemlock needles and red alder leaves in stream water Author: Ponce, Stanley L. Field studies indicate that accumulation of finely divided organic debris in the channels of mountain streams after clearcutting may be responsible for subsequent reduction in the dissolved oxygen concentration. The purpose of this study was to quantify the biochemical oxygen demand (BOD) of Douglas-fir needles and twigs, western hemlock needles and red alder leaves, ascertain the chemical characteristics of the leachate from these materials, and determine if such materials are toxic to fish. Long- and short-term BOD and BOD rate constants were determined for the different types of vegetation. A standard temperature BOD test was run 90 days for the leaf material and 45 days for the Douglas-fir twigs. Four replications were run for the leaves and three run for the twigs. Half the leaf samples were fixed with a nitrification inhibitor. However, later analyses proved nitrification did not occur. As a result, all the replications within a species were combined and one curve was fitted through each group of data. A BOD curve was constructed by least squares fit through the 90 days of leaf data and through 45 days of the twig data and extended to 90 days. The 90 day K1 and the B0D90 were calculated from this curve and were: 0. 125 and 110 mg 02/gm (dry weight) for Douglas-fir needles, 0.056 and 110 mg 02/gm (dry weight) for Douglas-fir twigs, 0.064 and 166 mg 02/gm (dry weight) for western hemlock needles, and 0. 046 and 286 mg 02/gm (dry weight) for red alder leaves. Further tests showed that these 90 day values could be accurately estimated by tests of shorter duration; 20 days for Douglas-fir and western hemlock, and 60 days for red alder. The 20-day western hemlock values may, in fact, yield a more precise estimate of the actual 90-day values than the composite fit. The 20-day western hemlock projections were 0.049 for K1 and 200 mg O2Igm (dry weight) for the B0D90. Leachates of the test materials were analyzed with respect to composition, concentration, and rate of nutrient release. This information was to be used in the explanation of the 90 day BOD values obtained. Half the samples were poisoned with 2. 7 mg/l mercuric chloride to inhibit microorganism growth while the rest of the samples remained untreated to show the effect of the microorganisms. These data were of limited use due to fungal growths appearing after 20 days and failure of half the twig samples to be adequately poisoned. The test was terminated after 20 days. Simple sugars and phenolic compounds were found in all the samples. Simple sugars present were arabinose, xylose, galactose, mannose, and glucose. Mean maximum sugar concentrations released in poisoned leaf samples varied from 21.5 mg glucose equivalent/gm (fresh weight) to 15. 0 mg/gm (fresh weight) for Douglas-fir and red alder. The mean maximum sugar concentrations in the non-poisoned samples were much less: 6. 0, 5. 0, and 8. 0 mg glucose equivalent/ gm (fresh weight) respectively for Douglas-fir, western hemlock, and red alder. The rate of sugar release was rapid for Douglas-fir needles, slow for red alder, and intermediate for western hemlock. The different types of phenolic compounds were not identified. The mean maximum concentration of phenolics in the poisoned samples were 0.72, 0.46, and 0.55 mg gallic acid/gm (fresh weight) respectively for Douglas-fir, western hemlock, and red alder leaves. There was little difference between mean concentrations of the poisoned and non-poisoned samples until day 10, at which time mean phenolic concentrations of the non-poisoned samples began to drop. The Douglas-fir twigs had a slow initial sugar release, followed by an increase in the rate; the maximum concentration reached was 10. 0 mg glucose equivalent/gm (fresh weight). The pattern of phenolic release was the same with a maximum concentration of about 1. 0 mg gallic acid/gm (fresh weight). The five-day BOD of leaf material was determined under conditions of fluctuating temperature (12. 8 to 35.00 C) similar to that observed in streams exposed by clearcutting. The BOD5 values were: 202 mg 02/gm (dry weight) for Douglas-fir, 109 mg 02/gm (dry weight) for western hemlock, and 249 mg 02/gm (dry weight) for red alder leaves. The BOD5 of samples incubated at standard temperature was much lower than those exposed to conditions of fluctuating temperature; it was 25, 42, and 24 percent of the temperature fluctuated BOD5 for Douglas-fir, western hemlock, and red alder leaves respectively. The toxicity of leachate extracted from 50 grams (fresh weight) per liter of water of each species was determined on guppies and steelhead fry. The 96-hr. LC5O to guppies from leachate of Douglas-fir, western hemlock, and red alder was 35, 65, and 18 percent of the original concentration as opposed to 26, 7. 5 and 25 percent of the original concentration for the steelhead fry. These are extremely low levels of toxicity to such a concentrated sample and pose no threat to the fish. Close

• 1862. [Article] Insights into the Geochemical Evolution of the Youngest Toba Tuff (Sumatra, Indonesia) Magma Chamber Through the Lens of Zircon-hosted Melt Inclusions

  Supervolcanic eruptions are among the most catastrophic phenomena on Earth, erupting 100s-1000s of cubic kilometers of magma, and producing devastating local effects and global climate perturbations. The ...

  Citation × Citation Citation Abstract Copy Title: Insights into the Geochemical Evolution of the Youngest Toba Tuff (Sumatra, Indonesia) Magma Chamber Through the Lens of Zircon-hosted Melt Inclusions Author: Lerner, Allan (Allan Henry) Supervolcanic eruptions are among the most catastrophic phenomena on Earth, erupting 100s-1000s of cubic kilometers of magma, and producing devastating local effects and global climate perturbations. The largest supervolcanic eruption of the last 28 Ma was the 74 ka Youngest Toba Tuff (YTT) eruption from Sumatra, Indonesia, which erupted 2,800 – 5,300 km³ of magma and may have pushed the human species to the brink of extinction. Despite the global significance of such events, the magmatic evolution that builds to super-eruptions remains poorly understood. The mineral zircon provides a unique potential to gain multidimensional insights into the pre-eruptive evolution of magma chambers by combining mineral and melt inclusion chemistry with U-series mineral dating. We combine zircon U-Th dating and trace element chemistry with zircon-hosted melt inclusion chemistries and volatile abundances to investigate the magmatic evolution preceding the YTT eruption To begin, we present the first detailed study of the susceptibility of zircon-hosted inclusions to syn- or post-entrapment modification of melt compositions. We conclude that boundary layer effects are negligible in even very small zircon-hosted inclusions owing to the slow growth rate of zircon crystals. Post-entrapment crystallization (PEC) of the zircon host phase is also a trivial concern, owing to the low Zr content of most melts. PEC of other daughter phases is recognized (< ~2% amphibole and sanidine), but these effects are also minor relative to melt inclusions in many major-phase minerals. The diffusive exchange of water from zircon-hosted melt inclusions is modeled to occur in less than 10 ka, and requilibration may occur within decades-centuries. Therefore, water contents of zircon-hosted inclusions represent late-stage storage conditions rather than long-term records of magmatic water. Zircon-hosted inclusions should remain diffusively sealed to all melt species, apart from H⁺, He, and Li⁺, over typical magmatic system timescales (104-105 yrs). Therefore, we conclude that zircon is a robust, albeit small, melt inclusion host and entrapped inclusions will be largely representative of the melt environments in which they formed. We then apply the multidimensional utility of zircon to gain insights into the pre-eruptive evolution of the YTT magmatic system. YTT zircon grains have U-Th crystallization ages spanning from the ~74 ka eruption age to > 375 ka, reinforcing earlier findings that the YTT system was long-lived. A progressive increase of U in zircon growth zones from < 500 to ~1,500 ppm indicates that the YTT system, or a portion of it, became highly fractionated between 130-200 ka. A lull in zircon formation between ~110-130 ka is contemporaneous with a previously recognized increase in chemical diversity of allanite, possibly reflecting a period of enhanced thermal input into the system. We identify two main populations of zircon-hosted melt inclusions. A low-MgO type is chemically evolved (> 280 ppm Rb, ~125 ppm Ba, 25-30 ppm Sr, < 0.03 wt% MgO) and has high water contents (3.8-5.7 wt% H₂O), consistent with formation and storage in a highly fractionated crystal mush ~4-9 km deep. A high-MgO type (250-260 ppm Rb, 160-450 ppm Ba, 35-55 ppm Sr, 0.04-0.07 wt% MgO) has compositions similar to matrix glasses, and is typically less hydrous (0.5-3.5 wt% H₂O), suggesting shallow (< 3 km) formation, storage, and syn-eruptive degassing in a less evolved melt. Melt inclusions dated via U-Th measurements of their entrapping zircon zones show no clear temporal differences between the two MgO populations. Rather, melt inclusions entrapped throughout the entire YTT history have relatively invariant major element compositions, and also have no discernible temporal trends in volatile abundances. We largely attribute these findings to the narrow stability field in which zircon crystallize, which inherently limits the compositional range of zircon-hosted inclusions. Zircon-hosted melt inclusions (particularly the high-MgO type) of many ages occur within sealed reentrant melt-channels. This suggests that melt inclusions in YTT zircon grains commonly formed as the system re-established zircon saturation following periods of zircon dissolution during thermal recharge events. A number of zircon grains have melt channels actively open to the grain exterior, which are rimmed with 1-3 μm of cathodoluminescence-bright (low-U) zircon growth. These dissolution/regrowth features are texturally similar to dissolution zones and high-temperature overgrowths described previously in YTT quartz; collectively, these textures provide evidence of a major thermal perturbation(s) 10s-100s of years before the YTT eruption. We conclude that high-T, mafic recharge events occurred throughout the pre-eruptive YTT evolution, and suggest that one or more large recharge events triggered the cataclysmic 74 ka YTT eruption. Title: Insights into the Geochemical Evolution of the Youngest Toba Tuff (Sumatra, Indonesia) Magma Chamber Through the Lens of Zircon-hosted Melt Inclusions Author: Lerner, Allan (Allan Henry) Supervolcanic eruptions are among the most catastrophic phenomena on Earth, erupting 100s-1000s of cubic kilometers of magma, and producing devastating local effects and global climate perturbations. The largest supervolcanic eruption of the last 28 Ma was the 74 ka Youngest Toba Tuff (YTT) eruption from Sumatra, Indonesia, which erupted 2,800 – 5,300 km³ of magma and may have pushed the human species to the brink of extinction. Despite the global significance of such events, the magmatic evolution that builds to super-eruptions remains poorly understood. The mineral zircon provides a unique potential to gain multidimensional insights into the pre-eruptive evolution of magma chambers by combining mineral and melt inclusion chemistry with U-series mineral dating. We combine zircon U-Th dating and trace element chemistry with zircon-hosted melt inclusion chemistries and volatile abundances to investigate the magmatic evolution preceding the YTT eruption To begin, we present the first detailed study of the susceptibility of zircon-hosted inclusions to syn- or post-entrapment modification of melt compositions. We conclude that boundary layer effects are negligible in even very small zircon-hosted inclusions owing to the slow growth rate of zircon crystals. Post-entrapment crystallization (PEC) of the zircon host phase is also a trivial concern, owing to the low Zr content of most melts. PEC of other daughter phases is recognized (< ~2% amphibole and sanidine), but these effects are also minor relative to melt inclusions in many major-phase minerals. The diffusive exchange of water from zircon-hosted melt inclusions is modeled to occur in less than 10 ka, and requilibration may occur within decades-centuries. Therefore, water contents of zircon-hosted inclusions represent late-stage storage conditions rather than long-term records of magmatic water. Zircon-hosted inclusions should remain diffusively sealed to all melt species, apart from H⁺, He, and Li⁺, over typical magmatic system timescales (104-105 yrs). Therefore, we conclude that zircon is a robust, albeit small, melt inclusion host and entrapped inclusions will be largely representative of the melt environments in which they formed. We then apply the multidimensional utility of zircon to gain insights into the pre-eruptive evolution of the YTT magmatic system. YTT zircon grains have U-Th crystallization ages spanning from the ~74 ka eruption age to > 375 ka, reinforcing earlier findings that the YTT system was long-lived. A progressive increase of U in zircon growth zones from < 500 to ~1,500 ppm indicates that the YTT system, or a portion of it, became highly fractionated between 130-200 ka. A lull in zircon formation between ~110-130 ka is contemporaneous with a previously recognized increase in chemical diversity of allanite, possibly reflecting a period of enhanced thermal input into the system. We identify two main populations of zircon-hosted melt inclusions. A low-MgO type is chemically evolved (> 280 ppm Rb, ~125 ppm Ba, 25-30 ppm Sr, < 0.03 wt% MgO) and has high water contents (3.8-5.7 wt% H₂O), consistent with formation and storage in a highly fractionated crystal mush ~4-9 km deep. A high-MgO type (250-260 ppm Rb, 160-450 ppm Ba, 35-55 ppm Sr, 0.04-0.07 wt% MgO) has compositions similar to matrix glasses, and is typically less hydrous (0.5-3.5 wt% H₂O), suggesting shallow (< 3 km) formation, storage, and syn-eruptive degassing in a less evolved melt. Melt inclusions dated via U-Th measurements of their entrapping zircon zones show no clear temporal differences between the two MgO populations. Rather, melt inclusions entrapped throughout the entire YTT history have relatively invariant major element compositions, and also have no discernible temporal trends in volatile abundances. We largely attribute these findings to the narrow stability field in which zircon crystallize, which inherently limits the compositional range of zircon-hosted inclusions. Zircon-hosted melt inclusions (particularly the high-MgO type) of many ages occur within sealed reentrant melt-channels. This suggests that melt inclusions in YTT zircon grains commonly formed as the system re-established zircon saturation following periods of zircon dissolution during thermal recharge events. A number of zircon grains have melt channels actively open to the grain exterior, which are rimmed with 1-3 μm of cathodoluminescence-bright (low-U) zircon growth. These dissolution/regrowth features are texturally similar to dissolution zones and high-temperature overgrowths described previously in YTT quartz; collectively, these textures provide evidence of a major thermal perturbation(s) 10s-100s of years before the YTT eruption. We conclude that high-T, mafic recharge events occurred throughout the pre-eruptive YTT evolution, and suggest that one or more large recharge events triggered the cataclysmic 74 ka YTT eruption. Close

• 1863. [Article] Hawaiian duck (Anas wyvilliana) behavior and response to wetland habitat management at Hanalei National Wildlife Refuge on Kaua'i

  The endangered Hawaiian Duck (koloa maoli; Anas wyvilliana), a non-migratory and island-endemic species, experienced a significant population decline during the twentieth century due to factors such as ...

  Citation × Citation Citation Abstract Copy Title: Hawaiian duck (Anas wyvilliana) behavior and response to wetland habitat management at Hanalei National Wildlife Refuge on Kaua'i Author: Malachowski, Christopher P. The endangered Hawaiian Duck (koloa maoli; Anas wyvilliana), a non-migratory and island-endemic species, experienced a significant population decline during the twentieth century due to factors such as habitat loss, overharvest, introduced mammalian predators, and hybridization with introduced feral Mallards (A. platyrhynchos). A key objective for Hawaiian Duck recovery is to establish a protected and managed network of wetland habitats; however, development of effective habitat management plans is stymied by the lack of information on patterns of habitat use in relation to fundamental resource requirements. Furthermore, many generalizations regarding dabbling duck behavior and resource requirements that guide seasonal wetland management objectives in North America may not apply to tropical regions and island systems. In this thesis, I compare the behavioral repertoire of the Hawaiian Duck with closely related island-endemic waterfowl and migratory North American Anas, I investigate the behavioral response of Hawaiian Ducks to wetland habitat management and taro cultivation, and I examine the effects of environmental, climatic, temporal, and social factors on the activity budgets of Hawaiian Ducks. I conducted instantaneous focal sampling (n = 984 observation sessions; 328.8 hr) throughout the annual cycle from September 2010 to August 2011 at managed wetlands and taro lo'i within Hanalei National Wildlife Refuge (NWR), Kaua'i. I documented 73 specific Hawaiian Duck behaviors in eight broad behavior categories including foraging, maintenance, resting, locomotion, alert, courtship, and intraspecific and interspecific agonistic interactions. I found that the behavioral repertoire of the Hawaiian Duck was similar to that of the Mallard; however, subtle variations in the form and linkage of certain courtship displays, such as nod-swimming, were observed. Additionally, male Hawaiian Ducks were occasionally associated with brood-rearing females (11% of brood observations), and this behavior appeared to be a male strategy whereby females received little perceived benefit , but males may have potentially garnered additional breeding attempts or maintained pair-bonds for subsequent breeding seasons. After accounting for sex, pair status, month, and time of day, the diurnal behavioral activities of Hawaiian Ducks differed between managed wetlands and taro habitats (F₆,₉₆₀ = 30.3, P < 0.001). Hawaiian Ducks utilized taro predominantly for resting (44%), maintenance (21%), and foraging (15%), while birds used managed wetlands for a variety of activities, including foraging (11%), maintenance (28%), resting (27%), and locomotion (22%). Social activities, particularly courtship, occurred more frequently in managed wetlands than in taro (H₁ = 11.9, P < 0.001). In managed wetlands, birds foraged slightly more with increasing cover of Cyperus spp. (r = 0.18, P < 0.001) and Fimbristylis littoralis (r = 0.17, P < 0.01) and decreasing cover of Urochloa mutica (r = -0.15, P < 0.01) and wetland vegetation height (r = -0.22, P < 0.001). Within taro habitat, the behavioral activities of Hawaiian Ducks differed significantly between birds in lo'i and on dikes (F₆,₄₆₈ = 142.8, P < 0.001); birds utilized lo‘i dikes for resting (60%) and maintenance activities (21%), whereas birds entered lo‘i primarily to forage (45%). The activity budget of Hawaiian Ducks was strongly influenced by time of day (F₁₈,₂₇₁₅.₇₈ = 6.4, P < 0.001), and birds spent more time engaged in active behaviors (i.e., foraging, locomotion, and alert) and less time resting during early morning and evening than during late morning and afternoon. While strong seasonal shifts in most behavioral patterns were not detected, males allocated more time to courting (1.1 vs. 0.3%; H1 = 6.92, P = 0.009) and mate-guarding (0.5 vs. <0.1%; H₁ = 9.83, P = 0.002) in managed wetlands between November and March than the remainder of the year. The effects of sex (F₆,₉₆₀ = 6.06, P < 0.001) and social status (F₆,₆₈₂ = 6.69, P < 0.001) on activity budgets were also significant. Females spent more time foraging (18 vs. 12%) and less time in alert, locomotor, and social behaviors than males. Paired birds allocated more time to aggression towards conspecifics, mate-guarding, and courtship, and within taro lo‘i, paired birds foraged more and rested less than unpaired birds. Overall, Hawaiian Duck allocated diurnal activity budgets differently in managed and cultivated wetland habitat at Hanalei NWR, suggesting that both systems may play an important role in fulfilling fundamental daily and seasonal resource requirements. The increased range of activities and foraging tactics used in managed wetlands may indicate the greater habitat diversity (e.g., vegetation structure, patchiness, plant species richness, range of water depths) provided by seasonal wetlands. In general, Hawaiian Duck allocated less time to diurnal foraging than North American Anas, such Mallard and Mottled Duck (A. fulvigula), suggesting that Hawaiian Duck may have lower daily and seasonal energy demands, have access to higher quality diet, or allot more time to nocturnal foraging activities. Also, unlike many North American migratory waterfowl that demonstrate significant behavioral plasticity in adjusting activity budgets to meet seasonal energy demands associated with breeding, molting, wintering, and migration, Hawaiian Duck did not exhibit a strong seasonal shift in most behaviors which may reflect their non-migratory nature and asynchronous life history cycle. Title: Hawaiian duck (Anas wyvilliana) behavior and response to wetland habitat management at Hanalei National Wildlife Refuge on Kaua'i Author: Malachowski, Christopher P. The endangered Hawaiian Duck (koloa maoli; Anas wyvilliana), a non-migratory and island-endemic species, experienced a significant population decline during the twentieth century due to factors such as habitat loss, overharvest, introduced mammalian predators, and hybridization with introduced feral Mallards (A. platyrhynchos). A key objective for Hawaiian Duck recovery is to establish a protected and managed network of wetland habitats; however, development of effective habitat management plans is stymied by the lack of information on patterns of habitat use in relation to fundamental resource requirements. Furthermore, many generalizations regarding dabbling duck behavior and resource requirements that guide seasonal wetland management objectives in North America may not apply to tropical regions and island systems. In this thesis, I compare the behavioral repertoire of the Hawaiian Duck with closely related island-endemic waterfowl and migratory North American Anas, I investigate the behavioral response of Hawaiian Ducks to wetland habitat management and taro cultivation, and I examine the effects of environmental, climatic, temporal, and social factors on the activity budgets of Hawaiian Ducks. I conducted instantaneous focal sampling (n = 984 observation sessions; 328.8 hr) throughout the annual cycle from September 2010 to August 2011 at managed wetlands and taro lo'i within Hanalei National Wildlife Refuge (NWR), Kaua'i. I documented 73 specific Hawaiian Duck behaviors in eight broad behavior categories including foraging, maintenance, resting, locomotion, alert, courtship, and intraspecific and interspecific agonistic interactions. I found that the behavioral repertoire of the Hawaiian Duck was similar to that of the Mallard; however, subtle variations in the form and linkage of certain courtship displays, such as nod-swimming, were observed. Additionally, male Hawaiian Ducks were occasionally associated with brood-rearing females (11% of brood observations), and this behavior appeared to be a male strategy whereby females received little perceived benefit , but males may have potentially garnered additional breeding attempts or maintained pair-bonds for subsequent breeding seasons. After accounting for sex, pair status, month, and time of day, the diurnal behavioral activities of Hawaiian Ducks differed between managed wetlands and taro habitats (F₆,₉₆₀ = 30.3, P < 0.001). Hawaiian Ducks utilized taro predominantly for resting (44%), maintenance (21%), and foraging (15%), while birds used managed wetlands for a variety of activities, including foraging (11%), maintenance (28%), resting (27%), and locomotion (22%). Social activities, particularly courtship, occurred more frequently in managed wetlands than in taro (H₁ = 11.9, P < 0.001). In managed wetlands, birds foraged slightly more with increasing cover of Cyperus spp. (r = 0.18, P < 0.001) and Fimbristylis littoralis (r = 0.17, P < 0.01) and decreasing cover of Urochloa mutica (r = -0.15, P < 0.01) and wetland vegetation height (r = -0.22, P < 0.001). Within taro habitat, the behavioral activities of Hawaiian Ducks differed significantly between birds in lo'i and on dikes (F₆,₄₆₈ = 142.8, P < 0.001); birds utilized lo‘i dikes for resting (60%) and maintenance activities (21%), whereas birds entered lo‘i primarily to forage (45%). The activity budget of Hawaiian Ducks was strongly influenced by time of day (F₁₈,₂₇₁₅.₇₈ = 6.4, P < 0.001), and birds spent more time engaged in active behaviors (i.e., foraging, locomotion, and alert) and less time resting during early morning and evening than during late morning and afternoon. While strong seasonal shifts in most behavioral patterns were not detected, males allocated more time to courting (1.1 vs. 0.3%; H1 = 6.92, P = 0.009) and mate-guarding (0.5 vs. <0.1%; H₁ = 9.83, P = 0.002) in managed wetlands between November and March than the remainder of the year. The effects of sex (F₆,₉₆₀ = 6.06, P < 0.001) and social status (F₆,₆₈₂ = 6.69, P < 0.001) on activity budgets were also significant. Females spent more time foraging (18 vs. 12%) and less time in alert, locomotor, and social behaviors than males. Paired birds allocated more time to aggression towards conspecifics, mate-guarding, and courtship, and within taro lo‘i, paired birds foraged more and rested less than unpaired birds. Overall, Hawaiian Duck allocated diurnal activity budgets differently in managed and cultivated wetland habitat at Hanalei NWR, suggesting that both systems may play an important role in fulfilling fundamental daily and seasonal resource requirements. The increased range of activities and foraging tactics used in managed wetlands may indicate the greater habitat diversity (e.g., vegetation structure, patchiness, plant species richness, range of water depths) provided by seasonal wetlands. In general, Hawaiian Duck allocated less time to diurnal foraging than North American Anas, such Mallard and Mottled Duck (A. fulvigula), suggesting that Hawaiian Duck may have lower daily and seasonal energy demands, have access to higher quality diet, or allot more time to nocturnal foraging activities. Also, unlike many North American migratory waterfowl that demonstrate significant behavioral plasticity in adjusting activity budgets to meet seasonal energy demands associated with breeding, molting, wintering, and migration, Hawaiian Duck did not exhibit a strong seasonal shift in most behaviors which may reflect their non-migratory nature and asynchronous life history cycle. Close

• 1864. [Article] Statistical Methods for Tissue Culture Medium Optimization and A Multiplexed Fingerprinting Set for Hazelnuts

  Hazelnut is one of the most important nuts in worldwide production and the European hazelnut (Corylus avellana L.) is the most economically important of the 11 recognized hazelnut species. Development ...

  Citation × Citation Citation Abstract Copy Title: Statistical Methods for Tissue Culture Medium Optimization and A Multiplexed Fingerprinting Set for Hazelnuts Author: Akin, Melekşen Hazelnut is one of the most important nuts in worldwide production and the European hazelnut (Corylus avellana L.) is the most economically important of the 11 recognized hazelnut species. Development of new cultivars is continuous, with emphasis on better nut quality, high yield and disease resistance. Hazelnuts are highly heterozygous, and clonally propagated. Traditional propagation methods in hazelnut are not rapid enough to provide the required nursery stock for newly released hazelnut cultivars, but micropropagation can provide rapid production of hazelnut planting stock. Several growth media are available for specific cultivars, but many are not suitable for the wide range of germplasm used in new cultivars. Micropropagation of hazelnuts remains challenging due to the various responses of diverse genotypes to in vitro growth. Several studies incrimentally improved the growth medium, but determining exact nutrient requirements was difficult. The aim of this study was to determine which statistical methods would make the growth medium optimization process more practical and to develop an optimal micropropagation medium for diverse hazelnuts by testing salts and ions as factors within the experimental design. In addition an SSR fingerprinting set suitable for a diverse group of hazelnuts was developed. The first study was designed to test the effect of salts on three hazelnut genotypes and compare two methods of data analysis. Driver and Kuniyuki Walnut medium (DKW) macro-salts (NH₄NO₃, Ca(NO₃)₂∙4H₂O, CaCl₂∙2H₂O, MgSO₄∙7H₂O, KH₂PO₄ and K₂SO₄) were varied from 0.5× to 3× DKW concentrations with 42 combinations in a IV-optimal design. Shoot quality, shoot length, multiplication and callus formation were rated and analyzed using Response Surface Methodology (RSM) and the Chi-Squared Automatic Interaction Detection (CHAID) data mining algorithm. Both analyses indicated that NH₄NO₃ was a predominant nutrient factor. RSM results were genotype dependent while CHAID included genotype as a factor in the analysis, allowing development of a common medium rather than several genotype-specific media. Overall, CHAID results were more specific and easier to interpret than RSM graphs. The optimal growth medium for diverse hazelnut genotypes was formulated as: 0.5× NH₄NO₃, 3× KH₂PO₄, 1.5× Ca(NO₃)₂ and and the rest of the macro salts set at 1× DKW with modified minor nutrients [4× H₃BO₃, 4× Na₂MoO₄∙2H₂O, 4× Zn(NO₃)₂∙6H₂O, 0.5× MnSO₄∙H₂O, 0.5× CuSO₄∙5H₂O]. The second study was to determine the effects of ions on tissue culture medium optimization. NH₄⁺, Ca²⁺, Mg²⁺, SO₄²⁻ and PO₄³⁻ ions were used as factors in a D-optimal design. K⁺ and NO₃⁻ ions were used to bring the pH level to neutral, and as factors in the statistical analysis. The CHAID data mining algorithm was used to analyze shoot growth responses of three hazelnut genotypes. The algorithm trees revealed significant variables and their interactions, and provided exact cut-off amounts for each of the ions for the related growth response by incorporating genotype as an independent factor. The critical cut-off values for good shoot quality, elongation, multiplication and medium callus formation were suggested to be: NO₃⁻ <88 mM, NH₄⁺ <20 mM, Ca²⁺ <5 mM, Mg²⁺ >5 mM and K⁺ <46 mM. Another step of the research was to develop a reliable and economical fingerprinting set consisting of high core-repeat SSRs (≥3) for genotype identification of 102 hazelnut accessions. Identification of trueness-to-type by phenotypic observation is very difficult and labeling mistakes during the several steps of micropropagation can result in costly errors. The use of SSRs for plant identification is preferred over other molecular markers because they are reproducible across laboratories, exhibit co-dominant inheritance, have a large number of alleles per locus and are randomly distributed throughout the genome. Twenty SSRs containing repeat motifs of three or more nucleotides distributed throughout the hazelnut genome were screened on eight genetically diverse cultivars to assess polymorphism, allele size range, and ease of scoring. Six SSRs were discarded after genotyping 96 hazelnut samples, either due to large allele bin widths and/or alleles that do not match the motifs, complicating allele scoring. Fourteen polymorphic, easy-to-score SSRs with non-overlapping alleles were selected and amplified in a single multiplex. The multiplexed set generated the same alleles that were obtained when amplifying each SSR individually in the eight test accessions. SSR primer concentrations were then optimized to generate a clear signal for each locus. This 14-SSR fingerprinting set was used to genotype 102 hazelnut accessions, and distinguished unique accessions mainly according to parentage and in some cases based on geographic origin. As a result of these studies, salt- and ion-based optimized tissue culture medium formulations were developed for diverse hazelnuts. The importance of salts and ions as factors within the experimental design and analysis was examined, and using salts as factors results in complexity within the design as the effects of ions can not be determined. Although salt optimization studies are still a powerful tool, and are experimentally easier, optimization at the ionic level provided a clearer evaluation of the ion-based growth responses, because the plants take up minerals as ions of the corresponding salts. Data mining (CHAID) was used to make the tissue culture optimization process more practical compared to analysis with the standard ANOVA, regression and RSM. CHAID delineated specific concentrations that were effective and allowed easier analysis of nutrient content for an improved medium. A reliable and cost-effective multiplexed fingerprinting set of 14 SSR markers was developed for confirming identity and paternity in diverse hazelnut cultivars and species and 102 accessions were fingerprinted. Title: Statistical Methods for Tissue Culture Medium Optimization and A Multiplexed Fingerprinting Set for Hazelnuts Author: Akin, Melekşen Hazelnut is one of the most important nuts in worldwide production and the European hazelnut (Corylus avellana L.) is the most economically important of the 11 recognized hazelnut species. Development of new cultivars is continuous, with emphasis on better nut quality, high yield and disease resistance. Hazelnuts are highly heterozygous, and clonally propagated. Traditional propagation methods in hazelnut are not rapid enough to provide the required nursery stock for newly released hazelnut cultivars, but micropropagation can provide rapid production of hazelnut planting stock. Several growth media are available for specific cultivars, but many are not suitable for the wide range of germplasm used in new cultivars. Micropropagation of hazelnuts remains challenging due to the various responses of diverse genotypes to in vitro growth. Several studies incrimentally improved the growth medium, but determining exact nutrient requirements was difficult. The aim of this study was to determine which statistical methods would make the growth medium optimization process more practical and to develop an optimal micropropagation medium for diverse hazelnuts by testing salts and ions as factors within the experimental design. In addition an SSR fingerprinting set suitable for a diverse group of hazelnuts was developed. The first study was designed to test the effect of salts on three hazelnut genotypes and compare two methods of data analysis. Driver and Kuniyuki Walnut medium (DKW) macro-salts (NH₄NO₃, Ca(NO₃)₂∙4H₂O, CaCl₂∙2H₂O, MgSO₄∙7H₂O, KH₂PO₄ and K₂SO₄) were varied from 0.5× to 3× DKW concentrations with 42 combinations in a IV-optimal design. Shoot quality, shoot length, multiplication and callus formation were rated and analyzed using Response Surface Methodology (RSM) and the Chi-Squared Automatic Interaction Detection (CHAID) data mining algorithm. Both analyses indicated that NH₄NO₃ was a predominant nutrient factor. RSM results were genotype dependent while CHAID included genotype as a factor in the analysis, allowing development of a common medium rather than several genotype-specific media. Overall, CHAID results were more specific and easier to interpret than RSM graphs. The optimal growth medium for diverse hazelnut genotypes was formulated as: 0.5× NH₄NO₃, 3× KH₂PO₄, 1.5× Ca(NO₃)₂ and and the rest of the macro salts set at 1× DKW with modified minor nutrients [4× H₃BO₃, 4× Na₂MoO₄∙2H₂O, 4× Zn(NO₃)₂∙6H₂O, 0.5× MnSO₄∙H₂O, 0.5× CuSO₄∙5H₂O]. The second study was to determine the effects of ions on tissue culture medium optimization. NH₄⁺, Ca²⁺, Mg²⁺, SO₄²⁻ and PO₄³⁻ ions were used as factors in a D-optimal design. K⁺ and NO₃⁻ ions were used to bring the pH level to neutral, and as factors in the statistical analysis. The CHAID data mining algorithm was used to analyze shoot growth responses of three hazelnut genotypes. The algorithm trees revealed significant variables and their interactions, and provided exact cut-off amounts for each of the ions for the related growth response by incorporating genotype as an independent factor. The critical cut-off values for good shoot quality, elongation, multiplication and medium callus formation were suggested to be: NO₃⁻ <88 mM, NH₄⁺ <20 mM, Ca²⁺ <5 mM, Mg²⁺ >5 mM and K⁺ <46 mM. Another step of the research was to develop a reliable and economical fingerprinting set consisting of high core-repeat SSRs (≥3) for genotype identification of 102 hazelnut accessions. Identification of trueness-to-type by phenotypic observation is very difficult and labeling mistakes during the several steps of micropropagation can result in costly errors. The use of SSRs for plant identification is preferred over other molecular markers because they are reproducible across laboratories, exhibit co-dominant inheritance, have a large number of alleles per locus and are randomly distributed throughout the genome. Twenty SSRs containing repeat motifs of three or more nucleotides distributed throughout the hazelnut genome were screened on eight genetically diverse cultivars to assess polymorphism, allele size range, and ease of scoring. Six SSRs were discarded after genotyping 96 hazelnut samples, either due to large allele bin widths and/or alleles that do not match the motifs, complicating allele scoring. Fourteen polymorphic, easy-to-score SSRs with non-overlapping alleles were selected and amplified in a single multiplex. The multiplexed set generated the same alleles that were obtained when amplifying each SSR individually in the eight test accessions. SSR primer concentrations were then optimized to generate a clear signal for each locus. This 14-SSR fingerprinting set was used to genotype 102 hazelnut accessions, and distinguished unique accessions mainly according to parentage and in some cases based on geographic origin. As a result of these studies, salt- and ion-based optimized tissue culture medium formulations were developed for diverse hazelnuts. The importance of salts and ions as factors within the experimental design and analysis was examined, and using salts as factors results in complexity within the design as the effects of ions can not be determined. Although salt optimization studies are still a powerful tool, and are experimentally easier, optimization at the ionic level provided a clearer evaluation of the ion-based growth responses, because the plants take up minerals as ions of the corresponding salts. Data mining (CHAID) was used to make the tissue culture optimization process more practical compared to analysis with the standard ANOVA, regression and RSM. CHAID delineated specific concentrations that were effective and allowed easier analysis of nutrient content for an improved medium. A reliable and cost-effective multiplexed fingerprinting set of 14 SSR markers was developed for confirming identity and paternity in diverse hazelnut cultivars and species and 102 accessions were fingerprinted. Close

• 1865. [Image] Dear concerned citizen

  	"Bureau of Land Management's (BLM) proposed decision and finding of no significant impact for the Lost River Management Framework Plan amendments."-- P. [1]; August 19, 1988."; "BLM-OR-PT-88-12-1792"--P. ...
  	Citation × Citation Citation Abstract Copy Title: Dear concerned citizen Year: 1988, 2005 "Bureau of Land Management's (BLM) proposed decision and finding of no significant impact for the Lost River Management Framework Plan amendments."-- P. [1]; August 19, 1988."; "BLM-OR-PT-88-12-1792"--P. 8 Title: Dear concerned citizen Year: 1988, 2005 "Bureau of Land Management's (BLM) proposed decision and finding of no significant impact for the Lost River Management Framework Plan amendments."-- P. [1]; August 19, 1988."; "BLM-OR-PT-88-12-1792"--P. 8 Close

• 1866. [Image] Effects of water quality on growth of juvenile shortnose suckers, Chasmistes brevirostris (Catostomidae: Cypriniformes), from Upper Klamath Lake, Oregon

  	One chapter of a seven chapter annual report from 1999 examining ecological issues regarding the shortnose and Lost River sucker populations in Upper Klamath Lake and Williamson River.
  	Citation × Citation Citation Abstract Copy Title: Effects of water quality on growth of juvenile shortnose suckers, Chasmistes brevirostris (Catostomidae: Cypriniformes), from Upper Klamath Lake, Oregon Author: Oregon Cooperative Wildlife Research Unit Year: 2000, 2005 One chapter of a seven chapter annual report from 1999 examining ecological issues regarding the shortnose and Lost River sucker populations in Upper Klamath Lake and Williamson River. Title: Effects of water quality on growth of juvenile shortnose suckers, Chasmistes brevirostris (Catostomidae: Cypriniformes), from Upper Klamath Lake, Oregon Author: Oregon Cooperative Wildlife Research Unit Year: 2000, 2005 One chapter of a seven chapter annual report from 1999 examining ecological issues regarding the shortnose and Lost River sucker populations in Upper Klamath Lake and Williamson River. Close

• 1867. [Image] Biological opinion Klamath Project operations

  	"May 31, 2002."; Includes bibliographical references.
  	Citation × Citation Citation Abstract Copy Title: Biological opinion Klamath Project operations Author: United States.; National Marine Fisheries Service. Year: 2002, 2008, 2005 "May 31, 2002."; Includes bibliographical references. Title: Biological opinion Klamath Project operations Author: United States.; National Marine Fisheries Service. Year: 2002, 2008, 2005 "May 31, 2002."; Includes bibliographical references. Close

• 1868. [Image] The Chemical and biological impact of Klamath Marsh on the Williamson River, Oregon

  	A comparative study of the Williamson River (before and after passage through Klamath Marsh) and the Sprague River (which is a major tributary of the Williamson River) in South Central Oregon has provided ...
  	Citation × Citation Citation Abstract Copy Title: The Chemical and biological impact of Klamath Marsh on the Williamson River, Oregon Author: Perdue, Edward M. Year: 1981, 2005 A comparative study of the Williamson River (before and after passage through Klamath Marsh) and the Sprague River (which is a major tributary of the Williamson River) in South Central Oregon has provided substantial insight into the effects of a marsh environment on the transport of iron and aquatic humus in river water. In the Sprague River and in the pre-marsh Williamson River, iron is transported primarily as 0.80 ym suspended particulate material. In Klamath Marsh, this coarse particulate material is "weathered11, yielding iron-aquatic humus "complexes'1. Thus, most iron and aquatic humus in the post-marsh Williamson River are in the 0.025 ?m size fraction. Presumably, other trace metals would be similarly affected. Klamath Marsh serves as an important source of biologically derived solutes such as amino acids and sugars. Fractionation studies have shown that amino acids are almost exclusively humic-bound in the Will-iamson River system, while sugars may be present as either polysacchar-ides (PS) or humic-bound saccharides (HS). The PS/HS ratio may reflect the relative importance of autochthonous and allochthonous sources of sugars. Major solute composition strongly indicates that ground waters flowing into the pre-marsh Williamson River and the Sprague River are derived from a different source than are ground waters which enter the post-marsh Williamson River from Big Springs, Spring Creek, and from unidentified springs below Klamath Marsh. Nutrient concentrations (H4SiO4, NO3, PO43) are significantly higher in spring waters than elsewhere in the system. While nitrate levels (3-11 ?m) were somewhat low, phosphate levels (1-3 ?m) were quite high throughout the Williamson River system. There was some evidence for nitrogen limitation of algal growth in the pre-marsh Williamson River. While Fragilaria construens was dominant throughout the Williamson River system, several Navicula spp. were restricted to the pre-marsh Williamson River and several Fragilaria spp. and Nitzschia, spp. were found only in the post-marsh Williamson River. In Upper Klamath Lake, Stephanodiscus astrea minuta, Fragilaria construens, and Aphanizomenon flos-aquae appeared in succession, with nuisance blooms of the latter organism occurring July-November. The cessation of flow of humic-rich water from Klamath Marsh during the summer months drastically decreased the flux of aquatic humus, iron, amino acids, and other marsh-derived solutes in the post-marsh Williamson River. At the time of cessation of flow from Klamath Marsh, nuisance blooms of Aphanizomenon flos-aquae appeared in Upper Klamath Lake. Furthermore, when flow from the marsh was re-established with the first major winter rains in November or December, Aphanizomenon flos-aquae abruptly ceased to grow in Upper Klamath Lake. Further studies are planned to determine whether this correlation is causal or coincidental. Title: The Chemical and biological impact of Klamath Marsh on the Williamson River, Oregon Author: Perdue, Edward M. Year: 1981, 2005 A comparative study of the Williamson River (before and after passage through Klamath Marsh) and the Sprague River (which is a major tributary of the Williamson River) in South Central Oregon has provided substantial insight into the effects of a marsh environment on the transport of iron and aquatic humus in river water. In the Sprague River and in the pre-marsh Williamson River, iron is transported primarily as 0.80 ym suspended particulate material. In Klamath Marsh, this coarse particulate material is "weathered11, yielding iron-aquatic humus "complexes'1. Thus, most iron and aquatic humus in the post-marsh Williamson River are in the 0.025 ?m size fraction. Presumably, other trace metals would be similarly affected. Klamath Marsh serves as an important source of biologically derived solutes such as amino acids and sugars. Fractionation studies have shown that amino acids are almost exclusively humic-bound in the Will-iamson River system, while sugars may be present as either polysacchar-ides (PS) or humic-bound saccharides (HS). The PS/HS ratio may reflect the relative importance of autochthonous and allochthonous sources of sugars. Major solute composition strongly indicates that ground waters flowing into the pre-marsh Williamson River and the Sprague River are derived from a different source than are ground waters which enter the post-marsh Williamson River from Big Springs, Spring Creek, and from unidentified springs below Klamath Marsh. Nutrient concentrations (H4SiO4, NO3, PO43) are significantly higher in spring waters than elsewhere in the system. While nitrate levels (3-11 ?m) were somewhat low, phosphate levels (1-3 ?m) were quite high throughout the Williamson River system. There was some evidence for nitrogen limitation of algal growth in the pre-marsh Williamson River. While Fragilaria construens was dominant throughout the Williamson River system, several Navicula spp. were restricted to the pre-marsh Williamson River and several Fragilaria spp. and Nitzschia, spp. were found only in the post-marsh Williamson River. In Upper Klamath Lake, Stephanodiscus astrea minuta, Fragilaria construens, and Aphanizomenon flos-aquae appeared in succession, with nuisance blooms of the latter organism occurring July-November. The cessation of flow of humic-rich water from Klamath Marsh during the summer months drastically decreased the flux of aquatic humus, iron, amino acids, and other marsh-derived solutes in the post-marsh Williamson River. At the time of cessation of flow from Klamath Marsh, nuisance blooms of Aphanizomenon flos-aquae appeared in Upper Klamath Lake. Furthermore, when flow from the marsh was re-established with the first major winter rains in November or December, Aphanizomenon flos-aquae abruptly ceased to grow in Upper Klamath Lake. Further studies are planned to determine whether this correlation is causal or coincidental. Close

• 1869. [Image] Evaluation of instream fish habitat restoration structures in Klamath River tributaries, 1988/1989

  	Annual Report For Interagency Agreement 14-16-0001-89508 EVALUATION OF INSTREAM FISH HABITAT RESTORATION STRUCTURES IN KLAMATH RIVER TRIBUTARIES 1988/1989 by A.D.Olson and J.R. West USDA-Forest Service, ...
  	Citation × Citation Citation Abstract Copy Title: Evaluation of instream fish habitat restoration structures in Klamath River tributaries, 1988/1989 Author: Olson, A. D. Year: 1989, 2008, 2006 Annual Report For Interagency Agreement 14-16-0001-89508 EVALUATION OF INSTREAM FISH HABITAT RESTORATION STRUCTURES IN KLAMATH RIVER TRIBUTARIES 1988/1989 by A.D.Olson and J.R. West USDA-Forest Service, Klamath National Forest 1312 Fairlane Road, Yreka, CA 96097 ABSTRACT Ten instream fish habitat techniques were evaluated to determine which most effectively restored salmonid spawning and/or rearing conditions. Structure stability was estimated based on how intact each structure remained (by percent) and its age, we then projected useful life for each structure type. Cost in 1989 dollars was used to determine cost per unit habitat area provided. Observed use by spawners was used to estimate total number of redds per structure (over its life). Cost of providing spawning habitat (cost per redd) was calculated by dividing estimated total redds by structure cost. Habitats resulting from instream structures were classified using the modified Bisson method and we determined the influence zone of each structure using physical variables to define habitat area. Structures were biologically sampled using direct underwater observation techniques described by Hankin and Reeves1 (1989). Two person dive teams used a "two-pass" method to enumerate and classify salmonids by species and age-class (0+, 1+ or older juveniles, and adults), noting the presence of other species. Fish use of structure affected habitat (post-modification) was compared to use of habitats like those present prior to structure placement (pre-modification). Comparison of "pre-modification" and "post-modification" fish standing crops resulted in a "net fish difference" which was divided by structure cost, yielding "cost per fish reared11. Boulder weirs, the most expensive structures investigated, did not affect enough surface area to make cost per unit of affected habitat reasonable. Cabled cover logs and digger logs (lowest cost structures) were very cost effective at altering physical habitat condition. We believe cost of physically modifying habitat area is only one factor that is important enough to effect success or failure of a large scale habitat restoration program. Assuming all other factors are of equal weight, lowest cost structures can provide the "best value". Modification prescribed to restore stable spawning habitat needs close scrutiny. We believe it is essential to know how the existing habitat is used by spawners by conducting spawning area use surveys which identify redd location and quantify habitat available during each spawning period. Boulder deflectors were best utilized by Chinook salmon spawners, however chinook spawner use of "traditional" structures (weirs backfilled with gravel) was disappointing. Backfilling of instream structures with suitable gravel is a practice that should be discontinued. Steelhead spawner use of structures which result in "pocket water" type spawning areas were heavily used. This habitat configuration proved most desirable when woody object cover was readily available to the spawners. The highest steelhead spawner use was associated with boulder groups with wood and boulder/rootwad groups. We found rearing structures which provided high habitat and cover diversity received the best response from juvenile fish. We observed fish use over one summer and saw dramatic unpredictable use changes even through this short time period. Fish rearing needs during other seasons may differ substantially from summer needs, therefore, suitability of modified habitat probably also changes. Digger logs, one of the least costly and simplest structures, provided the best increase in fish standing crop (fish/m2) for the lowest cost. We believe digger logs were well used by rearing fish because they are one of the most natural restoration structures investigated. Other structures which were well used (small weirs, deflectors, and boulder groups with attached wood) also seem to closely duplicate naturally productive habitats. Higher velocity habitat types associated with boulder groups with wood, boulder rootwad groups, and boulder deflectors were selected by juvenile steelhead and chinook salmon. Providing overhead cover, especially if it extends into the water where it may also be used as object cover, seemed most valuable for juvenile steelhead and salmon if it was placed in a habitat type which would normally receive high fish use. Placement of object cover in slow velocity areas (pool and glide edges) had questionable value for summer rearing habitat restoration, however we do not know what value these structures may have during colder water high flow periods when fish seek slow velocity, densely-covered habitats. We defined the most cost effective method as one meeting restoration objectives, providing the greatest increase in fish use (per surface area or volume), over the longest time period, for the lowest cost. We rank structures evaluated in this study (from most cost-effective to least cost effective) as follows: Digger Logs, Boulder deflectors, Small Boulder Weirs, Boulder Groups with Woody Cover, Free Boulder Weirs, Large Boulder Weirs, Boulder Groups, Boulder/Rootwad Groups, Boulder/Rootwad Deflectors, Small Boulder Weirs, and Cabled Cover Logs. Title: Evaluation of instream fish habitat restoration structures in Klamath River tributaries, 1988/1989 Author: Olson, A. D. Year: 1989, 2008, 2006 Annual Report For Interagency Agreement 14-16-0001-89508 EVALUATION OF INSTREAM FISH HABITAT RESTORATION STRUCTURES IN KLAMATH RIVER TRIBUTARIES 1988/1989 by A.D.Olson and J.R. West USDA-Forest Service, Klamath National Forest 1312 Fairlane Road, Yreka, CA 96097 ABSTRACT Ten instream fish habitat techniques were evaluated to determine which most effectively restored salmonid spawning and/or rearing conditions. Structure stability was estimated based on how intact each structure remained (by percent) and its age, we then projected useful life for each structure type. Cost in 1989 dollars was used to determine cost per unit habitat area provided. Observed use by spawners was used to estimate total number of redds per structure (over its life). Cost of providing spawning habitat (cost per redd) was calculated by dividing estimated total redds by structure cost. Habitats resulting from instream structures were classified using the modified Bisson method and we determined the influence zone of each structure using physical variables to define habitat area. Structures were biologically sampled using direct underwater observation techniques described by Hankin and Reeves1 (1989). Two person dive teams used a "two-pass" method to enumerate and classify salmonids by species and age-class (0+, 1+ or older juveniles, and adults), noting the presence of other species. Fish use of structure affected habitat (post-modification) was compared to use of habitats like those present prior to structure placement (pre-modification). Comparison of "pre-modification" and "post-modification" fish standing crops resulted in a "net fish difference" which was divided by structure cost, yielding "cost per fish reared11. Boulder weirs, the most expensive structures investigated, did not affect enough surface area to make cost per unit of affected habitat reasonable. Cabled cover logs and digger logs (lowest cost structures) were very cost effective at altering physical habitat condition. We believe cost of physically modifying habitat area is only one factor that is important enough to effect success or failure of a large scale habitat restoration program. Assuming all other factors are of equal weight, lowest cost structures can provide the "best value". Modification prescribed to restore stable spawning habitat needs close scrutiny. We believe it is essential to know how the existing habitat is used by spawners by conducting spawning area use surveys which identify redd location and quantify habitat available during each spawning period. Boulder deflectors were best utilized by Chinook salmon spawners, however chinook spawner use of "traditional" structures (weirs backfilled with gravel) was disappointing. Backfilling of instream structures with suitable gravel is a practice that should be discontinued. Steelhead spawner use of structures which result in "pocket water" type spawning areas were heavily used. This habitat configuration proved most desirable when woody object cover was readily available to the spawners. The highest steelhead spawner use was associated with boulder groups with wood and boulder/rootwad groups. We found rearing structures which provided high habitat and cover diversity received the best response from juvenile fish. We observed fish use over one summer and saw dramatic unpredictable use changes even through this short time period. Fish rearing needs during other seasons may differ substantially from summer needs, therefore, suitability of modified habitat probably also changes. Digger logs, one of the least costly and simplest structures, provided the best increase in fish standing crop (fish/m2) for the lowest cost. We believe digger logs were well used by rearing fish because they are one of the most natural restoration structures investigated. Other structures which were well used (small weirs, deflectors, and boulder groups with attached wood) also seem to closely duplicate naturally productive habitats. Higher velocity habitat types associated with boulder groups with wood, boulder rootwad groups, and boulder deflectors were selected by juvenile steelhead and chinook salmon. Providing overhead cover, especially if it extends into the water where it may also be used as object cover, seemed most valuable for juvenile steelhead and salmon if it was placed in a habitat type which would normally receive high fish use. Placement of object cover in slow velocity areas (pool and glide edges) had questionable value for summer rearing habitat restoration, however we do not know what value these structures may have during colder water high flow periods when fish seek slow velocity, densely-covered habitats. We defined the most cost effective method as one meeting restoration objectives, providing the greatest increase in fish use (per surface area or volume), over the longest time period, for the lowest cost. We rank structures evaluated in this study (from most cost-effective to least cost effective) as follows: Digger Logs, Boulder deflectors, Small Boulder Weirs, Boulder Groups with Woody Cover, Free Boulder Weirs, Large Boulder Weirs, Boulder Groups, Boulder/Rootwad Groups, Boulder/Rootwad Deflectors, Small Boulder Weirs, and Cabled Cover Logs. Close

• 1870. [Image] Environmental assessment for snowmobile rulemaking in Crater Lake National Park, January 2001

  	ill., maps; "00383.O1D-CRATER LAKE"; "NPSD-306 Jan 2001"; Includes bibliographical references
  	Citation × Citation Citation Abstract Copy Title: Environmental assessment for snowmobile rulemaking in Crater Lake National Park, January 2001 Author: Crater Lake National Park (Agency : U.S.) Year: 2001, 2010 ill., maps; "00383.O1D-CRATER LAKE"; "NPSD-306 Jan 2001"; Includes bibliographical references Title: Environmental assessment for snowmobile rulemaking in Crater Lake National Park, January 2001 Author: Crater Lake National Park (Agency : U.S.) Year: 2001, 2010 ill., maps; "00383.O1D-CRATER LAKE"; "NPSD-306 Jan 2001"; Includes bibliographical references Close

• 1871. [Image] Final supplemental environmental impact statement: for clarification of language in the 1994 record of decision for the Northwest Forest Plan; national forests and Bureau of Land Management districts within the range of the northern spotted owl: proposal to amend wording about the aquatic conservation strategy

  	Abstract The Secretaries of Agriculture and the Interior propose limited changes to language about how to demonstrate that projects follow the Aquatic Conservation Strategy, part of the Northwest Forest ...
  	Citation × Citation Citation Abstract Copy Title: Final supplemental environmental impact statement: for clarification of language in the 1994 record of decision for the Northwest Forest Plan; national forests and Bureau of Land Management districts within the range of the northern spotted owl: proposal to amend wording about the aquatic conservation strategy Author: United States. Department of Agriculture. Forest Service; United States. Department of the Interior. Bureau of Land Managemen Year: 2003, 2006, 2005 Abstract The Secretaries of Agriculture and the Interior propose limited changes to language about how to demonstrate that projects follow the Aquatic Conservation Strategy, part of the Northwest Forest Plan. Projects needed to achieve Northwest Forest Plan goals have been delayed or stopped due to misapplication of certain passages in the Aquatic Conservation Strategy. The agencies are responding to the underlying need for increased agency success planning and implementing projects, to the extent that the current wording has hindered the agencies ability to follow Northwest Forest Plan principles and achieve its goals. The goals of the Northwest Forest Plan cannot be achieved without project implementation. Three alternatives are considered in the Final Supplemental Environmental Impact Statement, No Action, the Proposed Action, and Alternative A. No Action would not change existing language within the Aquatic Conservation Strategy. The Proposed Action and Alternative A would make l Title: Final supplemental environmental impact statement: for clarification of language in the 1994 record of decision for the Northwest Forest Plan; national forests and Bureau of Land Management districts within the range of the northern spotted owl: proposal to amend wording about the aquatic conservation strategy Author: United States. Department of Agriculture. Forest Service; United States. Department of the Interior. Bureau of Land Managemen Year: 2003, 2006, 2005 Abstract The Secretaries of Agriculture and the Interior propose limited changes to language about how to demonstrate that projects follow the Aquatic Conservation Strategy, part of the Northwest Forest Plan. Projects needed to achieve Northwest Forest Plan goals have been delayed or stopped due to misapplication of certain passages in the Aquatic Conservation Strategy. The agencies are responding to the underlying need for increased agency success planning and implementing projects, to the extent that the current wording has hindered the agencies ability to follow Northwest Forest Plan principles and achieve its goals. The goals of the Northwest Forest Plan cannot be achieved without project implementation. Three alternatives are considered in the Final Supplemental Environmental Impact Statement, No Action, the Proposed Action, and Alternative A. No Action would not change existing language within the Aquatic Conservation Strategy. The Proposed Action and Alternative A would make l Close

• 1872. [Image] Biological assessment of Klamath Project's continuing operations on the endangered Lost River sucker and shortnose sucker

  	BIOLOGICAL ASSESSMENT OF KLAMATH PROJECT'S CONTINUING OPERATIONS ON THE ENDANGERED LOST RIVER SUCKER AND SHORTNOSE SUCKER U.S. Bureau of Reclamation Mid-Pacific Region Klamath Basin Area Office Klamath ...
  	Citation × Citation Citation Abstract Copy Title: Biological assessment of Klamath Project's continuing operations on the endangered Lost River sucker and shortnose sucker Author: United States. Bureau of Reclamation Year: 2001, 2005 BIOLOGICAL ASSESSMENT OF KLAMATH PROJECT'S CONTINUING OPERATIONS ON THE ENDANGERED LOST RIVER SUCKER AND SHORTNOSE SUCKER U.S. Bureau of Reclamation Mid-Pacific Region Klamath Basin Area Office Klamath Falls, Oregon February 13,2001 TABLE OF CONTENTS 1.0 INTRODUCTION 2 2.0 DESCRIPTION OF THE ACTION 3 3.0 DESCRIPTION OF HISTORIC OPERATIONS 6 4.0 ENDANGERED SPECIES POTENTIALLY AFFECTED BY THE KLAMATH PROJECT 16 5.0 ENVIRONMENTAL BASELINE 60 6.0 EFFECTS OF KLAMATH PROJECT ON BALD EAGLES 60 7.0 EFFECTS OF KLAMATH PROJECT ENDANGERED SUCKERS 63 8.0 PROPOSED CRITICAL HABITAT FOR ENDANGERED SUCKERS 82 9.0 CUMULATIVE EFFECTS 84 10.0 DETERMINATION OF EFFECTS 89 11.0 LITERATURE CITED 90 12.0 PERSONAL COMMUNICATIONS 100 13.0 APPENDIX 1 - ESA CONSULTATION REVIEW 101 Title: Biological assessment of Klamath Project's continuing operations on the endangered Lost River sucker and shortnose sucker Author: United States. Bureau of Reclamation Year: 2001, 2005 BIOLOGICAL ASSESSMENT OF KLAMATH PROJECT'S CONTINUING OPERATIONS ON THE ENDANGERED LOST RIVER SUCKER AND SHORTNOSE SUCKER U.S. Bureau of Reclamation Mid-Pacific Region Klamath Basin Area Office Klamath Falls, Oregon February 13,2001 TABLE OF CONTENTS 1.0 INTRODUCTION 2 2.0 DESCRIPTION OF THE ACTION 3 3.0 DESCRIPTION OF HISTORIC OPERATIONS 6 4.0 ENDANGERED SPECIES POTENTIALLY AFFECTED BY THE KLAMATH PROJECT 16 5.0 ENVIRONMENTAL BASELINE 60 6.0 EFFECTS OF KLAMATH PROJECT ON BALD EAGLES 60 7.0 EFFECTS OF KLAMATH PROJECT ENDANGERED SUCKERS 63 8.0 PROPOSED CRITICAL HABITAT FOR ENDANGERED SUCKERS 82 9.0 CUMULATIVE EFFECTS 84 10.0 DETERMINATION OF EFFECTS 89 11.0 LITERATURE CITED 90 12.0 PERSONAL COMMUNICATIONS 100 13.0 APPENDIX 1 - ESA CONSULTATION REVIEW 101 Close

• 1873. [Image] Annual survey of abundance and distribution of age 0 shortnose and Lost River suckers in Upper Klamath Lake

  	One chapter of a seven chapter annual report from 1999 examining ecological issues regarding the shortnose and Lost River sucker populations in Upper Klamath Lake and Williamson River.
  	Citation × Citation Citation Abstract Copy Title: Annual survey of abundance and distribution of age 0 shortnose and Lost River suckers in Upper Klamath Lake Author: Oregon Cooperative Wildlife Research Unit Year: 2000, 2005 One chapter of a seven chapter annual report from 1999 examining ecological issues regarding the shortnose and Lost River sucker populations in Upper Klamath Lake and Williamson River. Title: Annual survey of abundance and distribution of age 0 shortnose and Lost River suckers in Upper Klamath Lake Author: Oregon Cooperative Wildlife Research Unit Year: 2000, 2005 One chapter of a seven chapter annual report from 1999 examining ecological issues regarding the shortnose and Lost River sucker populations in Upper Klamath Lake and Williamson River. Close

• 1874. [Article] Evaluating the Efficacy of Predicting Bycatch Mortality Using Reflex Impairment through an Assessment of Crab Discards

  All animals that interact with fishing gear are not necessarily captured, and all animals that are captured are not necessarily retained. Fishing practices and gear configuration, management regulations, ...

  Citation × Citation Citation Abstract Copy Title: Evaluating the Efficacy of Predicting Bycatch Mortality Using Reflex Impairment through an Assessment of Crab Discards Author: Yochum, Noëlle All animals that interact with fishing gear are not necessarily captured, and all animals that are captured are not necessarily retained. Fishing practices and gear configuration, management regulations, and markets dictate which animals ultimately are retained or discarded. The impact of a fishery and the efficacy of management regulations can depend on the mortality rate of the animals that interact with the gear or are discarded. The Reflex Action Mortality Predictor (RAMP) is a simple, non-invasive, and inexpensive approach that has been used to evaluate this component of fishing mortality. The RAMP approach relates the degree of reflex impairment in an animal to the probability the animal will die. Since its introduction in 2006, the RAMP approach has been utilized in the U.S. and abroad to evaluate mortality for a variety of species, fishing gear types, and stressors. Although there have been numerous applications of the RAMP approach in mortality estimation studies, there has been limited research to directly evaluate RAMP estimates and some skepticism remains in the fisheries science and management communities about the reliability and accuracy of the approach. The goal of this dissertation was to conduct research to assess RAMP and to synthesize findings from previously completed RAMP studies. The three research studies described in this dissertation consider: (1) the accuracy of applying an established relationship between reflex impairment and mortality probability to predict overall mortality attributed to novel stressors; (2) the development and utilization of a RAMP relationship to evaluate discard mortality in a fishery with management regulations that mandate discarding of certain categories of animals; and (3) whether the RAMP approach produces accurate estimates of mortality if survival is determined through laboratory captive holding. The first study estimated a relationship between reflex impairment and mortality probability for Tanner crab (Chionoecetes bairdi) discarded from the groundfish bottom trawl fishery in the Gulf of Alaska. This relationship was then compared to one previously established for Tanner crab in the Bering Sea bottom trawl fishery that encountered the fishing gear, but remained on the seafloor ('unobserved bycatch'). While mortality probabilities were similar between the two studies for crab with no or full reflex impairment, discarded crab with intermediate levels of reflex impairment had lower mortality probabilities than those from the unobserved bycatch study. Results from this study indicate the importance of describing all stressors to which animals are exposed and detailing the study methodology when initially creating a RAMP relationship. Failure to do so may result in inaccurate mortality estimates when the RAMP is applied to animals exposed to stressors not included in the original calibration. The second study developed a RAMP relationship using laboratory captive holding for Dungeness crab (Cancer magister) discarded in the Oregon commercial and recreational Dungeness fisheries and estimated that the discard mortality rate is lower than previously determined. This supports the goal of the '3-S' management strategy currently employed for these fisheries to protect sub-legal males (Size), females (Sex), and soft-shell (Season) crab by discarding them from the catch. For the commercial ocean Dungeness fishery, the estimated overall discard mortality rates (five days after release) varied by sex and shell-hardness, and reflex impairment was a significant predictor of mortality for both the commercial and recreational fisheries. In addition, results indicated that, when evaluating the role of discard mortality in '3-S' management with respect to fishery impact and sustainability, it is important to look not only at mortality rates, but also at the mortality- and bycatch- per retained ratios, and temporal trends relative to changes in effort, animal condition, and catch composition. This study also highlighted the (i) importance of evaluating the influence of biological, environmental, and fishing variables on mortality, (ii) complications that arise when establishing a RAMP relationship for a low impact fishery, and (iii) limitations of determining mortality through laboratory captive holding. The third study used mark-recapture methods to evaluate the reliability of results generated using the RAMP relationship established in the second study, which was based on the survival of crab held in captivity in the laboratory. Given the unnatural conditions for determining survival in captivity and the short-term duration of the experiment, mortality probability estimates may be biased. Similarities in patterns of relative survival rates between the studies lend support to the ability of the RAMP relationship to estimate discard mortality rates using captive holding. The laboratory-based RAMP approach was superior in its ability to provide direct estimates of mortality rates, whereas the mark-recapture study was limited to providing relative survival rates between reflex impairment levels that were imprecise due to low numbers of recaptured crab. This study highlighted the complications associated with tagging discarded animals and conducting a RAMP study with a fishery that has highly variable seasonal fishing effort. A synthesis of the research described in this dissertation and published work by other researchers highlights the limitations of the RAMP approach so that future researchers can avoid pitfalls in its application, and leads to suggestions on how to standardize some of the methodological steps. This analysis aims to increase the reliability of future RAMP studies and their production of high quality estimates of discard mortality rates that promote sustainable fisheries. Title: Evaluating the Efficacy of Predicting Bycatch Mortality Using Reflex Impairment through an Assessment of Crab Discards Author: Yochum, Noëlle All animals that interact with fishing gear are not necessarily captured, and all animals that are captured are not necessarily retained. Fishing practices and gear configuration, management regulations, and markets dictate which animals ultimately are retained or discarded. The impact of a fishery and the efficacy of management regulations can depend on the mortality rate of the animals that interact with the gear or are discarded. The Reflex Action Mortality Predictor (RAMP) is a simple, non-invasive, and inexpensive approach that has been used to evaluate this component of fishing mortality. The RAMP approach relates the degree of reflex impairment in an animal to the probability the animal will die. Since its introduction in 2006, the RAMP approach has been utilized in the U.S. and abroad to evaluate mortality for a variety of species, fishing gear types, and stressors. Although there have been numerous applications of the RAMP approach in mortality estimation studies, there has been limited research to directly evaluate RAMP estimates and some skepticism remains in the fisheries science and management communities about the reliability and accuracy of the approach. The goal of this dissertation was to conduct research to assess RAMP and to synthesize findings from previously completed RAMP studies. The three research studies described in this dissertation consider: (1) the accuracy of applying an established relationship between reflex impairment and mortality probability to predict overall mortality attributed to novel stressors; (2) the development and utilization of a RAMP relationship to evaluate discard mortality in a fishery with management regulations that mandate discarding of certain categories of animals; and (3) whether the RAMP approach produces accurate estimates of mortality if survival is determined through laboratory captive holding. The first study estimated a relationship between reflex impairment and mortality probability for Tanner crab (Chionoecetes bairdi) discarded from the groundfish bottom trawl fishery in the Gulf of Alaska. This relationship was then compared to one previously established for Tanner crab in the Bering Sea bottom trawl fishery that encountered the fishing gear, but remained on the seafloor ('unobserved bycatch'). While mortality probabilities were similar between the two studies for crab with no or full reflex impairment, discarded crab with intermediate levels of reflex impairment had lower mortality probabilities than those from the unobserved bycatch study. Results from this study indicate the importance of describing all stressors to which animals are exposed and detailing the study methodology when initially creating a RAMP relationship. Failure to do so may result in inaccurate mortality estimates when the RAMP is applied to animals exposed to stressors not included in the original calibration. The second study developed a RAMP relationship using laboratory captive holding for Dungeness crab (Cancer magister) discarded in the Oregon commercial and recreational Dungeness fisheries and estimated that the discard mortality rate is lower than previously determined. This supports the goal of the '3-S' management strategy currently employed for these fisheries to protect sub-legal males (Size), females (Sex), and soft-shell (Season) crab by discarding them from the catch. For the commercial ocean Dungeness fishery, the estimated overall discard mortality rates (five days after release) varied by sex and shell-hardness, and reflex impairment was a significant predictor of mortality for both the commercial and recreational fisheries. In addition, results indicated that, when evaluating the role of discard mortality in '3-S' management with respect to fishery impact and sustainability, it is important to look not only at mortality rates, but also at the mortality- and bycatch- per retained ratios, and temporal trends relative to changes in effort, animal condition, and catch composition. This study also highlighted the (i) importance of evaluating the influence of biological, environmental, and fishing variables on mortality, (ii) complications that arise when establishing a RAMP relationship for a low impact fishery, and (iii) limitations of determining mortality through laboratory captive holding. The third study used mark-recapture methods to evaluate the reliability of results generated using the RAMP relationship established in the second study, which was based on the survival of crab held in captivity in the laboratory. Given the unnatural conditions for determining survival in captivity and the short-term duration of the experiment, mortality probability estimates may be biased. Similarities in patterns of relative survival rates between the studies lend support to the ability of the RAMP relationship to estimate discard mortality rates using captive holding. The laboratory-based RAMP approach was superior in its ability to provide direct estimates of mortality rates, whereas the mark-recapture study was limited to providing relative survival rates between reflex impairment levels that were imprecise due to low numbers of recaptured crab. This study highlighted the complications associated with tagging discarded animals and conducting a RAMP study with a fishery that has highly variable seasonal fishing effort. A synthesis of the research described in this dissertation and published work by other researchers highlights the limitations of the RAMP approach so that future researchers can avoid pitfalls in its application, and leads to suggestions on how to standardize some of the methodological steps. This analysis aims to increase the reliability of future RAMP studies and their production of high quality estimates of discard mortality rates that promote sustainable fisheries. Close

• 1875. [Article] Mitochondrial decay in the aging rat heart : changes in fatty acid-supported bioenergetics and macromolecular organization of the electron transport system

  Decline in cardiac pump function is a hallmark of aging where mitochondrial decay is an important underlying cause. Although certainly multifactorial in nature, both dysfunction of the machinery involved ...

  Citation × Citation Citation Abstract Copy Title: Mitochondrial decay in the aging rat heart : changes in fatty acid-supported bioenergetics and macromolecular organization of the electron transport system Author: Gomez Ramirez, Luis A. (Luis Alejandro) Decline in cardiac pump function is a hallmark of aging where mitochondrial decay is an important underlying cause. Although certainly multifactorial in nature, both dysfunction of the machinery involved in the chemiosmotic process of energy transduction and lower capacity to maintain fatty acid-driven respiration are identified as intrinsic factors of mitochondrial decay in the aged myocardium. Age-associated destabilization of electron transport supercomplexes as a potential factor of mitochondrial decay in the rat heart. Defective operation of the electron transport chain (ETC) constitutes a key mechanism involved in the age-associated loss of mitochondrial energy metabolism. Nevertheless, the molecular events underlying inefficient electron flux that ultimately leads to higher superoxide appearance and impaired respiration are not fully known. As recent biophysical evidence shows that the ETC may form large macromolecular assemblies (i.e. supercomplexes) that disintegrate in certain pathologies (e.g. heart failure or Barth syndrome) reminiscent of aging, we investigated the hypothesis that alterations in supercomplexes are partly responsible for the age-related loss of cardiac ETC function. In this dissertation, age-associated changes in supercomplex organization and stability were investigated in subsarcolemmal (SSM) and interfibrillary (IFM) mitochondria isolated from cardiac tissue from young (3-5 months) and old (24-28 months) male Fischer 344 rats. Blue native-PAGE (BN-PAGE) analysis of digitonin-solubilized mitochondrial membranes coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to investigate supercomplex organization. Results show that both SSM and IFM display supercomplexes comprised of various stoichiometries of complexes I, III and IV (never complex II), which typically organize as high mass (1500-2300 kDa) assemblies containing up to four copies of complex IV (i.e. I₁III₂IV[subscript N]-type supercomplexes). Interestingly, analysis of IFM proteins showed that, in general, supercomplex levels declined by up to 15 % (p < 0.05) with age; however, different degrees of supercomplex deterioration were observed, depending on the particular supercomplex investigated. Supercomplexes of the highest molecular weights (i.e. 1900-2300 kDa), which were also composed of the most complex stoichiometries (i.e. I1III2IVN, N ≥ 2), were primarily lost with age. In particular, I₁III₂IV₂, I₁III₂IV₃ and I₁III₂IV₄ supercomplexes were found to decline by 13% (p < 0.05), 30% (p < 0.05) and 45% (p < 0.05), respectively, on an age basis. Therefore, the age-associated loss of supercomplexes in IFM stems from destabilization of the assemblies that comprise several copies of complex IV, which could partially limit proper electron transfer to O₂ for its reduction, affecting mitochondrial respiratory capacity. In contrast to IFM, the aging defects of SSM supercomplexes appeared to be confined to the assembly comprised of only one copy of complex IV (I₁III₂IV₁, 1700 kDa) (37% loss; p = 0.06), while the higher molecular weight supercomplex sub-types that were most affected in IFM (i.e. I₁III₂IV[subscript N], N ≥ 2) were not significantly altered with age. Thus, the results from this dissertation indicate that mitochondria from different subcellular locations in the myocyte show different degrees of supercomplex destabilization in the aging rat heart. The more robust supercomplex deficits noted for IFM fit well with previous observations that electron transport characteristics of this subpopulation are more adversely affected with age than SSM. Although the underlying factor(s) of supercomplex deterioration are not fully known, the hypothesis that age-related alterations of certain constituents of the IMM (e.g. cardiolipin) may be important factors of supercomplex destabilization in cardiac mitochondria was investigated in this dissertation. To this end, LC-MS/MS characterization of supercomplex proteins and HPLC analysis of cardiolipin were used as approaches to elucidate potential factor(s) of supercomplex destabilization in the aging rat heart. Age-related alterations of cardiolipin levels and its acyl-chain content showed a strong parallel to the age-associated destabilization of supercomplexes. Specifically, cardiolipin levels declined by 10% (p < 0.05) in IFM, the mitochondrial subpopulation displaying the highest degree of supercomplex deterioration. In addition, the content of (18:2)₄-cardiolipin, the predominant species in the heart, was found to decline by 50% (p < 0.05) on average in both populations of cardiac mitochondria. Therefore, the data presented in this dissertation indicate that changes in cardiolipin may be at least one of the factors involved in supercomplex destabilization in the aging heart. Age-related decline in carnitine palmitoyltransferase I (CPT1) activity as a mitochondrial lesion that limits fatty acid catabolism in the rat heart. Loss of fatty acid utilization, another intrinsic factor of mitochondrial decay in the aged myocardium, has been associated with age-related alterations in the activity of carnitine palmitoyltransferase 1 (CPT1), the rate-controlling enzyme for overall fatty acid β-oxidation. Nevertheless, the exact molecular mechanism involved in the age-related loss of fatty acid-driven bioenergetics is not fully understood. In this dissertation, it was also investigated whether the aging lesion for fatty oxidation lies in a particular mitochondrial subpopulation or more generally results from cardiac decrements in L-carnitine levels. In order to clarify the role of each one of these factors, the effect of long-term dietary supplementation with the L-carnitine analogue, acetyl-L-carnitine (ALCAR), was also investigated. Results show that aging selectively decreases CPT1 activity in IFM by reducing enzyme catalytic efficiency for palmitoyl-CoA. IFM displayed a 28% (p < 0.05) loss of CPT1 activity, which correlated with a decline (41%, p < 0.05) in palmitoyl-CoA-driven state 3 respiration. Interestingly, SSM had preserved enzyme function and efficiently utilized palmitate. Analysis of IFM CPT1 kinetics showed both diminished V[subscript max] and K[subscript m] (60% and 49% respectively, p < 0.05) when palmitoyl-CoA was the substrate. However, no age-related changes in enzyme kinetics were evident with respect to L-carnitine. ALCAR supplementation restored CPT1 activity in heart IFM, but not apparently through remediation of L-carnitine levels. Rather, ALCAR influenced enzyme activity over time, potentially by modulating conditions in the aging heart that ultimately affect palmitoyl-CoA binding and CPT1 kinetics. In conclusion, this dissertation presents a characterization of age-associated alterations in the macromolecular organization of the IMM components that could partly explain the loss of mitochondrial oxidative capacity that affects the aging heart. In addition, the characterization of an age-related lesion of the controlling enzyme for β-oxidation is presented as another important factor that limits mitochondrial function and energy metabolism in cardiac mitochondria. Title: Mitochondrial decay in the aging rat heart : changes in fatty acid-supported bioenergetics and macromolecular organization of the electron transport system Author: Gomez Ramirez, Luis A. (Luis Alejandro) Decline in cardiac pump function is a hallmark of aging where mitochondrial decay is an important underlying cause. Although certainly multifactorial in nature, both dysfunction of the machinery involved in the chemiosmotic process of energy transduction and lower capacity to maintain fatty acid-driven respiration are identified as intrinsic factors of mitochondrial decay in the aged myocardium. Age-associated destabilization of electron transport supercomplexes as a potential factor of mitochondrial decay in the rat heart. Defective operation of the electron transport chain (ETC) constitutes a key mechanism involved in the age-associated loss of mitochondrial energy metabolism. Nevertheless, the molecular events underlying inefficient electron flux that ultimately leads to higher superoxide appearance and impaired respiration are not fully known. As recent biophysical evidence shows that the ETC may form large macromolecular assemblies (i.e. supercomplexes) that disintegrate in certain pathologies (e.g. heart failure or Barth syndrome) reminiscent of aging, we investigated the hypothesis that alterations in supercomplexes are partly responsible for the age-related loss of cardiac ETC function. In this dissertation, age-associated changes in supercomplex organization and stability were investigated in subsarcolemmal (SSM) and interfibrillary (IFM) mitochondria isolated from cardiac tissue from young (3-5 months) and old (24-28 months) male Fischer 344 rats. Blue native-PAGE (BN-PAGE) analysis of digitonin-solubilized mitochondrial membranes coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to investigate supercomplex organization. Results show that both SSM and IFM display supercomplexes comprised of various stoichiometries of complexes I, III and IV (never complex II), which typically organize as high mass (1500-2300 kDa) assemblies containing up to four copies of complex IV (i.e. I₁III₂IV[subscript N]-type supercomplexes). Interestingly, analysis of IFM proteins showed that, in general, supercomplex levels declined by up to 15 % (p < 0.05) with age; however, different degrees of supercomplex deterioration were observed, depending on the particular supercomplex investigated. Supercomplexes of the highest molecular weights (i.e. 1900-2300 kDa), which were also composed of the most complex stoichiometries (i.e. I1III2IVN, N ≥ 2), were primarily lost with age. In particular, I₁III₂IV₂, I₁III₂IV₃ and I₁III₂IV₄ supercomplexes were found to decline by 13% (p < 0.05), 30% (p < 0.05) and 45% (p < 0.05), respectively, on an age basis. Therefore, the age-associated loss of supercomplexes in IFM stems from destabilization of the assemblies that comprise several copies of complex IV, which could partially limit proper electron transfer to O₂ for its reduction, affecting mitochondrial respiratory capacity. In contrast to IFM, the aging defects of SSM supercomplexes appeared to be confined to the assembly comprised of only one copy of complex IV (I₁III₂IV₁, 1700 kDa) (37% loss; p = 0.06), while the higher molecular weight supercomplex sub-types that were most affected in IFM (i.e. I₁III₂IV[subscript N], N ≥ 2) were not significantly altered with age. Thus, the results from this dissertation indicate that mitochondria from different subcellular locations in the myocyte show different degrees of supercomplex destabilization in the aging rat heart. The more robust supercomplex deficits noted for IFM fit well with previous observations that electron transport characteristics of this subpopulation are more adversely affected with age than SSM. Although the underlying factor(s) of supercomplex deterioration are not fully known, the hypothesis that age-related alterations of certain constituents of the IMM (e.g. cardiolipin) may be important factors of supercomplex destabilization in cardiac mitochondria was investigated in this dissertation. To this end, LC-MS/MS characterization of supercomplex proteins and HPLC analysis of cardiolipin were used as approaches to elucidate potential factor(s) of supercomplex destabilization in the aging rat heart. Age-related alterations of cardiolipin levels and its acyl-chain content showed a strong parallel to the age-associated destabilization of supercomplexes. Specifically, cardiolipin levels declined by 10% (p < 0.05) in IFM, the mitochondrial subpopulation displaying the highest degree of supercomplex deterioration. In addition, the content of (18:2)₄-cardiolipin, the predominant species in the heart, was found to decline by 50% (p < 0.05) on average in both populations of cardiac mitochondria. Therefore, the data presented in this dissertation indicate that changes in cardiolipin may be at least one of the factors involved in supercomplex destabilization in the aging heart. Age-related decline in carnitine palmitoyltransferase I (CPT1) activity as a mitochondrial lesion that limits fatty acid catabolism in the rat heart. Loss of fatty acid utilization, another intrinsic factor of mitochondrial decay in the aged myocardium, has been associated with age-related alterations in the activity of carnitine palmitoyltransferase 1 (CPT1), the rate-controlling enzyme for overall fatty acid β-oxidation. Nevertheless, the exact molecular mechanism involved in the age-related loss of fatty acid-driven bioenergetics is not fully understood. In this dissertation, it was also investigated whether the aging lesion for fatty oxidation lies in a particular mitochondrial subpopulation or more generally results from cardiac decrements in L-carnitine levels. In order to clarify the role of each one of these factors, the effect of long-term dietary supplementation with the L-carnitine analogue, acetyl-L-carnitine (ALCAR), was also investigated. Results show that aging selectively decreases CPT1 activity in IFM by reducing enzyme catalytic efficiency for palmitoyl-CoA. IFM displayed a 28% (p < 0.05) loss of CPT1 activity, which correlated with a decline (41%, p < 0.05) in palmitoyl-CoA-driven state 3 respiration. Interestingly, SSM had preserved enzyme function and efficiently utilized palmitate. Analysis of IFM CPT1 kinetics showed both diminished V[subscript max] and K[subscript m] (60% and 49% respectively, p < 0.05) when palmitoyl-CoA was the substrate. However, no age-related changes in enzyme kinetics were evident with respect to L-carnitine. ALCAR supplementation restored CPT1 activity in heart IFM, but not apparently through remediation of L-carnitine levels. Rather, ALCAR influenced enzyme activity over time, potentially by modulating conditions in the aging heart that ultimately affect palmitoyl-CoA binding and CPT1 kinetics. In conclusion, this dissertation presents a characterization of age-associated alterations in the macromolecular organization of the IMM components that could partly explain the loss of mitochondrial oxidative capacity that affects the aging heart. In addition, the characterization of an age-related lesion of the controlling enzyme for β-oxidation is presented as another important factor that limits mitochondrial function and energy metabolism in cardiac mitochondria. Close

• 1876. [Article] Brown Marmorated Stink Bug (BMSB), Halyomorpha halys Taint in Wine : Impact on Wine Sensory, Effect of Wine-processing and Management Techniques

  Brown marmorated stink bug (BMSB), (Halyomorpha halys, Hemiptera: Pentatomidae) is an invasive species that damages numerous agricultural crops including grapes. Related damage include lower ...

  Citation × Citation Citation Abstract Copy Title: Brown Marmorated Stink Bug (BMSB), Halyomorpha halys Taint in Wine : Impact on Wine Sensory, Effect of Wine-processing and Management Techniques Author: Mohekar, Pallavi, 1985- Brown marmorated stink bug (BMSB), (Halyomorpha halys, Hemiptera: Pentatomidae) is an invasive species that damages numerous agricultural crops including grapes. Related damage include lower berry weight with increased exposure and cracked berries as a result of BMSB feeding activity. The insect is currently detected in 43 US states including Oregon, Washington, California, and New York. The grape and wine industries in these areas hold significant economic value. BMSB damage has already resulted in major economic loss in the agricultural industry. Current data indicates that the infestation is spreading to new regions and its population density is increasing in regions where it has been detected. Surveys show BMSB in vineyards of Oregon, Virginia and New York where BMSB can damage grapes, lowering their yield and quality. When harvested with grape clusters, BMSB can introduce volatile compounds, trans-2-decenal and tridecane, into wine. Prior work has shown that the presence of these compounds alters wine sensory. In this thesis, the focus is on analyzing BMSB’s impact on wine quality and consumer preference. Additionally, this work determines the action threshold (AT) for BMSB in the vineyard, which is likely to prove important to the grape and wine industry in designing control limits and maintaining wine quality. The first contribution of this work establishes the sensory detection threshold (DT) and consumer rejection thresholds (CRT) for trans-2-decenal in red wine. Trans-2-decenal is one of the main aroma compounds in BMSB taint, having green, cilantro-like aroma characteristics that is undesirable in wine. Results conclusively show that trans-2-decenal in wine has a negative effect on its quality. In Pinot noir, consumers were able to perceive trans-2-decenal at 1.92 µg/L (DT). Consumer preference for Pinot noir and Merlot containing trans-2-decenal decreased significantly above the concentration of 4.8 µg/L (CRT). Pinot noir containing trans-2-decenal above CRT was described as green, herbal, musty and less fruity by wine professionals. Based on such findings, the use of CRT is recommended when establishing consumer tolerance levels of trans-2-decenal in wine. The second contribution relates BMSB presence in vineyard with sensory threshold of trans-2-decenal in the finished wine. Pinot noir, Merlot and Pinot gris were produced using different densities of BMSB in grape clusters. The results of this study indicate BMSB density of three per cluster can result in Pinot noir containing trans-2-decenal at its DT and below its CRT. This density can be used as AT for BMSB in the vineyard since wines made from grapes contaminated at or greater than 3 BMSB per cluster are likely to experience low preference by wine consumers. The same BMSB density can be used to devise control measures for Merlot since trans-2-decenal CRT was found to be similar for both Pinot noir and Merlot. Pinot gris was found to be free of trans-2-decenal even at BMSB density of 1 per cluster. Therefore, we believe that BMSB may not be a concern for white wines. The third contribution provides methods to reduce BMSB taint in finished wine. This can be done by modifying the winemaking process or by applying corrective measures in the wine. During winemaking, destemming and pressing were identified to be the steps responsible for increasing BMSB taint levels in wine whereas alcoholic fermentation decreases taint levels. Consequently, finished white wine was found to be free of trans-2-decenal since fermentation occurs after pressing. However, trans-2-decenal was present in finished red wine since pressing occurs after fermentation. Taint levels in finished red wine are also affected by different pressing variants (free run versus press fraction, bladder press versus basket press), with press fraction and bladder press introducing more BMSB taint compared to free run and basket press. This information will allow winemakers to adjust processing steps in order to minimize BMSB taint levels in red wines. Further reduction in taint levels was shown to be possible through the use of reverse osmosis filtration. Alternatively, oak addition can be used to mask the sensory attributes of trans-2-decenal at the risk of introducing spicy notes into wine. None of the other common fining agents tested were found to be effective against trans-2-decenal. Taken together, this thesis contributes a number of novel insights into the impact of BMSB on red and white wine. By relating consumer thresholds and descriptive analysis with chemical and wine processing, we are able to establish control densities for the pest in the vineyard, identify key processing steps and post-fermentation treatments to reduce BMSB taint. The information contained in this thesis is likely to prove valuable to the wine industry in its struggle against BMSB. Title: Brown Marmorated Stink Bug (BMSB), Halyomorpha halys Taint in Wine : Impact on Wine Sensory, Effect of Wine-processing and Management Techniques Author: Mohekar, Pallavi, 1985- Brown marmorated stink bug (BMSB), (Halyomorpha halys, Hemiptera: Pentatomidae) is an invasive species that damages numerous agricultural crops including grapes. Related damage include lower berry weight with increased exposure and cracked berries as a result of BMSB feeding activity. The insect is currently detected in 43 US states including Oregon, Washington, California, and New York. The grape and wine industries in these areas hold significant economic value. BMSB damage has already resulted in major economic loss in the agricultural industry. Current data indicates that the infestation is spreading to new regions and its population density is increasing in regions where it has been detected. Surveys show BMSB in vineyards of Oregon, Virginia and New York where BMSB can damage grapes, lowering their yield and quality. When harvested with grape clusters, BMSB can introduce volatile compounds, trans-2-decenal and tridecane, into wine. Prior work has shown that the presence of these compounds alters wine sensory. In this thesis, the focus is on analyzing BMSB’s impact on wine quality and consumer preference. Additionally, this work determines the action threshold (AT) for BMSB in the vineyard, which is likely to prove important to the grape and wine industry in designing control limits and maintaining wine quality. The first contribution of this work establishes the sensory detection threshold (DT) and consumer rejection thresholds (CRT) for trans-2-decenal in red wine. Trans-2-decenal is one of the main aroma compounds in BMSB taint, having green, cilantro-like aroma characteristics that is undesirable in wine. Results conclusively show that trans-2-decenal in wine has a negative effect on its quality. In Pinot noir, consumers were able to perceive trans-2-decenal at 1.92 µg/L (DT). Consumer preference for Pinot noir and Merlot containing trans-2-decenal decreased significantly above the concentration of 4.8 µg/L (CRT). Pinot noir containing trans-2-decenal above CRT was described as green, herbal, musty and less fruity by wine professionals. Based on such findings, the use of CRT is recommended when establishing consumer tolerance levels of trans-2-decenal in wine. The second contribution relates BMSB presence in vineyard with sensory threshold of trans-2-decenal in the finished wine. Pinot noir, Merlot and Pinot gris were produced using different densities of BMSB in grape clusters. The results of this study indicate BMSB density of three per cluster can result in Pinot noir containing trans-2-decenal at its DT and below its CRT. This density can be used as AT for BMSB in the vineyard since wines made from grapes contaminated at or greater than 3 BMSB per cluster are likely to experience low preference by wine consumers. The same BMSB density can be used to devise control measures for Merlot since trans-2-decenal CRT was found to be similar for both Pinot noir and Merlot. Pinot gris was found to be free of trans-2-decenal even at BMSB density of 1 per cluster. Therefore, we believe that BMSB may not be a concern for white wines. The third contribution provides methods to reduce BMSB taint in finished wine. This can be done by modifying the winemaking process or by applying corrective measures in the wine. During winemaking, destemming and pressing were identified to be the steps responsible for increasing BMSB taint levels in wine whereas alcoholic fermentation decreases taint levels. Consequently, finished white wine was found to be free of trans-2-decenal since fermentation occurs after pressing. However, trans-2-decenal was present in finished red wine since pressing occurs after fermentation. Taint levels in finished red wine are also affected by different pressing variants (free run versus press fraction, bladder press versus basket press), with press fraction and bladder press introducing more BMSB taint compared to free run and basket press. This information will allow winemakers to adjust processing steps in order to minimize BMSB taint levels in red wines. Further reduction in taint levels was shown to be possible through the use of reverse osmosis filtration. Alternatively, oak addition can be used to mask the sensory attributes of trans-2-decenal at the risk of introducing spicy notes into wine. None of the other common fining agents tested were found to be effective against trans-2-decenal. Taken together, this thesis contributes a number of novel insights into the impact of BMSB on red and white wine. By relating consumer thresholds and descriptive analysis with chemical and wine processing, we are able to establish control densities for the pest in the vineyard, identify key processing steps and post-fermentation treatments to reduce BMSB taint. The information contained in this thesis is likely to prove valuable to the wine industry in its struggle against BMSB. Close

• 1877. [Image] Anomalies of larval and juvenile shortnose and Lost River suckers in Upper Klamath Lake, Oregon

  	Abstract-Larval and juvenile shortnose {Chasmistes brevirostris) and Lost River (Deltistes luxatus) suckers from Upper Klamath Lake, OR, were examined to determine anomaly rates for fins, eyes, spinal ...
  	Citation × Citation Citation Abstract Copy Title: Anomalies of larval and juvenile shortnose and Lost River suckers in Upper Klamath Lake, Oregon Author: Plunkett, Steven R.; Snyder-Conn, Elaine Year: 2000, 2005 Abstract-Larval and juvenile shortnose {Chasmistes brevirostris) and Lost River (Deltistes luxatus) suckers from Upper Klamath Lake, OR, were examined to determine anomaly rates for fins, eyes, spinal column, vertebrae, and osteocranium, and their possible associations with water quality and pesticides. X-rays of 1,550 fish and 1,395 matching specimens, collected in 1993, were ranked on the severity of anomalies. One or more anomalies were observed in 15.9% of shortnose suckers and 8.2% of Lost River suckers. Anomaly rates exceeding 1.0%, greater than rates expected from high water quality systems, were observed for lordosis and scoliosis, and abnormalities of the vertebrae, opercula, and pectoral and pelvic fins in shortnose suckers, and abnormalities of vertebrae and opercula in Lost River suckers. The highest rates of anomalies were in vertebrae, pelvic fins, and opercula in shortnose suckers, and opercula and vertebrae in Lost River suckers. Shortnose suckers exhibited higher rates than Lost River suckers for almost all anomalies. Particular anomaly rates differed significantly among sites. There were also substantially more anomalies found in larvae and small juveniles than in larger juveniles. Based on the high anomaly rates observed in this study, it is possible that 0-aged sucker cohorts in Upper Klamath Lake are far more vulnerable to mortality. Title: Anomalies of larval and juvenile shortnose and Lost River suckers in Upper Klamath Lake, Oregon Author: Plunkett, Steven R.; Snyder-Conn, Elaine Year: 2000, 2005 Abstract-Larval and juvenile shortnose {Chasmistes brevirostris) and Lost River (Deltistes luxatus) suckers from Upper Klamath Lake, OR, were examined to determine anomaly rates for fins, eyes, spinal column, vertebrae, and osteocranium, and their possible associations with water quality and pesticides. X-rays of 1,550 fish and 1,395 matching specimens, collected in 1993, were ranked on the severity of anomalies. One or more anomalies were observed in 15.9% of shortnose suckers and 8.2% of Lost River suckers. Anomaly rates exceeding 1.0%, greater than rates expected from high water quality systems, were observed for lordosis and scoliosis, and abnormalities of the vertebrae, opercula, and pectoral and pelvic fins in shortnose suckers, and abnormalities of vertebrae and opercula in Lost River suckers. The highest rates of anomalies were in vertebrae, pelvic fins, and opercula in shortnose suckers, and opercula and vertebrae in Lost River suckers. Shortnose suckers exhibited higher rates than Lost River suckers for almost all anomalies. Particular anomaly rates differed significantly among sites. There were also substantially more anomalies found in larvae and small juveniles than in larger juveniles. Based on the high anomaly rates observed in this study, it is possible that 0-aged sucker cohorts in Upper Klamath Lake are far more vulnerable to mortality. Close

• 1878. [Image] Guidance for evaluating and recommending temperature regimes to protect fish

  	Abstract. Procedures are presented for evaluating temperature regimes for fish. Although examples pertain to spring chinook salmon (Oncorhynchus tshawytscha), the principles apply to other species. Basic ...
  	Citation × Citation Citation Abstract Copy Title: Guidance for evaluating and recommending temperature regimes to protect fish Author: Armour, Carl L. Year: 1991, 2005 Abstract. Procedures are presented for evaluating temperature regimes for fish. Although examples pertain to spring chinook salmon (Oncorhynchus tshawytscha), the principles apply to other species. Basic temperature tolerance relationships for fish are explained and three options are described for comparing alternative temperature regimes. The options are to base comparisons on experimental temperature tolerance results, suitability of a simulated temperature regime for key life stages, or population statistics and predicted responses to simulated temperatures. Key words: Chinook salmon, water temperature, alternative temperature regimes. Title: Guidance for evaluating and recommending temperature regimes to protect fish Author: Armour, Carl L. Year: 1991, 2005 Abstract. Procedures are presented for evaluating temperature regimes for fish. Although examples pertain to spring chinook salmon (Oncorhynchus tshawytscha), the principles apply to other species. Basic temperature tolerance relationships for fish are explained and three options are described for comparing alternative temperature regimes. The options are to base comparisons on experimental temperature tolerance results, suitability of a simulated temperature regime for key life stages, or population statistics and predicted responses to simulated temperatures. Key words: Chinook salmon, water temperature, alternative temperature regimes. Close

• 1879. [Image] The Water Report. The ESA and water takings: $16.7 million settlement shakes up water world

  	Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. This is an interview with attorney Roger Marzulla. See the full report at http://www.thewaterreport.com/...
  	Citation × Citation Citation Abstract Copy Title: The Water Report. The ESA and water takings: $16.7 million settlement shakes up water world Author: Envirotech Publications Year: 2005, 2008, 2006 Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. This is an interview with attorney Roger Marzulla. See the full report at http://www.thewaterreport.com/ Title: The Water Report. The ESA and water takings: $16.7 million settlement shakes up water world Author: Envirotech Publications Year: 2005, 2008, 2006 Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. This is an interview with attorney Roger Marzulla. See the full report at http://www.thewaterreport.com/ Close

• 1880. [Image] Restoring Harmony in the Klamath Basin

  	"January 2003."; Includes bibliographical references (p. 25-28)
  	Citation × Citation Citation Abstract Copy Title: Restoring Harmony in the Klamath Basin Author: Meiners, Roger E; Kosnik, Lea-Rachel D., 1972- Year: 2003, 2007, 2005 "January 2003."; Includes bibliographical references (p. 25-28) Title: Restoring Harmony in the Klamath Basin Author: Meiners, Roger E; Kosnik, Lea-Rachel D., 1972- Year: 2003, 2007, 2005 "January 2003."; Includes bibliographical references (p. 25-28) Close

• 1881. [Image] Crater Lake limnological studies 1985 annual report

  	1982-2002; ill., maps; Title covers calendar years 1985-1987; CA 9000-3-0003 Subagreement 12; Includes bibliographic references; Issues lack volume numbering
  	Citation × Citation Citation Abstract Copy Title: Crater Lake limnological studies 1985 annual report Author: Oregon State University; in collaboration with Crater Lake National Park Year: 1985, 2009 1982-2002; ill., maps; Title covers calendar years 1985-1987; CA 9000-3-0003 Subagreement 12; Includes bibliographic references; Issues lack volume numbering Title: Crater Lake limnological studies 1985 annual report Author: Oregon State University; in collaboration with Crater Lake National Park Year: 1985, 2009 1982-2002; ill., maps; Title covers calendar years 1985-1987; CA 9000-3-0003 Subagreement 12; Includes bibliographic references; Issues lack volume numbering Close

• 1882. [Article] The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem

  Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of ...

  Citation × Citation Citation Abstract Copy Title: The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem Author: Diemer, Geoffrey Scott Year: 2014 Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of establishing a more comprehensive view of virus diversity and evolution, as vast amounts of new sequence data becomes available for comparative analysis.Metagenomic DNA from virus-sized particles (smaller than 0.2 microns in diameter) was isolated from approximately 20 liters of sediment obtained from Boiling Springs Lake (BSL) and sequenced. BSL is a large, acidic hot-spring (with a pH of 2.2, and temperatures ranging from 50°C to 96°C) located in Lassen Volcanic National Park, USA. BSL supports a purely microbial ecosystem comprised largely of Archaea and Bacteria, however, the lower temperature regions permit the growth of acid- and thermo-tolerant Eukarya. This distinctive feature of the BSL microbial ecosystem ensures that virus types infecting all domains of life will be present. The metagenomic sequence data was used to characterize the types of viruses present within the microbial ecosystem, to ascertain the extent of genetic diversity and novelty comprising the BSL virus assemblage, and to explore the genomic and structural modalities of virus evolution.Metagenomic surveys of natural virus assemblages, including the survey of BSL, have revealed that the diversity within the virosphere far exceeds what has currently been determined through the detailed study of viruses that are relevant to human health and agriculture. The number of as-yet-uncharacterized virus protein families present in the BSL assemblage was estimated by clustering analysis. Genomic context analysis of the predicted viral protein sequences in the BSL dataset indicates that most of the putative uncharacterized proteins are endemic or unique to BSL, and are largely harbored by known virus types. A comparative metagenomic analysis approach identified a set of conserved, yet uncharacterized BSL protein sequences that are commonly found in other similar and dissimilar environments.New sequence data from metagenomic surveys of natural virus assemblages was also used to better characterize and define known virus protein families, as some of the viruses found in the BSL environment represent distant relatives of well-characterized isolates. By comparing viral genes and protein sequences from these highly divergent species, it is possible to better understand the dynamics of adaptation and evolution in the virosphere. Additionally, as structures of virus proteins continue to be experimentally determined by X-ray crystallography and cryo-electron microscopy, a merger of structural and metagenomic sequence data allows the opportunity to observe the structural dynamics underlying virus protein evolution.Capsid (structural) proteins from two distinct Microviridae strains; a globally ubiquitous and highly sequence-diverse virus family, were identified in, and isolated from the BSL metagenomic DNA sample. These BSL capsid protein sequences, along with several other homologous sequences derived from metagenomic surveys and laboratory isolates, were mapped to the solved structure of a closely related capsid protein from the Spiroplasma phage-4 microvirus. Patterns of amino acid sequence conservation, unveiled by structure-based homology modeling analysis, revealed that the protein sequences within this family exhibit a remarkable level of plasticity, while remaining structurally and functionally congruent.Lateral gene transfer is thought to have had a significant impact on the genomic evolution and adaptation of virus families. Genomic context analysis was also utilized to identify interviral gene transfer within the BSL virus assemblage. An ostensibly rare interviral gene transfer event, having transpired between single-stranded RNA and DNA virus types, was detected in the BSL metagenome. Similar genomes were subsequently detected in other ecosystems around the globe. The discovery of this new virus genome dramatically underscores the scope and importance of genetic mobility and genomic mosaicism as major forces driving the evolution of viruses.The analyses conducted herein demonstrate the many ways in which viral metagenomic sequence data may be utilized to not only evaluate the composition of a natural virus assemblage, but to discover new viral genes, and to better understand the dynamics of both genomic and structural evolution within the virosphere. Title: The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem Author: Diemer, Geoffrey Scott Year: 2014 Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of establishing a more comprehensive view of virus diversity and evolution, as vast amounts of new sequence data becomes available for comparative analysis.Metagenomic DNA from virus-sized particles (smaller than 0.2 microns in diameter) was isolated from approximately 20 liters of sediment obtained from Boiling Springs Lake (BSL) and sequenced. BSL is a large, acidic hot-spring (with a pH of 2.2, and temperatures ranging from 50°C to 96°C) located in Lassen Volcanic National Park, USA. BSL supports a purely microbial ecosystem comprised largely of Archaea and Bacteria, however, the lower temperature regions permit the growth of acid- and thermo-tolerant Eukarya. This distinctive feature of the BSL microbial ecosystem ensures that virus types infecting all domains of life will be present. The metagenomic sequence data was used to characterize the types of viruses present within the microbial ecosystem, to ascertain the extent of genetic diversity and novelty comprising the BSL virus assemblage, and to explore the genomic and structural modalities of virus evolution.Metagenomic surveys of natural virus assemblages, including the survey of BSL, have revealed that the diversity within the virosphere far exceeds what has currently been determined through the detailed study of viruses that are relevant to human health and agriculture. The number of as-yet-uncharacterized virus protein families present in the BSL assemblage was estimated by clustering analysis. Genomic context analysis of the predicted viral protein sequences in the BSL dataset indicates that most of the putative uncharacterized proteins are endemic or unique to BSL, and are largely harbored by known virus types. A comparative metagenomic analysis approach identified a set of conserved, yet uncharacterized BSL protein sequences that are commonly found in other similar and dissimilar environments.New sequence data from metagenomic surveys of natural virus assemblages was also used to better characterize and define known virus protein families, as some of the viruses found in the BSL environment represent distant relatives of well-characterized isolates. By comparing viral genes and protein sequences from these highly divergent species, it is possible to better understand the dynamics of adaptation and evolution in the virosphere. Additionally, as structures of virus proteins continue to be experimentally determined by X-ray crystallography and cryo-electron microscopy, a merger of structural and metagenomic sequence data allows the opportunity to observe the structural dynamics underlying virus protein evolution.Capsid (structural) proteins from two distinct Microviridae strains; a globally ubiquitous and highly sequence-diverse virus family, were identified in, and isolated from the BSL metagenomic DNA sample. These BSL capsid protein sequences, along with several other homologous sequences derived from metagenomic surveys and laboratory isolates, were mapped to the solved structure of a closely related capsid protein from the Spiroplasma phage-4 microvirus. Patterns of amino acid sequence conservation, unveiled by structure-based homology modeling analysis, revealed that the protein sequences within this family exhibit a remarkable level of plasticity, while remaining structurally and functionally congruent.Lateral gene transfer is thought to have had a significant impact on the genomic evolution and adaptation of virus families. Genomic context analysis was also utilized to identify interviral gene transfer within the BSL virus assemblage. An ostensibly rare interviral gene transfer event, having transpired between single-stranded RNA and DNA virus types, was detected in the BSL metagenome. Similar genomes were subsequently detected in other ecosystems around the globe. The discovery of this new virus genome dramatically underscores the scope and importance of genetic mobility and genomic mosaicism as major forces driving the evolution of viruses.The analyses conducted herein demonstrate the many ways in which viral metagenomic sequence data may be utilized to not only evaluate the composition of a natural virus assemblage, but to discover new viral genes, and to better understand the dynamics of both genomic and structural evolution within the virosphere. Close

• 1883. [Article] Conservation genetics of Kincaid's lupine : a threatened plant of western Oregon and southwest Washington grasslands

  Kincaid's lupine (Lupinus oreganus Heller) is a federally listed threatened species native to remnant grassland of western Oregon and southwestern Washington, and is the primary larval host plant of a ...

  Citation × Citation Citation Abstract Copy Title: Conservation genetics of Kincaid's lupine : a threatened plant of western Oregon and southwest Washington grasslands Author: Severns, Paul M. Kincaid's lupine (Lupinus oreganus Heller) is a federally listed threatened species native to remnant grassland of western Oregon and southwestern Washington, and is the primary larval host plant of a once thought extinct butterfly, Plebejus icarioides fenderi Macy. Past studies concerning Kincaid's lupine reproduction suggested that populations may suffer reductions in fitness and progeny vigor due to inbreeding depression, but no direct investigation into range-wide patterns of genetic variation has been undertaken. I used nuclear DNA and chloroplast DNA simple sequence repeat (SSR) markers to determine genet size and patterns of non-adventitious rhizomatous lupine spread, to estimate the number of genets within Kincaid's lupine populations, and to assess whether seed transfer for the purpose of genetic rescue is an appropriate genetics management strategy for Kincaid's lupine. Patterns of allelic diversity at nDNA SSR loci within study patches revealed that non-adventitious spread of rhizomes can extend to at least 27 m and may dominate a portion of a lupine patch or small population. However, genet spread and arrangement in study patches were sufficiently integrated such that interplantlet Bombus foraging flights exceeding 2 m had > 90% probability of occurring between different genets. Within-lupine patch genetic diversity was well-undersampled, refuting the supposition that Kincaid's lupine populations suffer from inbreeding depression due to small effective population sizes. Estimation of Kincaid's lupine abundance through leaf cover and inflorescence number was tightly correlated with plantlet number, a unit of vegetative and sexual growth, within lupine patches but the relationship was not consistent between patches within populations or between populations. We used genet to plantlet ratios (determined through genotyping) and plantlet density to estimate genet population size in Kincaid's lupine patches. Because of the strong correlation between cover and plantlet density, historically collected lupine abundance data could be used to estimate genet population size provided that plantlet density is calibrated to patch-specific cover measurements. Within patches and populations across the range of Kincaid's lupine there was little DNA evidence suggesting severe inbreeding. Only one of 24 populations and five study patches had strong statistical evidence of a recent genetic bottleneck despite the range-wide fragmentation of lupine populations and habitat. Mean population fixation index values for nearly half of the populations were near Hardy-Weinberg equilibrium expectations and only one small lupine population had a F-value > 0.20, suggestive of high inbreeding levels. Half of the populations actually had an excess of heterozygotes, suggesting that genetic diversity is not being lost. Chloroplast DNA coincides well with the observation that genetic diversity is not being lost through inbreeding or genetic bottlenecking in Kincaid's lupine. The mean number of cpDNA haplotypes per population was approximately 4 maternal lineages, which is very high for an animal pollinated plant with heavy seeds that have limited dispersal. Even relatively small populations of Kincaid's lupine had 2 or more cpDNA haplotypes, indicating that populations are not severely inbred. Both nuclear and chloroplast DNA SSR genetic marker diversity suggests that Kincaid's lupine does not require genetic rescue for effective conservation. Due to the longevity of Kincaid's lupine and the apparently large amount of within population genetic diversity, the encouragement of natural recruitment from vegetation management that improves habitat conditions is likely to maintain the relatively large amount of genetic diversity within Kincaid's lupine populations. Title: Conservation genetics of Kincaid's lupine : a threatened plant of western Oregon and southwest Washington grasslands Author: Severns, Paul M. Kincaid's lupine (Lupinus oreganus Heller) is a federally listed threatened species native to remnant grassland of western Oregon and southwestern Washington, and is the primary larval host plant of a once thought extinct butterfly, Plebejus icarioides fenderi Macy. Past studies concerning Kincaid's lupine reproduction suggested that populations may suffer reductions in fitness and progeny vigor due to inbreeding depression, but no direct investigation into range-wide patterns of genetic variation has been undertaken. I used nuclear DNA and chloroplast DNA simple sequence repeat (SSR) markers to determine genet size and patterns of non-adventitious rhizomatous lupine spread, to estimate the number of genets within Kincaid's lupine populations, and to assess whether seed transfer for the purpose of genetic rescue is an appropriate genetics management strategy for Kincaid's lupine. Patterns of allelic diversity at nDNA SSR loci within study patches revealed that non-adventitious spread of rhizomes can extend to at least 27 m and may dominate a portion of a lupine patch or small population. However, genet spread and arrangement in study patches were sufficiently integrated such that interplantlet Bombus foraging flights exceeding 2 m had > 90% probability of occurring between different genets. Within-lupine patch genetic diversity was well-undersampled, refuting the supposition that Kincaid's lupine populations suffer from inbreeding depression due to small effective population sizes. Estimation of Kincaid's lupine abundance through leaf cover and inflorescence number was tightly correlated with plantlet number, a unit of vegetative and sexual growth, within lupine patches but the relationship was not consistent between patches within populations or between populations. We used genet to plantlet ratios (determined through genotyping) and plantlet density to estimate genet population size in Kincaid's lupine patches. Because of the strong correlation between cover and plantlet density, historically collected lupine abundance data could be used to estimate genet population size provided that plantlet density is calibrated to patch-specific cover measurements. Within patches and populations across the range of Kincaid's lupine there was little DNA evidence suggesting severe inbreeding. Only one of 24 populations and five study patches had strong statistical evidence of a recent genetic bottleneck despite the range-wide fragmentation of lupine populations and habitat. Mean population fixation index values for nearly half of the populations were near Hardy-Weinberg equilibrium expectations and only one small lupine population had a F-value > 0.20, suggestive of high inbreeding levels. Half of the populations actually had an excess of heterozygotes, suggesting that genetic diversity is not being lost. Chloroplast DNA coincides well with the observation that genetic diversity is not being lost through inbreeding or genetic bottlenecking in Kincaid's lupine. The mean number of cpDNA haplotypes per population was approximately 4 maternal lineages, which is very high for an animal pollinated plant with heavy seeds that have limited dispersal. Even relatively small populations of Kincaid's lupine had 2 or more cpDNA haplotypes, indicating that populations are not severely inbred. Both nuclear and chloroplast DNA SSR genetic marker diversity suggests that Kincaid's lupine does not require genetic rescue for effective conservation. Due to the longevity of Kincaid's lupine and the apparently large amount of within population genetic diversity, the encouragement of natural recruitment from vegetation management that improves habitat conditions is likely to maintain the relatively large amount of genetic diversity within Kincaid's lupine populations. Close

• 1884. [Article] The determination of 4-Pyridoxic acid in urine ; an investigation into the recovery of 4-pyridoxic acid and the lactone of 4-pyridoxic acid from two Dowex ion exchange resins

  4-Pyridoxic acid is the major metabolite of all forms of vitamin B₆ in mammalian species. The determination of 4-pyridoxic acid, therefore, is important in the investigation of vitamin B₆ metabolism and ...

  Citation × Citation Citation Abstract Copy Title: The determination of 4-Pyridoxic acid in urine ; an investigation into the recovery of 4-pyridoxic acid and the lactone of 4-pyridoxic acid from two Dowex ion exchange resins Author: Rohrer, Martha Jane 4-Pyridoxic acid is the major metabolite of all forms of vitamin B₆ in mammalian species. The determination of 4-pyridoxic acid, therefore, is important in the investigation of vitamin B₆ metabolism and for the establishment of human requirements for the vitamin. Although 4-pyridoxic acid is itself fluorescent, Huff and Perlzweig (1944) developed a classic method for its determination based on the conversion of the metabolite to the even more highly fluorescent lactone. Sarett in 1951 recognized that there are many substances in urine other than 4-pyridoxic acid which are fluorescent and which may interfere with its determination. His attempts to remove the extraneous fluorescent compounds with Decalso or with charcoal were not entirely satisfactory. He proposed, therefore, the administration of a test dose of 4-pyridoxic acid to subjects whose urine was to be analyzed for the metabolite of vitamin B₆, thus rendering the foreign fluorescence less significant by dilution. In 1955, Fujita and associates employed ion exchange chromatography as a means of separating 4-pyridoxic acid from other fluorescent compounds in urine and in 1958 Reddy, Reynolds and Price developed a chromatographic method using Dowex 1 (Cl⁻), a strongly basic anion exchange resin and Dowex 5OW (H⁺), a strongly acidic cation exchange resin for the separation of 4-pyridoxic acid from extraneous fluorescent materials in urine. Eluates from the latter of the two columns, used in sequence, were subjected to a chemical procedure to oxidize the 4-pyridoxic acid to the more highly fluorescent lactone form. The Reddy, Reynolds and Price procedure has provided the means for achieving more valid results than had been possible previously. Because of the importance of this procedure, the dynamics of the ion exchange method of Reddy and associates was investigated. Standards of 4-pyridoxic acid, or 4-pyridoxic acid lactone, and of urine were subjected to ion exchange chromatography using their procedure. Conversion of the 4-pyridoxic acid to the lactone was accomplished by means of the microprocedure of Woodring, Fisher and Storvick (1964). Effluent, wash, and eluate fractions were collected to determine the pattern of elution of the 4-pyridoxic acid, as well as to determine the effect of interfering fluorescence from the resins and from reagents. Eluates of urine from the second in the series of two Dowex ion exchange resins were subjected to paper and thin layer chromatography along with standards of 4-pyridoxic acid and the lactone of 4-pyridoxic acid. Eluates from influents of hydrolyzed urine produced highly fluorescent zones which did not correspond to those of standards of 4-pyridoxic acid or its lactone. A tryptophan load test is often used to diagnose vitamin B₆ deficiency but some of the metabolites of tryptophan are highly fluorescent and may interfere with the fluorometric measurement of 4-pyridoxic acid even after its conversion to the more fluorescent lactone. To study the effect of the presence of tryptophan metabolites on the determination of 4-pyridoxic acid in urine, a test dose of L-tryptophan was administered to one subject and the subsequent 24-hour urine collection was treated according to the chromatographic procedure of Reddy et al. The final eluate was analyzed for 4- pyridoxic acid using the raicroprocedure of Woodring and associates. Readings of fluorescence indicated that much foreign fluorescence remained even after the lactonization procedure. Recovery of 4- pyridoxic acid was 65.5 percent. Therefore, for the determination of 4-pyridoxic acid following a test dose of L-tryptophan, a recovery curve would have to be used for calculation of 4-pyridoxic acid excretion. It was made emphatically clear that there are highly fluorescent compounds present in the resin itself, even after extensive treatment, which cannot be removed. The results of this study emphasize the great importance of maintaining a constant rate of flow, and thus a constant rate of leaching, during chromatography to minimize the effect of the interfering fluorescence. Dowex 5OW (H⁺) will not retain 4-pyridoxic acid well unless the resin has been rendered strongly acidic. It was ascertained that this procedure should be accomplished just before use. 4-Pyridoxic acid and the lactone of 4-pyridoxic acid are eluted almost at once from the Dowex 1 resin but are released in the middle fractions during elution from freshly activated Dowex 50W, with 50 ml. of elutriant. It was determined that chromatography could be undertaken at a relatively rapid flow rate, thus allowing the entire chromatogtaphic procedure and analysis of eluates to be completed in one day. Title: The determination of 4-Pyridoxic acid in urine ; an investigation into the recovery of 4-pyridoxic acid and the lactone of 4-pyridoxic acid from two Dowex ion exchange resins Author: Rohrer, Martha Jane 4-Pyridoxic acid is the major metabolite of all forms of vitamin B₆ in mammalian species. The determination of 4-pyridoxic acid, therefore, is important in the investigation of vitamin B₆ metabolism and for the establishment of human requirements for the vitamin. Although 4-pyridoxic acid is itself fluorescent, Huff and Perlzweig (1944) developed a classic method for its determination based on the conversion of the metabolite to the even more highly fluorescent lactone. Sarett in 1951 recognized that there are many substances in urine other than 4-pyridoxic acid which are fluorescent and which may interfere with its determination. His attempts to remove the extraneous fluorescent compounds with Decalso or with charcoal were not entirely satisfactory. He proposed, therefore, the administration of a test dose of 4-pyridoxic acid to subjects whose urine was to be analyzed for the metabolite of vitamin B₆, thus rendering the foreign fluorescence less significant by dilution. In 1955, Fujita and associates employed ion exchange chromatography as a means of separating 4-pyridoxic acid from other fluorescent compounds in urine and in 1958 Reddy, Reynolds and Price developed a chromatographic method using Dowex 1 (Cl⁻), a strongly basic anion exchange resin and Dowex 5OW (H⁺), a strongly acidic cation exchange resin for the separation of 4-pyridoxic acid from extraneous fluorescent materials in urine. Eluates from the latter of the two columns, used in sequence, were subjected to a chemical procedure to oxidize the 4-pyridoxic acid to the more highly fluorescent lactone form. The Reddy, Reynolds and Price procedure has provided the means for achieving more valid results than had been possible previously. Because of the importance of this procedure, the dynamics of the ion exchange method of Reddy and associates was investigated. Standards of 4-pyridoxic acid, or 4-pyridoxic acid lactone, and of urine were subjected to ion exchange chromatography using their procedure. Conversion of the 4-pyridoxic acid to the lactone was accomplished by means of the microprocedure of Woodring, Fisher and Storvick (1964). Effluent, wash, and eluate fractions were collected to determine the pattern of elution of the 4-pyridoxic acid, as well as to determine the effect of interfering fluorescence from the resins and from reagents. Eluates of urine from the second in the series of two Dowex ion exchange resins were subjected to paper and thin layer chromatography along with standards of 4-pyridoxic acid and the lactone of 4-pyridoxic acid. Eluates from influents of hydrolyzed urine produced highly fluorescent zones which did not correspond to those of standards of 4-pyridoxic acid or its lactone. A tryptophan load test is often used to diagnose vitamin B₆ deficiency but some of the metabolites of tryptophan are highly fluorescent and may interfere with the fluorometric measurement of 4-pyridoxic acid even after its conversion to the more fluorescent lactone. To study the effect of the presence of tryptophan metabolites on the determination of 4-pyridoxic acid in urine, a test dose of L-tryptophan was administered to one subject and the subsequent 24-hour urine collection was treated according to the chromatographic procedure of Reddy et al. The final eluate was analyzed for 4- pyridoxic acid using the raicroprocedure of Woodring and associates. Readings of fluorescence indicated that much foreign fluorescence remained even after the lactonization procedure. Recovery of 4- pyridoxic acid was 65.5 percent. Therefore, for the determination of 4-pyridoxic acid following a test dose of L-tryptophan, a recovery curve would have to be used for calculation of 4-pyridoxic acid excretion. It was made emphatically clear that there are highly fluorescent compounds present in the resin itself, even after extensive treatment, which cannot be removed. The results of this study emphasize the great importance of maintaining a constant rate of flow, and thus a constant rate of leaching, during chromatography to minimize the effect of the interfering fluorescence. Dowex 5OW (H⁺) will not retain 4-pyridoxic acid well unless the resin has been rendered strongly acidic. It was ascertained that this procedure should be accomplished just before use. 4-Pyridoxic acid and the lactone of 4-pyridoxic acid are eluted almost at once from the Dowex 1 resin but are released in the middle fractions during elution from freshly activated Dowex 50W, with 50 ml. of elutriant. It was determined that chromatography could be undertaken at a relatively rapid flow rate, thus allowing the entire chromatogtaphic procedure and analysis of eluates to be completed in one day. Close

• 1885. [Article] Epichloë typhina (fungus) - Botanophila lobata (fly) interaction : an invasive "pollinator" system in its introduced range in western Oregon

  Epichloë typhina (Ascomycetes: Clavicipitaceae) is an endophytic fungus that infects perennial Pooid grasses and is the causal agent of choke disease. It is endemic to Europe and was inadvertently introduced ...

  Citation × Citation Citation Abstract Copy Title: Epichloë typhina (fungus) - Botanophila lobata (fly) interaction : an invasive "pollinator" system in its introduced range in western Oregon Author: Kaser, Joseph M. Epichloë typhina (Ascomycetes: Clavicipitaceae) is an endophytic fungus that infects perennial Pooid grasses and is the causal agent of choke disease. It is endemic to Europe and was inadvertently introduced into orchardgrass seed production fields in western Oregon. Choke disease, which was first recorded in Oregon in 1996, currently infects ~90% of cultivated orchardgrass seed fields in the region, resulting in yield losses >65%. Infective propagules (i.e. ascospores) are produced sexually by the bipolar heterothallic fungus and gamete outcross has been shown to be facilitated in the wild by Botanophila spp. (Diptera: Anthomyiidae), including Botanophila lobata. The fly - fungus interaction is generally considered to be one of obligatory mutualism based on studies conducted in areas endemism. However, recent evidence suggests that the fungus is able to sexually outcross in cultivated Oregon orchardgrass fields without the aid of fly "pollinators." Additionally, ascosporic fertilization has recently been implicated as an alternative mechanism for gamete transfer and might have important impacts on fungal reproduction in Oregon. The objectives of this study were to: 1) explore how two tightly linked species, which appear to have an obligate mutualistic relationship in areas of endemism, interact in a non-native context; 2) quantitatively examine the seasonal and diurnal presence of E. typhina ascospores in a cultivated Oregon orchardgrass field; and 3) test alternative transfer mechanisms of fungal spermatia for E. typhina. To address objective 1), the spatial variability and reproductive success of E. typhina and B. lobata were estimated during surveys of ten cultivated orchardgrass fields in 2008 and four fields in 2009. Fungal distributions were spatially aggregated at five of the study sites in 2008 and three in 2009. Fly distributions were spatially aggregated at three sites in 2008 and one in 2009. Botanophila lobata density exhibited a positive linear relationship with E. typhina density, suggestive of positive density dependence of fly oviposition with fungal density. However, fungal reproductive success was not affected by fly density or fungal density within the range of distributions observed in this study. To address objective 2), airborne ascospores were monitored in a single cultivated orchardgrass field during 2008 and 2009 using a Burkard volumetric spore trap. Ascospore production began in early to middle May and continued into late July during both years of the study. Daily ascospore production exhibited a circadian rhythm, with production peaking on average at 1:08 am and 12:36 am, in 2008 and 2009, respectively. The prolonged duration and high intensity of ascospore production during the growing season suggest a large window within which new plants are at risk to infection, and within which preventative management strategies must be adopted. To address objective 3), splash fertilization, contact fertilization and B. lobata fertilization were tested in the greenhouse. Although only two replicates were completed, both contact and splash fertilization appeared to be viable mechanisms of sexual outcross for E. typhina. The results of this study strongly indicate that E. typhina can successfully reproduce without the presence of B. lobata. Splash and contact fertilization, as well as ascosporic fertilization, provide opportunities for reproduction of the fungus in absence of fly pollinators. It appears that the fly - fungus interaction has shifted from an obligatory mutualism to facultative mutualism or simple fungivory within the introduced range in western Oregon. Title: Epichloë typhina (fungus) - Botanophila lobata (fly) interaction : an invasive "pollinator" system in its introduced range in western Oregon Author: Kaser, Joseph M. Epichloë typhina (Ascomycetes: Clavicipitaceae) is an endophytic fungus that infects perennial Pooid grasses and is the causal agent of choke disease. It is endemic to Europe and was inadvertently introduced into orchardgrass seed production fields in western Oregon. Choke disease, which was first recorded in Oregon in 1996, currently infects ~90% of cultivated orchardgrass seed fields in the region, resulting in yield losses >65%. Infective propagules (i.e. ascospores) are produced sexually by the bipolar heterothallic fungus and gamete outcross has been shown to be facilitated in the wild by Botanophila spp. (Diptera: Anthomyiidae), including Botanophila lobata. The fly - fungus interaction is generally considered to be one of obligatory mutualism based on studies conducted in areas endemism. However, recent evidence suggests that the fungus is able to sexually outcross in cultivated Oregon orchardgrass fields without the aid of fly "pollinators." Additionally, ascosporic fertilization has recently been implicated as an alternative mechanism for gamete transfer and might have important impacts on fungal reproduction in Oregon. The objectives of this study were to: 1) explore how two tightly linked species, which appear to have an obligate mutualistic relationship in areas of endemism, interact in a non-native context; 2) quantitatively examine the seasonal and diurnal presence of E. typhina ascospores in a cultivated Oregon orchardgrass field; and 3) test alternative transfer mechanisms of fungal spermatia for E. typhina. To address objective 1), the spatial variability and reproductive success of E. typhina and B. lobata were estimated during surveys of ten cultivated orchardgrass fields in 2008 and four fields in 2009. Fungal distributions were spatially aggregated at five of the study sites in 2008 and three in 2009. Fly distributions were spatially aggregated at three sites in 2008 and one in 2009. Botanophila lobata density exhibited a positive linear relationship with E. typhina density, suggestive of positive density dependence of fly oviposition with fungal density. However, fungal reproductive success was not affected by fly density or fungal density within the range of distributions observed in this study. To address objective 2), airborne ascospores were monitored in a single cultivated orchardgrass field during 2008 and 2009 using a Burkard volumetric spore trap. Ascospore production began in early to middle May and continued into late July during both years of the study. Daily ascospore production exhibited a circadian rhythm, with production peaking on average at 1:08 am and 12:36 am, in 2008 and 2009, respectively. The prolonged duration and high intensity of ascospore production during the growing season suggest a large window within which new plants are at risk to infection, and within which preventative management strategies must be adopted. To address objective 3), splash fertilization, contact fertilization and B. lobata fertilization were tested in the greenhouse. Although only two replicates were completed, both contact and splash fertilization appeared to be viable mechanisms of sexual outcross for E. typhina. The results of this study strongly indicate that E. typhina can successfully reproduce without the presence of B. lobata. Splash and contact fertilization, as well as ascosporic fertilization, provide opportunities for reproduction of the fungus in absence of fly pollinators. It appears that the fly - fungus interaction has shifted from an obligatory mutualism to facultative mutualism or simple fungivory within the introduced range in western Oregon. Close

• 1886. [Article] Integrating traceability with onboard handling to enhance product quality and marketability of Eastern Pacific troll-caught albacore tuna (Thunnus alalunga)

  The fishing industry in the Pacific Northwest is a dynamic and highly competitive industry that must constantly respond to rapidly changing resource, regulatory and market forces. These forces have already ...

  Citation × Citation Citation Abstract Copy Title: Integrating traceability with onboard handling to enhance product quality and marketability of Eastern Pacific troll-caught albacore tuna (Thunnus alalunga) Author: Thompson, Michael J. The fishing industry in the Pacific Northwest is a dynamic and highly competitive industry that must constantly respond to rapidly changing resource, regulatory and market forces. These forces have already had a significant impact on our fisheries and will continue to do so as we learn more about the biology and ecology of harvested species, and how this information can be used to effectively manage our fisheries. In addition, market forces, both here and abroad, including the push by some governments to improve food safety and consumer confidence, are also having an impact on the U.S. seafood industry. In an attempt to address these issues, the European Union (E.U.) recently enacted traceability legislation, now mandatory for seafood, which will require all U.S. businesses exporting to the E.U. to provide adequate traceability documentation on their products. This legislation will have an impact on many U.S. fisheries, including the troll-caught albacore fishery in the Eastern Pacific Ocean, which, after losing its traditional market, has recently relied heavily on exporting. Although the term traceability has been around for some time it is relatively new to the U.S. food industry and many in the seafood sector, who now face the possibility of mandatory traceability, have not yet considered all its implications. Another issue facing the Eastern Pacific albacore fishery is that of product quality. Traditionally, this fishery has concentrated on producing albacore for the high-volume cannery market, which does not require the same stringent quality control standards as other market sectors. Albacore tuna (Thunnus alalunga), members of the Scrombroid family, are capable of thermoregulation and can exhibit internal temperatures of more than 15º C above ambient seawater. High internal temperatures, if sustained, and residual blood content can stimulate bacterial growth, which can eventually lead to scrombroid poisoning in humans. This makes the time immediately after landing critical in attaining and preserving important quality traits. In order to develop new markets for Eastern Pacific troll-caught albacore, quality needs to be improved and/or maintained within the industry at a sufficient level to supply market demands. This would require at least a portion of the industry to implement a set of onboard handling procedures designed to preserve and maintain quality. Although guidelines for handling albacore are available there is no industry “standard” for producing high quality products and only limited research presently exists into preserving quality traits of albacore onboard a vessel. The first paper in this thesis explores the concepts of traceability, current traceability legislation, and the potential applications of traceability systems to improve quality and marketing of U.S. seafood products. The second paper evaluates different onboard bleeding and handling techniques, which can affect product quality, currently used in the albacore industry and their ability to remove blood from the muscle tissues. Thirty-two different combinations of handling techniques and their affect on residual blood content were investigated by examining blood concentrations within the muscle tissue, using spectrophotometry methods, and cutaneous blood vessel coverage, by computer-aided digital color analysis. The results of the statistical analysis indicate that three of the five factors investigated had some influence on residual blood content. The third paper in this thesis evaluates the design and development of a computer-based onboard traceability system with integrated barcode technology, capable of efficiently recording capture and handling data. Two system trials were conducted, during normal fishing operations, where a total of 450 albacore tuna were successfully entered into the traceability database through the use of the Fishery Data Interface application. Documentation supplied by this system, which includes both spatial and temporal data, as well as information on product activities, will enable businesses to meet existing traceability requirements while also providing a new tool for the marketing of seafood products produced in the United States. Title: Integrating traceability with onboard handling to enhance product quality and marketability of Eastern Pacific troll-caught albacore tuna (Thunnus alalunga) Author: Thompson, Michael J. The fishing industry in the Pacific Northwest is a dynamic and highly competitive industry that must constantly respond to rapidly changing resource, regulatory and market forces. These forces have already had a significant impact on our fisheries and will continue to do so as we learn more about the biology and ecology of harvested species, and how this information can be used to effectively manage our fisheries. In addition, market forces, both here and abroad, including the push by some governments to improve food safety and consumer confidence, are also having an impact on the U.S. seafood industry. In an attempt to address these issues, the European Union (E.U.) recently enacted traceability legislation, now mandatory for seafood, which will require all U.S. businesses exporting to the E.U. to provide adequate traceability documentation on their products. This legislation will have an impact on many U.S. fisheries, including the troll-caught albacore fishery in the Eastern Pacific Ocean, which, after losing its traditional market, has recently relied heavily on exporting. Although the term traceability has been around for some time it is relatively new to the U.S. food industry and many in the seafood sector, who now face the possibility of mandatory traceability, have not yet considered all its implications. Another issue facing the Eastern Pacific albacore fishery is that of product quality. Traditionally, this fishery has concentrated on producing albacore for the high-volume cannery market, which does not require the same stringent quality control standards as other market sectors. Albacore tuna (Thunnus alalunga), members of the Scrombroid family, are capable of thermoregulation and can exhibit internal temperatures of more than 15º C above ambient seawater. High internal temperatures, if sustained, and residual blood content can stimulate bacterial growth, which can eventually lead to scrombroid poisoning in humans. This makes the time immediately after landing critical in attaining and preserving important quality traits. In order to develop new markets for Eastern Pacific troll-caught albacore, quality needs to be improved and/or maintained within the industry at a sufficient level to supply market demands. This would require at least a portion of the industry to implement a set of onboard handling procedures designed to preserve and maintain quality. Although guidelines for handling albacore are available there is no industry “standard” for producing high quality products and only limited research presently exists into preserving quality traits of albacore onboard a vessel. The first paper in this thesis explores the concepts of traceability, current traceability legislation, and the potential applications of traceability systems to improve quality and marketing of U.S. seafood products. The second paper evaluates different onboard bleeding and handling techniques, which can affect product quality, currently used in the albacore industry and their ability to remove blood from the muscle tissues. Thirty-two different combinations of handling techniques and their affect on residual blood content were investigated by examining blood concentrations within the muscle tissue, using spectrophotometry methods, and cutaneous blood vessel coverage, by computer-aided digital color analysis. The results of the statistical analysis indicate that three of the five factors investigated had some influence on residual blood content. The third paper in this thesis evaluates the design and development of a computer-based onboard traceability system with integrated barcode technology, capable of efficiently recording capture and handling data. Two system trials were conducted, during normal fishing operations, where a total of 450 albacore tuna were successfully entered into the traceability database through the use of the Fishery Data Interface application. Documentation supplied by this system, which includes both spatial and temporal data, as well as information on product activities, will enable businesses to meet existing traceability requirements while also providing a new tool for the marketing of seafood products produced in the United States. Close

• 1887. [Article] Caspian tern (Hydroprogne caspia) foraging ecology and predation on juvenile salmonids in San Francisco Bay, California

  Brooks Island, located in central San Francisco Bay, California, currently supports the largest breeding colony of Caspian terns (Hydroprogne caspia) in the Bay Area, and is one of several proposed relocation ...

  Citation × Citation Citation Abstract Copy Title: Caspian tern (Hydroprogne caspia) foraging ecology and predation on juvenile salmonids in San Francisco Bay, California Author: Adrean, Lindsay J. Brooks Island, located in central San Francisco Bay, California, currently supports the largest breeding colony of Caspian terns (Hydroprogne caspia) in the Bay Area, and is one of several proposed relocation sites for some Caspian terns from the world's largest colony in the Columbia River estuary of Oregon. Juvenile salmonids have been identified in the diet of Caspian terns nesting at Brooks Island, so I investigated whether the colony, at its current or an enhanced size, poses a threat to the recovery of several runs of salmonids (Oncorhynchus spp.) in San Francisco Bay that are listed under the U.S. Endangered Species Act (ESA). I also examined the foraging ecology of Brooks Island Caspian terns to 1) determine whether the colony is suitable for expansion based on availability of forage fish resources, a factor potentially limiting the size and productivity of the colony, and 2) investigate how Caspian terns nesting at this colony exploit forage fish resources. I used a bioenergetics modeling approach, employing estimates of tern energy requirements and proportions of energy supplied by various prey types, to estimate consumption of juvenile salmonids by Caspian terns nesting on Brooks Island during 2008 and 2009. Estimated salmonid consumption was 205,000 smolts (95% CI: 175,000 – 245,000 smolts) in 2008 and 167,000 smolts (95% CI: 144,000 – 191,000 smolts) in 2009. Predation rates on ESA-listed Central Valley spring-run Chinook salmon (O. tshawytscha; 0.08%) were lower than those on unlisted fall-run Chinook salmon (1.0%). Average per capita predation rates on juvenile salmonids by Brooks Island Caspian terns (2008: 126 fish; 2009: 123 fish) were less than half those of Caspian terns nesting in the Columbia River estuary. If the current downward trend in the number of Caspian terns nesting on Brooks Island continues until the colony is no longer extant, the resulting declines in predation on salmonids would lead to increases in annual population growth rates (Δλ) of salmonid runs of just small fractions of one percentage point. The proposed enhancement of the Brooks Island Caspian tern colony to 3,000 individuals would at most cause declines in annual population growth rates of 0.3% for fall-run Chinook salmon and 0.02% for threatened spring-run Chinook salmon, assuming that smolt mortality from tern predation is 100% additive. This level of impact to the ESA-listed spring-run Chinook salmon stock is less than the level considered acceptable by the National Marine Fisheries Service (Δλ = 0.05%). Radio-tracking of Caspian terns nesting on Brooks Island revealed that the maximum foraging distance from the colony was 80 km. The median foraging distance from the colony was greater in 2009 compared to 2008 (20.6 km vs. 14.0 km), average number of foraging trips per day was higher (4.4 vs. 3.4 foraging trips), and average adult colony attendance was lower (43% vs. 52% of daylight hours). These results indicate that the colony was more food-limited during the 2009 breeding season, concurrent with anomalous downwelling along the coast of northern California and reduced availability and size of marine forage fishes, such as herring, sardines, and anchovies. Caspian terns used a number of core foraging areas within 30 km of the Brooks Island colony, both inside and just outside the Bay. Two large core foraging areas were close to or overlapped with the release site for juvenile salmonids in eastern San Pablo Bay, where > 10 million hatchery-raised smolts were released from net pens during both the 2008 and 2009 tern nesting seasons. This finding supports the hypothesis that most juvenile salmonids consumed by terns nesting at the Brooks Island colony were captured at or near the release site. Individual Caspian terns displayed foraging site fidelity, suggesting that foraging at the release site for hatchery-raised salmonids was a learned behavior by some terns. The Brooks Island colony site is within foraging distance of adequate marine forage fish resources in most years, and Caspian terns nesting there are not dependent on juvenile salmonids as a food resource. Consumption of juvenile salmonids by Brooks Island terns would be largely curtailed by modification of hatchery release practices. Title: Caspian tern (Hydroprogne caspia) foraging ecology and predation on juvenile salmonids in San Francisco Bay, California Author: Adrean, Lindsay J. Brooks Island, located in central San Francisco Bay, California, currently supports the largest breeding colony of Caspian terns (Hydroprogne caspia) in the Bay Area, and is one of several proposed relocation sites for some Caspian terns from the world's largest colony in the Columbia River estuary of Oregon. Juvenile salmonids have been identified in the diet of Caspian terns nesting at Brooks Island, so I investigated whether the colony, at its current or an enhanced size, poses a threat to the recovery of several runs of salmonids (Oncorhynchus spp.) in San Francisco Bay that are listed under the U.S. Endangered Species Act (ESA). I also examined the foraging ecology of Brooks Island Caspian terns to 1) determine whether the colony is suitable for expansion based on availability of forage fish resources, a factor potentially limiting the size and productivity of the colony, and 2) investigate how Caspian terns nesting at this colony exploit forage fish resources. I used a bioenergetics modeling approach, employing estimates of tern energy requirements and proportions of energy supplied by various prey types, to estimate consumption of juvenile salmonids by Caspian terns nesting on Brooks Island during 2008 and 2009. Estimated salmonid consumption was 205,000 smolts (95% CI: 175,000 – 245,000 smolts) in 2008 and 167,000 smolts (95% CI: 144,000 – 191,000 smolts) in 2009. Predation rates on ESA-listed Central Valley spring-run Chinook salmon (O. tshawytscha; 0.08%) were lower than those on unlisted fall-run Chinook salmon (1.0%). Average per capita predation rates on juvenile salmonids by Brooks Island Caspian terns (2008: 126 fish; 2009: 123 fish) were less than half those of Caspian terns nesting in the Columbia River estuary. If the current downward trend in the number of Caspian terns nesting on Brooks Island continues until the colony is no longer extant, the resulting declines in predation on salmonids would lead to increases in annual population growth rates (Δλ) of salmonid runs of just small fractions of one percentage point. The proposed enhancement of the Brooks Island Caspian tern colony to 3,000 individuals would at most cause declines in annual population growth rates of 0.3% for fall-run Chinook salmon and 0.02% for threatened spring-run Chinook salmon, assuming that smolt mortality from tern predation is 100% additive. This level of impact to the ESA-listed spring-run Chinook salmon stock is less than the level considered acceptable by the National Marine Fisheries Service (Δλ = 0.05%). Radio-tracking of Caspian terns nesting on Brooks Island revealed that the maximum foraging distance from the colony was 80 km. The median foraging distance from the colony was greater in 2009 compared to 2008 (20.6 km vs. 14.0 km), average number of foraging trips per day was higher (4.4 vs. 3.4 foraging trips), and average adult colony attendance was lower (43% vs. 52% of daylight hours). These results indicate that the colony was more food-limited during the 2009 breeding season, concurrent with anomalous downwelling along the coast of northern California and reduced availability and size of marine forage fishes, such as herring, sardines, and anchovies. Caspian terns used a number of core foraging areas within 30 km of the Brooks Island colony, both inside and just outside the Bay. Two large core foraging areas were close to or overlapped with the release site for juvenile salmonids in eastern San Pablo Bay, where > 10 million hatchery-raised smolts were released from net pens during both the 2008 and 2009 tern nesting seasons. This finding supports the hypothesis that most juvenile salmonids consumed by terns nesting at the Brooks Island colony were captured at or near the release site. Individual Caspian terns displayed foraging site fidelity, suggesting that foraging at the release site for hatchery-raised salmonids was a learned behavior by some terns. The Brooks Island colony site is within foraging distance of adequate marine forage fish resources in most years, and Caspian terns nesting there are not dependent on juvenile salmonids as a food resource. Consumption of juvenile salmonids by Brooks Island terns would be largely curtailed by modification of hatchery release practices. Close

• 1888. [Article] Chemical labeling methods and mass spectrometry of mitochondrial thiol proteomes

  Dysfunction of mitochondria has been linked to aging and the pathogenesis of many degenerative diseases. Aside from their primary function in energy production, mitochondria are considered as a major source ...

  Citation × Citation Citation Abstract Copy Title: Chemical labeling methods and mass spectrometry of mitochondrial thiol proteomes Author: Wang, Jing Dysfunction of mitochondria has been linked to aging and the pathogenesis of many degenerative diseases. Aside from their primary function in energy production, mitochondria are considered as a major source and target of reactive oxygen and nitrogen species (ROS/RNS) in cells as well. The mitochondrial thiol proteome is a subset of proteins inside mitochondria particularly vulnerable to oxidative modifications often caused by ROS/RNS due to the high reactivity of thiol groups. In this dissertation, we used chemoselective labeling approaches to target mitochondrial thiol proteomes with two distinct purposes. In the first part of our study, a mitochondria-targeted cationic sulfhydryl reagent, (4-iodobutyl)triphenyl- phosphonium (IBTP), was used to label the protein thiols. This study was focused on the investigation of the tandem mass spectrometric behaviors of the thiol peptides modified by IBTP. In the latter part of the dissertation, we tested the hypothesis that the thiol proteomes of cardiac mitochondria undergo chemical changes as a consequence of aging. The thiol-reactive isotope-coded affinity tags (ICATs) were utilized to estimate the possible age-related impacts on the relative abundances of protein thiols in two mitochondrial subpopulations present in rat myocardium, respectively. Fixed charge chemical modifications on peptides and proteins can have significant effects on the ion fragmentation behaviors in tandem mass spectrometry (MS/MS). The MS/MS fragmentation behavior of butyltriphenylphosphonium (BTP)-modified peptides was evaluated via the comparison to their carbamidomethylated (CAM) analogues using a quadrupole ion trap mass spectrometer (LCQ) and/or a quadrupole time-of-flight (QTOF) instrument under conditions of low energy collision-induced dissociation (CID). Besides the expected higher charge states observed in peptides and fragment ions containing the BTP moiety, the charged BTP group also had a significant effect on the amide bond fragmentation products of modified cysteine-containing peptides. The presence of a phosphonium ion was speculated to reduce the tendency for the protonation of the proximal amide bonds in the peptide backbones, and consequently decrease the product ion abundances at the corresponding cleavage sites when compared to those from the CAM-modified derivatives. This effect was particularly noticeable when an Xxx-Pro bond was in the vicinity of a BTP group. Calculations indicated that proton affinities were generally 20-50 kcal/mol lower for BTP-modified peptides in contrast to the respective unmodified or CAM-modified analogues. In the latter part of the dissertation, we focused on the evaluation of age-related effects on protein thiol abundances in cardiac subsarcolemmal and interfibrillar mitochondria (SSM/IFM). A total of 243 cysteine residues from 115 proteins in SSM and 149 cysteine sites from 65 proteins in IFM were identified from both young and old rats using ICAT labeling approach, respectively. Significant age-related differences (p-value < 0.05) in protein thiol abundances were only observed for five proteins from IFM. These proteins were associated with the functional pathways of the oxidative phosphorylation (NDUV1 and QCR1), the tricarboxylic acid cycle (MDHM and ODPB) and fatty acid beta-oxidation (ACSL1). Additionally, five other proteins in SSM and two proteins in IFM were detected with potentially significant age-related effects (0.05 < p-value < 0.1) with regard to their respective protein thiol abundances, however, no common protein was identified from both subpopulations. These results demonstrated the differences in age-related effects on protein thiol abundances between cardiac SSM and IFM. Further, the reactivities of cysteine residues, identified in the current ICAT reaction, were evaluated and sorted into high (78 in SSM vs. 47 in IFM), moderate (30 vs. 32) and low (135 vs. 70) labeling frequency groups. Thirty eight thiol groups were also identified from other cysteine-targeted studies conducted in our group, i.e., Michael addition by 2-alkenals and disulfide exchange via glutathionylation. The comparative results from these three studies revealed eight cysteine residues as the common modification sites targeted by three distinct reaction mechanisms. This resulted in the identification of candidates of vulnerable cysteine residues in the aging heart mitochondria. Title: Chemical labeling methods and mass spectrometry of mitochondrial thiol proteomes Author: Wang, Jing Dysfunction of mitochondria has been linked to aging and the pathogenesis of many degenerative diseases. Aside from their primary function in energy production, mitochondria are considered as a major source and target of reactive oxygen and nitrogen species (ROS/RNS) in cells as well. The mitochondrial thiol proteome is a subset of proteins inside mitochondria particularly vulnerable to oxidative modifications often caused by ROS/RNS due to the high reactivity of thiol groups. In this dissertation, we used chemoselective labeling approaches to target mitochondrial thiol proteomes with two distinct purposes. In the first part of our study, a mitochondria-targeted cationic sulfhydryl reagent, (4-iodobutyl)triphenyl- phosphonium (IBTP), was used to label the protein thiols. This study was focused on the investigation of the tandem mass spectrometric behaviors of the thiol peptides modified by IBTP. In the latter part of the dissertation, we tested the hypothesis that the thiol proteomes of cardiac mitochondria undergo chemical changes as a consequence of aging. The thiol-reactive isotope-coded affinity tags (ICATs) were utilized to estimate the possible age-related impacts on the relative abundances of protein thiols in two mitochondrial subpopulations present in rat myocardium, respectively. Fixed charge chemical modifications on peptides and proteins can have significant effects on the ion fragmentation behaviors in tandem mass spectrometry (MS/MS). The MS/MS fragmentation behavior of butyltriphenylphosphonium (BTP)-modified peptides was evaluated via the comparison to their carbamidomethylated (CAM) analogues using a quadrupole ion trap mass spectrometer (LCQ) and/or a quadrupole time-of-flight (QTOF) instrument under conditions of low energy collision-induced dissociation (CID). Besides the expected higher charge states observed in peptides and fragment ions containing the BTP moiety, the charged BTP group also had a significant effect on the amide bond fragmentation products of modified cysteine-containing peptides. The presence of a phosphonium ion was speculated to reduce the tendency for the protonation of the proximal amide bonds in the peptide backbones, and consequently decrease the product ion abundances at the corresponding cleavage sites when compared to those from the CAM-modified derivatives. This effect was particularly noticeable when an Xxx-Pro bond was in the vicinity of a BTP group. Calculations indicated that proton affinities were generally 20-50 kcal/mol lower for BTP-modified peptides in contrast to the respective unmodified or CAM-modified analogues. In the latter part of the dissertation, we focused on the evaluation of age-related effects on protein thiol abundances in cardiac subsarcolemmal and interfibrillar mitochondria (SSM/IFM). A total of 243 cysteine residues from 115 proteins in SSM and 149 cysteine sites from 65 proteins in IFM were identified from both young and old rats using ICAT labeling approach, respectively. Significant age-related differences (p-value < 0.05) in protein thiol abundances were only observed for five proteins from IFM. These proteins were associated with the functional pathways of the oxidative phosphorylation (NDUV1 and QCR1), the tricarboxylic acid cycle (MDHM and ODPB) and fatty acid beta-oxidation (ACSL1). Additionally, five other proteins in SSM and two proteins in IFM were detected with potentially significant age-related effects (0.05 < p-value < 0.1) with regard to their respective protein thiol abundances, however, no common protein was identified from both subpopulations. These results demonstrated the differences in age-related effects on protein thiol abundances between cardiac SSM and IFM. Further, the reactivities of cysteine residues, identified in the current ICAT reaction, were evaluated and sorted into high (78 in SSM vs. 47 in IFM), moderate (30 vs. 32) and low (135 vs. 70) labeling frequency groups. Thirty eight thiol groups were also identified from other cysteine-targeted studies conducted in our group, i.e., Michael addition by 2-alkenals and disulfide exchange via glutathionylation. The comparative results from these three studies revealed eight cysteine residues as the common modification sites targeted by three distinct reaction mechanisms. This resulted in the identification of candidates of vulnerable cysteine residues in the aging heart mitochondria. Close

• 1889. [Article] Biochemical and Physical Characterization of Fish Protein Isolate and Surimi for their Compatibility

  There are presently two successful methods used to refine fish muscle proteins: surimi and fish protein isolate (FPI). Both surimi and FPI have the ability to form an elastic gel upon comminution and heating. ...

  Citation × Citation Citation Abstract Copy Title: Biochemical and Physical Characterization of Fish Protein Isolate and Surimi for their Compatibility Author: Kobayashi, Yuka There are presently two successful methods used to refine fish muscle proteins: surimi and fish protein isolate (FPI). Both surimi and FPI have the ability to form an elastic gel upon comminution and heating. However, their gelation behaviors are different as they are refined in a biochemically opposite way based on the nature of protein denaturation. The focus of this study was to compare surimi and FPI under various processing conditions, such as rigor mortis, frozen storage, comminution conditions, and blending effect, and how these conditions can affect their functional properties including gel texture. The structural changes and rheological properties of tilapia protein prepared using FPI and surimi with pre- and post-rigor muscle were evaluated. No rigor effect was observed on the gel-forming ability of FPI, although higher storage modulus (G’) and better gel texture were obtained in surimi made from pre-rigor tilapia compared to surimi made from post-rigor tilapia. Results suggested pre-rigor processing may improve gel-formation properties of surimi, but not as much for the gelation of FPI. Storing fish in a freezer for extended periods of time can adversely affect the gel-forming ability of muscle proteins. The effect of frozen storage (0, 1, and 3 mo) on the biochemical and physical characterization of FPI and surimi made from tilapia was elucidated. The Ca²⁺ATPase activity of tilapia fillet continuously reduced throughout the frozen storage; however, the decline trend of its activity was slower than cold or temperate water species. As reported by storage modulus (G’), storing whole fish frozen for 3 mo did not affect the gelling ability of FPI and surimi. The results from surface hydrophobicity, surface reactive sulfhydryl (SRSH) content, and differential scanning calorimetry also corresponded to the results from storage modulus. Thus, frozen tilapia, if stored up to 3 mo, may be used like fresh fish in the processing of FPI and surimi and no negative effects on gel qualities. The uniqueness of tropical fish tilapia was thought due to its high thermal stability. The quality of surimi gels was affected more so under various rigor stages and frozen storage compared to FPI gels. Conversely, the addition of salt into FPI induced a higher degree of unfolding protein structure prior to gelation compared to surimi. In addition, comminution conditions affected the quality of FPI gel more than that of surimi gel. A significant increase in puncture gel texture was observed when FPI and surimi were chopped at 25°C for 18 min compared to samples chopped at 5°C for 6 min. The comparable results were detected as measured by storage modulus. FPI chopped with 3% salt at 5°C for 6 min showed the lowest gel texture among all treatments, possibly because protein structure was not disintegrated appropriately and formed larger protein aggregates and coarser gels demonstrated by microscopic analyses. Results suggested controlling chopping temperature and time, and the addition of salt, may be significant factors to enhance production of high quality gel in FPI and surimi. Moreover, the effect of various comminution conditions on structural changes were investigated using Fourier transform infrared (FT-IR) and Raman spectroscopy. Both procedures exhibited increasing chopping temperature and time, adding salt, promoted a higher degree of unfolding protein structure in FPI and surimi paste made from tilapia, when they were chopped at 25°C for 18 min compared to samples chopped at 5°C for 6 min. Also, FPI and surimi gels prepared after chopping at 25°C for 18 min revealed higher β-sheet contents and more chemical bonds such as hydrophobic interactions and disulfide bonds than those at 5°C for 6 min. Controlling comminution conditions may be one of the important factors to produce high quality gels from FPI and surimi using tropical fish like tilapia. Additionally, FT-IR and Raman spectroscopy are useful complementary tools, allowing a better interpretation of the structural changes in FPI and surimi under various comminution conditions. The gelation properties of blending two different fish proteins obtained from surimi and FPI at different ratios was evaluated. Effects of blending surimi and FPI on gel functionality (whiteness, hardness, and cohesiveness) demonstrated a linear pattern when the proportion of surimi is larger than or equal to that of FPI. Also, breaking force and penetration distance decreased significantly when the ratio of surimi to FPI decreased. Results indicated gels cooked in a water bath tended to exhibit a higher breaking force than gels cooked ohmically. On the other hand, a higher penetration distance was observed for gels cooked ohmically compared to gels cooked in a water bath. Blending surimi and FPI did not affect the inter-molecular interactions of protein in a linear pattern, like mixing various grades of surimi, but this might be feasible only when the proportion of FPI does not exceed 50%. Title: Biochemical and Physical Characterization of Fish Protein Isolate and Surimi for their Compatibility Author: Kobayashi, Yuka There are presently two successful methods used to refine fish muscle proteins: surimi and fish protein isolate (FPI). Both surimi and FPI have the ability to form an elastic gel upon comminution and heating. However, their gelation behaviors are different as they are refined in a biochemically opposite way based on the nature of protein denaturation. The focus of this study was to compare surimi and FPI under various processing conditions, such as rigor mortis, frozen storage, comminution conditions, and blending effect, and how these conditions can affect their functional properties including gel texture. The structural changes and rheological properties of tilapia protein prepared using FPI and surimi with pre- and post-rigor muscle were evaluated. No rigor effect was observed on the gel-forming ability of FPI, although higher storage modulus (G’) and better gel texture were obtained in surimi made from pre-rigor tilapia compared to surimi made from post-rigor tilapia. Results suggested pre-rigor processing may improve gel-formation properties of surimi, but not as much for the gelation of FPI. Storing fish in a freezer for extended periods of time can adversely affect the gel-forming ability of muscle proteins. The effect of frozen storage (0, 1, and 3 mo) on the biochemical and physical characterization of FPI and surimi made from tilapia was elucidated. The Ca²⁺ATPase activity of tilapia fillet continuously reduced throughout the frozen storage; however, the decline trend of its activity was slower than cold or temperate water species. As reported by storage modulus (G’), storing whole fish frozen for 3 mo did not affect the gelling ability of FPI and surimi. The results from surface hydrophobicity, surface reactive sulfhydryl (SRSH) content, and differential scanning calorimetry also corresponded to the results from storage modulus. Thus, frozen tilapia, if stored up to 3 mo, may be used like fresh fish in the processing of FPI and surimi and no negative effects on gel qualities. The uniqueness of tropical fish tilapia was thought due to its high thermal stability. The quality of surimi gels was affected more so under various rigor stages and frozen storage compared to FPI gels. Conversely, the addition of salt into FPI induced a higher degree of unfolding protein structure prior to gelation compared to surimi. In addition, comminution conditions affected the quality of FPI gel more than that of surimi gel. A significant increase in puncture gel texture was observed when FPI and surimi were chopped at 25°C for 18 min compared to samples chopped at 5°C for 6 min. The comparable results were detected as measured by storage modulus. FPI chopped with 3% salt at 5°C for 6 min showed the lowest gel texture among all treatments, possibly because protein structure was not disintegrated appropriately and formed larger protein aggregates and coarser gels demonstrated by microscopic analyses. Results suggested controlling chopping temperature and time, and the addition of salt, may be significant factors to enhance production of high quality gel in FPI and surimi. Moreover, the effect of various comminution conditions on structural changes were investigated using Fourier transform infrared (FT-IR) and Raman spectroscopy. Both procedures exhibited increasing chopping temperature and time, adding salt, promoted a higher degree of unfolding protein structure in FPI and surimi paste made from tilapia, when they were chopped at 25°C for 18 min compared to samples chopped at 5°C for 6 min. Also, FPI and surimi gels prepared after chopping at 25°C for 18 min revealed higher β-sheet contents and more chemical bonds such as hydrophobic interactions and disulfide bonds than those at 5°C for 6 min. Controlling comminution conditions may be one of the important factors to produce high quality gels from FPI and surimi using tropical fish like tilapia. Additionally, FT-IR and Raman spectroscopy are useful complementary tools, allowing a better interpretation of the structural changes in FPI and surimi under various comminution conditions. The gelation properties of blending two different fish proteins obtained from surimi and FPI at different ratios was evaluated. Effects of blending surimi and FPI on gel functionality (whiteness, hardness, and cohesiveness) demonstrated a linear pattern when the proportion of surimi is larger than or equal to that of FPI. Also, breaking force and penetration distance decreased significantly when the ratio of surimi to FPI decreased. Results indicated gels cooked in a water bath tended to exhibit a higher breaking force than gels cooked ohmically. On the other hand, a higher penetration distance was observed for gels cooked ohmically compared to gels cooked in a water bath. Blending surimi and FPI did not affect the inter-molecular interactions of protein in a linear pattern, like mixing various grades of surimi, but this might be feasible only when the proportion of FPI does not exceed 50%. Close

• 1890. [Article] Overstory composition and stand structure shifts within inter-mixed ponderosa pine and lodgepole pine stands of the south-central Oregon pumice zone

  Ponderosa pine (Pinus ponderosa) and lodgepole pine (Pinus contorta var. murrayana) forests of south-central Oregon have been extensively researched over the last century. However, little information has ...

  Citation × Citation Citation Abstract Copy Title: Overstory composition and stand structure shifts within inter-mixed ponderosa pine and lodgepole pine stands of the south-central Oregon pumice zone Author: Shuffield, Chaylon D. Ponderosa pine (Pinus ponderosa) and lodgepole pine (Pinus contorta var. murrayana) forests of south-central Oregon have been extensively researched over the last century. However, little information has been reported on overstory composition and stand structure shifts associated with fire exclusion within inter-mixed ponderosa pine and lodgepole pine stands of the south-central Oregon pumice zone. In recent time, the lack of disturbance history and quantitative information needed to reconstruct historic stand conditions has become a growing concern for many ecologists. The need to collect quantitative information from remnant old-growth stands is imperative to improve restoration activities, incorporate stand-level diversity, identify the degree of successional departure, and to ensure valuable data is archived for future reference and ecological analysis. In Chapter 1, an exhaustive search for published information on early land-use practices specific to our study area was performed to: (1) identify the degree of Native American influence on vegetation; (2) identify direct and indirect Euro-American disturbances involving the loss of natural processes; and (3) establish a reference period for appropriate representation of historic conditions. In Chapter 2, remnant old-growth stands were analyzed using dendrochronological techniques and statistical comparisons to quantify: (1) shifts in overstory composition and stand structure; (2) growth and development of ponderosa pine and lodgepole pine across time; and to (3) characterize the influence of climate and fire on species recruitment. Our analysis indicated successional trajectory shifts occurred shortly after the loss of Native American influence beginning around 1850 and associated affects of intensive grazing following 1880. Age reconstruction displayed an exponential pattern of recruitment between 1880 and 1950. Since 1850, our analysis revealed a reduction in average tree basal area growth and height development of understory ponderosa pine and lodgepole pine. Ponderosa pine greater than 150 years old accounted for less than 5.0% of the total contemporary density, but composed 45.0% of the total basal area. Lodgepole pine greater than 100 years old accounted for approximately 3.0% of the total contemporary density and composed 12.8% of the total basal area. Stand density for our study area averaged 25.3 trees per hectare for ponderosa pine greater than 53.3 centimeters diameter at 1.4 meters. We report low levels of lodgepole pine recruitment (2/hectare/decade) prior to 1880 and suggest the long-term development of less fire-resistant lodgepole pine has been favored since fire exclusion. Furthermore, contemporary settings support conditions associated to atypical mountain pine beetle outbreaks and fire behavior known to cause mortality of large diameter ponderosa pine. Restoration of remnant inter-mixed stands requires the aggressive removal of lodgepole pine and re-introduction of fire to provide long-term sustainability of ecosystem health and preservation of large diameter ponderosa pine. Title: Overstory composition and stand structure shifts within inter-mixed ponderosa pine and lodgepole pine stands of the south-central Oregon pumice zone Author: Shuffield, Chaylon D. Ponderosa pine (Pinus ponderosa) and lodgepole pine (Pinus contorta var. murrayana) forests of south-central Oregon have been extensively researched over the last century. However, little information has been reported on overstory composition and stand structure shifts associated with fire exclusion within inter-mixed ponderosa pine and lodgepole pine stands of the south-central Oregon pumice zone. In recent time, the lack of disturbance history and quantitative information needed to reconstruct historic stand conditions has become a growing concern for many ecologists. The need to collect quantitative information from remnant old-growth stands is imperative to improve restoration activities, incorporate stand-level diversity, identify the degree of successional departure, and to ensure valuable data is archived for future reference and ecological analysis. In Chapter 1, an exhaustive search for published information on early land-use practices specific to our study area was performed to: (1) identify the degree of Native American influence on vegetation; (2) identify direct and indirect Euro-American disturbances involving the loss of natural processes; and (3) establish a reference period for appropriate representation of historic conditions. In Chapter 2, remnant old-growth stands were analyzed using dendrochronological techniques and statistical comparisons to quantify: (1) shifts in overstory composition and stand structure; (2) growth and development of ponderosa pine and lodgepole pine across time; and to (3) characterize the influence of climate and fire on species recruitment. Our analysis indicated successional trajectory shifts occurred shortly after the loss of Native American influence beginning around 1850 and associated affects of intensive grazing following 1880. Age reconstruction displayed an exponential pattern of recruitment between 1880 and 1950. Since 1850, our analysis revealed a reduction in average tree basal area growth and height development of understory ponderosa pine and lodgepole pine. Ponderosa pine greater than 150 years old accounted for less than 5.0% of the total contemporary density, but composed 45.0% of the total basal area. Lodgepole pine greater than 100 years old accounted for approximately 3.0% of the total contemporary density and composed 12.8% of the total basal area. Stand density for our study area averaged 25.3 trees per hectare for ponderosa pine greater than 53.3 centimeters diameter at 1.4 meters. We report low levels of lodgepole pine recruitment (2/hectare/decade) prior to 1880 and suggest the long-term development of less fire-resistant lodgepole pine has been favored since fire exclusion. Furthermore, contemporary settings support conditions associated to atypical mountain pine beetle outbreaks and fire behavior known to cause mortality of large diameter ponderosa pine. Restoration of remnant inter-mixed stands requires the aggressive removal of lodgepole pine and re-introduction of fire to provide long-term sustainability of ecosystem health and preservation of large diameter ponderosa pine. Close

• 1891. [Article] Measuring costs of sequestering carbon in forest stands with different management regimes in western Oregon

  This project was a part of larger work that compared major factors controlling patterns of carbon dynamics in two regions of the globe, the Pacific Northwest, USA and northwestern Russia. It was funded ...

  Citation × Citation Citation Abstract Copy Title: Measuring costs of sequestering carbon in forest stands with different management regimes in western Oregon Author: Zyrina, Olga A. This project was a part of larger work that compared major factors controlling patterns of carbon dynamics in two regions of the globe, the Pacific Northwest, USA and northwestern Russia. It was funded through the NASA foundation (grant # NAG5- 6242). Human economic activity is causing the release of pollutants such as carbon dioxide. The increased concentration of pollutants in the atmosphere is thought to cause greenhouse effect, in other words - the warming of the earth and lower atmosphere. Different methods are proposed to reduce concentration of greenhouse gases (GHG) in the atmosphere. Some involve development of more clean technologies. Some involve reductions in the use of fossil fuels. Another possibility is to store carbon (C) as live biomass. Plants use C for growth and development. Using forests to sequester C is one strategy for mitigating effects of GHG emissions. There are many methods in forestry to grow trees and produce wood products. Some of them include clearcutting, thinning, fertilizing, burning, and partial cutting. This project had three purposes. First, was to investigate the effect of a wide variety of silvicultural treatments on C storage and the economic value of harvested forest products. We measured economic value as soil expectation value. Second, was to use Data Envelopment Analysis to determine the efficient set of treatments, which make up the Production Possibility Frontier (PPF) in terms of C and economic value. Third, was to use the PPF to measure the marginal cost of carbon storage in moving from high SEV and relatively low C storage to lower SEV and relatively high C storage. C storage and timber harvest were simulated using the STANDCARB model for forest types common in north-western Oregon with two tree species, Douglas fir (Pseudotsuga menziesii) and Western hemlock (Tsuga heterophylla). Fifty silvicultural regimes were investigated. They included clearcutting with rotations of 50, 70, 90, 110, 130, and 150. Each of the six rotation ages had eight combinations of silvicultural treatments consisting of artificial and natural regeneration, growth enhancement (GE) and thinning. Two partial cutting regimes: group selection and single-tree selection were also used in the analysis. C storage was calculated for every output year of each model run as a sum of live, dead, and stable C. C storage for each silvicultural regime was measured as the average over five full rotations from the steady state portion of the run. The analysis showed that average C increases with rotation age from 335.99 MgC/ha with 50-year rotation with natural regeneration and thinning to 826.36 MgCIha with 150-year rotation with artificial regeneration and GE. The use of artificial regeneration compared to natural regeneration gave a 20-30 MgC/ha improvement for all regimes. The total harvest from thinning and clearcutting over the rotation period averaged for several runs varied from 505.34 m3/ha (with 50-year rotation no treatment) to 1782.24 m3/ha (with 150-year rotation with GE and thinning) The use of artificial compared to natural regeneration gave a 20-50 m3/ha increase in harvest for all regimes. SEV is the present value of net revenues from perpetually growing tree crops following the specified regime. It measures the economic value of each regime. Generally, SEV has a negative correlation with rotation length. Using a 3.5 percent real discount rate, the maximum SEV ($7904.3/hectare) was obtained from 50-year rotation with artificial regeneration, GE and thinning In contrast, SEV for 130-year rotation with artificial regeneration was only $446.68/hectare. Using Data Envelopment Analysis (OnFront software) we found that 8 of the 50 regimes investigated were efficient in their ability to store C and produce economic value. The efficient regimes included 50, 110, 130 and 150-year rotations with artificial regeneration, GE and thinning; 110, 130 and 150-year rotations with natural regeneration, GE and thinning, and the 150-year rotation with natural regeneration and GE. When regimes with GE were excluded, we found 7 efficient regimes: 50 and 150-year rotations with artificial regeneration and thinning, 50, 110, 130 and 150-year rotations with natural regeneration and thinning, and the 150-year rotation with natural regeneration. The marginal cost of C storage is the SEV lost per unit of C due to change in silvicultural regimes that results in increase of average C stored. Marginal cost analysis indicated that marginal cost values were similar for regimes with GE and without. As C storage increased, the marginal cost generally increased. The increase in C storage from 428 MgC/ha to 589 MgC/ha implied a marginal cost of $13.28IMgC. In case of increasing C storage from 683 MgC/ha to 802.7 MgC/ha, the marginal cost would increase to $32.79JMgC. Title: Measuring costs of sequestering carbon in forest stands with different management regimes in western Oregon Author: Zyrina, Olga A. This project was a part of larger work that compared major factors controlling patterns of carbon dynamics in two regions of the globe, the Pacific Northwest, USA and northwestern Russia. It was funded through the NASA foundation (grant # NAG5- 6242). Human economic activity is causing the release of pollutants such as carbon dioxide. The increased concentration of pollutants in the atmosphere is thought to cause greenhouse effect, in other words - the warming of the earth and lower atmosphere. Different methods are proposed to reduce concentration of greenhouse gases (GHG) in the atmosphere. Some involve development of more clean technologies. Some involve reductions in the use of fossil fuels. Another possibility is to store carbon (C) as live biomass. Plants use C for growth and development. Using forests to sequester C is one strategy for mitigating effects of GHG emissions. There are many methods in forestry to grow trees and produce wood products. Some of them include clearcutting, thinning, fertilizing, burning, and partial cutting. This project had three purposes. First, was to investigate the effect of a wide variety of silvicultural treatments on C storage and the economic value of harvested forest products. We measured economic value as soil expectation value. Second, was to use Data Envelopment Analysis to determine the efficient set of treatments, which make up the Production Possibility Frontier (PPF) in terms of C and economic value. Third, was to use the PPF to measure the marginal cost of carbon storage in moving from high SEV and relatively low C storage to lower SEV and relatively high C storage. C storage and timber harvest were simulated using the STANDCARB model for forest types common in north-western Oregon with two tree species, Douglas fir (Pseudotsuga menziesii) and Western hemlock (Tsuga heterophylla). Fifty silvicultural regimes were investigated. They included clearcutting with rotations of 50, 70, 90, 110, 130, and 150. Each of the six rotation ages had eight combinations of silvicultural treatments consisting of artificial and natural regeneration, growth enhancement (GE) and thinning. Two partial cutting regimes: group selection and single-tree selection were also used in the analysis. C storage was calculated for every output year of each model run as a sum of live, dead, and stable C. C storage for each silvicultural regime was measured as the average over five full rotations from the steady state portion of the run. The analysis showed that average C increases with rotation age from 335.99 MgC/ha with 50-year rotation with natural regeneration and thinning to 826.36 MgCIha with 150-year rotation with artificial regeneration and GE. The use of artificial regeneration compared to natural regeneration gave a 20-30 MgC/ha improvement for all regimes. The total harvest from thinning and clearcutting over the rotation period averaged for several runs varied from 505.34 m3/ha (with 50-year rotation no treatment) to 1782.24 m3/ha (with 150-year rotation with GE and thinning) The use of artificial compared to natural regeneration gave a 20-50 m3/ha increase in harvest for all regimes. SEV is the present value of net revenues from perpetually growing tree crops following the specified regime. It measures the economic value of each regime. Generally, SEV has a negative correlation with rotation length. Using a 3.5 percent real discount rate, the maximum SEV ($7904.3/hectare) was obtained from 50-year rotation with artificial regeneration, GE and thinning In contrast, SEV for 130-year rotation with artificial regeneration was only $446.68/hectare. Using Data Envelopment Analysis (OnFront software) we found that 8 of the 50 regimes investigated were efficient in their ability to store C and produce economic value. The efficient regimes included 50, 110, 130 and 150-year rotations with artificial regeneration, GE and thinning; 110, 130 and 150-year rotations with natural regeneration, GE and thinning, and the 150-year rotation with natural regeneration and GE. When regimes with GE were excluded, we found 7 efficient regimes: 50 and 150-year rotations with artificial regeneration and thinning, 50, 110, 130 and 150-year rotations with natural regeneration and thinning, and the 150-year rotation with natural regeneration. The marginal cost of C storage is the SEV lost per unit of C due to change in silvicultural regimes that results in increase of average C stored. Marginal cost analysis indicated that marginal cost values were similar for regimes with GE and without. As C storage increased, the marginal cost generally increased. The increase in C storage from 428 MgC/ha to 589 MgC/ha implied a marginal cost of $13.28IMgC. In case of increasing C storage from 683 MgC/ha to 802.7 MgC/ha, the marginal cost would increase to $32.79JMgC. Close

• 1892. [Article] Response of Soil Microbially Mediated Nutrient Cycling and Community Structure to Timber Harvest in the Pacific Northwest

  Forest harvest persists as one of the most globally important industries, and crucially provides raw wood products for both building and fuel materials. Mechanistically complex abiotic and biotic processes ...

  Citation × Citation Citation Abstract Copy Title: Response of Soil Microbially Mediated Nutrient Cycling and Community Structure to Timber Harvest in the Pacific Northwest Author: Danielson, Rachel E. Forest harvest persists as one of the most globally important industries, and crucially provides raw wood products for both building and fuel materials. Mechanistically complex abiotic and biotic processes curb ecosystem recovery following timber harvest and it is of great importance to understand the effects of this practice on biogeochemical cycling and ecosystem function to determine the potential for long-term sustainability. This thesis was motivated by a lack of comprehensive understanding as to the consistency of preexisting and post-harvest microbially mediated process rates and community composition across a large region of the same dominant vegetation type. I sought to determine how timber harvest across the Pacific Northwest impacts microbial biogeochemical cycling activity and community structure of both prokaryotic and fungal communities in response to harvest. At nine managed Douglas-fir forests, samples were collected from exact locations within sites one year prior to and twelve to fifteen months following clear-cut harvesting. The objective of the first study was to determine the degree of variability in microbially mediated process rates and pools of C and N, and generalized trends that are evident across sites one year following harvest. Samples were analyzed for various C and N pools, and the potential activities of biogeochemically important extracellular enzymes were measured. Soil incubations were performed to determine respiration rate and N production over time. Soil DNA isolates were used to quantify 16S rRNA and ITS gene copy numbers using qPCR, and all measurements were statistically compared between pre-and post-harvest samples. Total soil C and N did not change significantly following harvest, but the C: N ratio of dissolved components decreased consistently and biomass C: N ratios generally increased. Activities of β-glucosidase and cellobiohydrolase increased significantly whereas activities of phenol oxidase and peroxidase decreased significantly. Cumulative respiration over the incubation period declined substantially, and total N pools changed from primarily DON pre-harvest, to primarily NO₃⁻post-harvest. Changes in activity rates and pool sizes following harvest were generally related to C to N balances. Pre-harvest measurements suggested communities may be co-limited by C and N, while the emergence of strong C limitation was evident post-harvest. The generalized trends identified from this study can be used in future research as reference points for ecosystem status during forest succession, and for correlation with an investigation of changes in microbial community composition and structure. The objective of the second study was to determine the factors shaping soil microbial communities of Douglas-fir forests in the Pacific Northwest, and to identify generalized short-term effects of timber harvest on the richness, diversity, and structureof these communities. DNA was extracted from soils and sequenced using the Illumina® Miseq platform to determine differences in prokaryotic and fungal communities. When communities were considered separately pre-and post-harvest, pH most consistently explained community dissimilarity among sites. Although community dispersion did not vary between pre-and post-harvest samples, OTU richness was consistently and significantly higher following tree removal. Both prokaryotic and fungal community structures were significantly different in post-compared to pre-harvest soils, even when just OTUs representing the top 50% of sequences were considered. Relative abundance of the dominant three bacterial phyla (Proteobacteria, Acidobacteria, and Verrucomicrobia) did not change significantly following harvest, but some less-represented phyla decreased (Actinobacteria) or increased (Bacteroidetes) significantly in relative abundance. Basidiomycota abundance decreased significantly whereas Ascomycota and Zygomycota abundance increased. Ectomycorrhizal fungi were enriched across pre-harvest samples, whereas many known saprotrophic species were enriched post-harvest. In conclusion, general alterations in fungal communities, as well as select bacterial and archaeal taxa, may serve as appropriate indicators of disturbance and ecosystem status across this region. Title: Response of Soil Microbially Mediated Nutrient Cycling and Community Structure to Timber Harvest in the Pacific Northwest Author: Danielson, Rachel E. Forest harvest persists as one of the most globally important industries, and crucially provides raw wood products for both building and fuel materials. Mechanistically complex abiotic and biotic processes curb ecosystem recovery following timber harvest and it is of great importance to understand the effects of this practice on biogeochemical cycling and ecosystem function to determine the potential for long-term sustainability. This thesis was motivated by a lack of comprehensive understanding as to the consistency of preexisting and post-harvest microbially mediated process rates and community composition across a large region of the same dominant vegetation type. I sought to determine how timber harvest across the Pacific Northwest impacts microbial biogeochemical cycling activity and community structure of both prokaryotic and fungal communities in response to harvest. At nine managed Douglas-fir forests, samples were collected from exact locations within sites one year prior to and twelve to fifteen months following clear-cut harvesting. The objective of the first study was to determine the degree of variability in microbially mediated process rates and pools of C and N, and generalized trends that are evident across sites one year following harvest. Samples were analyzed for various C and N pools, and the potential activities of biogeochemically important extracellular enzymes were measured. Soil incubations were performed to determine respiration rate and N production over time. Soil DNA isolates were used to quantify 16S rRNA and ITS gene copy numbers using qPCR, and all measurements were statistically compared between pre-and post-harvest samples. Total soil C and N did not change significantly following harvest, but the C: N ratio of dissolved components decreased consistently and biomass C: N ratios generally increased. Activities of β-glucosidase and cellobiohydrolase increased significantly whereas activities of phenol oxidase and peroxidase decreased significantly. Cumulative respiration over the incubation period declined substantially, and total N pools changed from primarily DON pre-harvest, to primarily NO₃⁻post-harvest. Changes in activity rates and pool sizes following harvest were generally related to C to N balances. Pre-harvest measurements suggested communities may be co-limited by C and N, while the emergence of strong C limitation was evident post-harvest. The generalized trends identified from this study can be used in future research as reference points for ecosystem status during forest succession, and for correlation with an investigation of changes in microbial community composition and structure. The objective of the second study was to determine the factors shaping soil microbial communities of Douglas-fir forests in the Pacific Northwest, and to identify generalized short-term effects of timber harvest on the richness, diversity, and structureof these communities. DNA was extracted from soils and sequenced using the Illumina® Miseq platform to determine differences in prokaryotic and fungal communities. When communities were considered separately pre-and post-harvest, pH most consistently explained community dissimilarity among sites. Although community dispersion did not vary between pre-and post-harvest samples, OTU richness was consistently and significantly higher following tree removal. Both prokaryotic and fungal community structures were significantly different in post-compared to pre-harvest soils, even when just OTUs representing the top 50% of sequences were considered. Relative abundance of the dominant three bacterial phyla (Proteobacteria, Acidobacteria, and Verrucomicrobia) did not change significantly following harvest, but some less-represented phyla decreased (Actinobacteria) or increased (Bacteroidetes) significantly in relative abundance. Basidiomycota abundance decreased significantly whereas Ascomycota and Zygomycota abundance increased. Ectomycorrhizal fungi were enriched across pre-harvest samples, whereas many known saprotrophic species were enriched post-harvest. In conclusion, general alterations in fungal communities, as well as select bacterial and archaeal taxa, may serve as appropriate indicators of disturbance and ecosystem status across this region. Close

• 1893. [Article] Four centuries of soil carbon and nitrogen change after severe fire in a Western Cascades forest landscape

  Fire is a major disturbance process in many forests. Long-term studies of the biogeochemical effects of fires, especially on soils, are very rare. Consequently, long-term effects of fire on soils are often ...

  Citation × Citation Citation Abstract Copy Title: Four centuries of soil carbon and nitrogen change after severe fire in a Western Cascades forest landscape Author: Giesen, Thomas William Fire is a major disturbance process in many forests. Long-term studies of the biogeochemical effects of fires, especially on soils, are very rare. Consequently, long-term effects of fire on soils are often hypothesized from short-term effects. In a chronosequence study, I studied 24 western Cascades (Oregon) forest stands thought to have been initiated in fire. Twelve of those burned about 150 years ago (“young” sites), and the other 12 burned an average of 550 years ago (“old” sites). I hypothesized that young stands would have less carbon (C) and nitrogen (N) in forest floor and in 0 -10 cm mineral soil than old stands. I found that forest floor N pools of old sites (average = 1,823 kg/ha ± s.e. = 132 kg/ha) were significantly greater than young sites (1,450 ± 98 kg/ha). Similarly, forest floor C pools of old sites (62,980 ± 5,403 kg/ha) were significantly greater than young sites (49,032 ± 2,965 kg/ha). Greater N and C pools in forest floor of old sites resulted from greater forest floor mass in old sites; concentrations of both N and C, and C:N ratios, did not differ significantly by forest age class. In mineral soil, neither concentrations nor pools of N and C differed between young and old sites. Despite overall similarity of C:N ratios in young versus old sites, potential N mineralization rates were twice as high in forest floor of old sites (average = 60 ± 7.3 mg N / g soil) than young sites (26 ± 3.5 mg N / g soil), . Nitrate accounted for only 2% or less of total N mineralized in forest floor samples. In mineral soil, potential net N mineralization did not differ by forest age class. The pattern of high net N mineralization and low nitrification in old forests is consistent with other studies of fire-prone forests, yet contrasts with many studies of forests that lack fire, and suggests that ammonium is not the sole control over nitrification in fire-prone ecosystems. Overall, fire appears to impart a longterm legacy of reduced forest floor N and C pools in this western Oregon Cascades landscape, which suggests that current fire-suppression activities in the region may increase forest floor N and C storage over historical conditions within several centuries. The differences in forest floor and soil N cycling processes that I observed by forest age class raise the further possibility that fire exclusion in these forests may change the relative abundance of soil inorganic N forms to favor ammonium over nitrate. Such changes may have unknown consequences for relative competitive abilities of plant and microbial species that rely preferentially on different N-forms to meet N nutrition requirements. While forest floor N and C pools increase from young to old stands, forest floor and soil N and C pools are not different, or decline, between 450 year old stands and the oldest stands at 800+ years, That, and other, anomalous changes in values from ~450 to 800+ years, suggest possible changes in ecosystem functions, and may indicate that this landscape could be a fruitful study area for examinations of a mature, steady-state ecosystem Title: Four centuries of soil carbon and nitrogen change after severe fire in a Western Cascades forest landscape Author: Giesen, Thomas William Fire is a major disturbance process in many forests. Long-term studies of the biogeochemical effects of fires, especially on soils, are very rare. Consequently, long-term effects of fire on soils are often hypothesized from short-term effects. In a chronosequence study, I studied 24 western Cascades (Oregon) forest stands thought to have been initiated in fire. Twelve of those burned about 150 years ago (“young” sites), and the other 12 burned an average of 550 years ago (“old” sites). I hypothesized that young stands would have less carbon (C) and nitrogen (N) in forest floor and in 0 -10 cm mineral soil than old stands. I found that forest floor N pools of old sites (average = 1,823 kg/ha ± s.e. = 132 kg/ha) were significantly greater than young sites (1,450 ± 98 kg/ha). Similarly, forest floor C pools of old sites (62,980 ± 5,403 kg/ha) were significantly greater than young sites (49,032 ± 2,965 kg/ha). Greater N and C pools in forest floor of old sites resulted from greater forest floor mass in old sites; concentrations of both N and C, and C:N ratios, did not differ significantly by forest age class. In mineral soil, neither concentrations nor pools of N and C differed between young and old sites. Despite overall similarity of C:N ratios in young versus old sites, potential N mineralization rates were twice as high in forest floor of old sites (average = 60 ± 7.3 mg N / g soil) than young sites (26 ± 3.5 mg N / g soil), . Nitrate accounted for only 2% or less of total N mineralized in forest floor samples. In mineral soil, potential net N mineralization did not differ by forest age class. The pattern of high net N mineralization and low nitrification in old forests is consistent with other studies of fire-prone forests, yet contrasts with many studies of forests that lack fire, and suggests that ammonium is not the sole control over nitrification in fire-prone ecosystems. Overall, fire appears to impart a longterm legacy of reduced forest floor N and C pools in this western Oregon Cascades landscape, which suggests that current fire-suppression activities in the region may increase forest floor N and C storage over historical conditions within several centuries. The differences in forest floor and soil N cycling processes that I observed by forest age class raise the further possibility that fire exclusion in these forests may change the relative abundance of soil inorganic N forms to favor ammonium over nitrate. Such changes may have unknown consequences for relative competitive abilities of plant and microbial species that rely preferentially on different N-forms to meet N nutrition requirements. While forest floor N and C pools increase from young to old stands, forest floor and soil N and C pools are not different, or decline, between 450 year old stands and the oldest stands at 800+ years, That, and other, anomalous changes in values from ~450 to 800+ years, suggest possible changes in ecosystem functions, and may indicate that this landscape could be a fruitful study area for examinations of a mature, steady-state ecosystem Close

• 1894. [Article] Road networks, timber harvest, and the spread of Phytophthora root rot infestations of Port-Orford-­cedar in southwest Oregon

  Phytophthora lateralis is the causal agent of cedar root rot, a fatal forest pathogen whose principal host is Chamaecyparis lawsoniana (Port-Orford-cedar), a predominantly riparian-restricted endemic tree ...

  Citation × Citation Citation Abstract Copy Title: Road networks, timber harvest, and the spread of Phytophthora root rot infestations of Port-Orford-­cedar in southwest Oregon Author: Clark, William C. Phytophthora lateralis is the causal agent of cedar root rot, a fatal forest pathogen whose principal host is Chamaecyparis lawsoniana (Port-Orford-cedar), a predominantly riparian-restricted endemic tree species of ecological, economical, and cultural importance to coastal Oregon and California. Local scale distribution of P. lateralis is thought to be associated with timber harvest and road-building disturbances. However, knowledge of the landscape-scale factors that contribute to successful invasions of P. lateralis is also important for effective land management of Port-Orford-cedar. P. lateralis is able to infest in wet conditions via stream networks (zoospore) and dry conditions via road networks (resting spore). This study tested the hypothesis that vehicles spread P. lateralis by relating its distribution to traffic intensive, anthropogenic disturbances (i.e. a road network, timber harvest) over a 31-yr period in a 3,910-km² portion of the Rogue River-Siskiyou National Forest in the Siskiyou Mountains of Oregon. Indices of road disturbance (presence/absence, configuration, length, density, road-stream network connectivity) and timber harvest (presence/absence, area, density, frequency) were related to locations of infested cedar populations from a USFS survey dataset using a geographic information system (GIS). About 40% of 934 7th-field catchments were infested with the pathogen. Total road length of the study site was 5,070 km; maximum road density was 8.2 km/km2 and averaged 1.6 km/km² in roaded catchments (n = 766). Timber activities extracted 17,370 ha (2,338 cutting units) of forest across 509 catchments; 345 catchments were cut ≥ twice. Maximum harvest density was 0.92 km²/km² ([mean] = 0.04). Both road networks and timber harvest patchworks were significantly related to cedar root rot heterogeneity. Chi-squared contingency tables showed that infestation rates were 2.2 times higher in catchments with roads compared to roadless catchments and 1.4 times higher in catchments with road-stream intersections compared to those that were unconnected. Infestation was twice as likely in catchments with both harvest and road presence than road presence alone. Single-variable logistic regression showed that a one percent increase in harvest density increased infestation odds 25% and a one-unit (km/km²) increase in road density increased infestation odds 80%. Road and stream network configuration was also important to pathogen distribution: 1) uninfested catchments are most likely to be spatially removed from infested, roaded catchments, 2) only 11% of 287 roaded catchments downstream of infested, roaded catchments were uninfested, and 3) only 12% of 319 catchments downstream of infested catchments were uninfested. Road networks and timber harvest patchworks appear to reduce landscape heterogeneity by providing up-catchment and down-catchment access to host populations by linking pathogenic materials to the stream network. Timber harvest data suggest that while infestation risk to Port-Orford-cedar populations remains high, management policies may have curbed infestation risk in timber-harvested catchments; if this is a result of specific P. lateralis mitigation policies adopted in the late 1980's or broader, region-wide conservation policies (i.e. the Northwest Forest Plan) is yet unclear. Title: Road networks, timber harvest, and the spread of Phytophthora root rot infestations of Port-Orford-­cedar in southwest Oregon Author: Clark, William C. Phytophthora lateralis is the causal agent of cedar root rot, a fatal forest pathogen whose principal host is Chamaecyparis lawsoniana (Port-Orford-cedar), a predominantly riparian-restricted endemic tree species of ecological, economical, and cultural importance to coastal Oregon and California. Local scale distribution of P. lateralis is thought to be associated with timber harvest and road-building disturbances. However, knowledge of the landscape-scale factors that contribute to successful invasions of P. lateralis is also important for effective land management of Port-Orford-cedar. P. lateralis is able to infest in wet conditions via stream networks (zoospore) and dry conditions via road networks (resting spore). This study tested the hypothesis that vehicles spread P. lateralis by relating its distribution to traffic intensive, anthropogenic disturbances (i.e. a road network, timber harvest) over a 31-yr period in a 3,910-km² portion of the Rogue River-Siskiyou National Forest in the Siskiyou Mountains of Oregon. Indices of road disturbance (presence/absence, configuration, length, density, road-stream network connectivity) and timber harvest (presence/absence, area, density, frequency) were related to locations of infested cedar populations from a USFS survey dataset using a geographic information system (GIS). About 40% of 934 7th-field catchments were infested with the pathogen. Total road length of the study site was 5,070 km; maximum road density was 8.2 km/km2 and averaged 1.6 km/km² in roaded catchments (n = 766). Timber activities extracted 17,370 ha (2,338 cutting units) of forest across 509 catchments; 345 catchments were cut ≥ twice. Maximum harvest density was 0.92 km²/km² ([mean] = 0.04). Both road networks and timber harvest patchworks were significantly related to cedar root rot heterogeneity. Chi-squared contingency tables showed that infestation rates were 2.2 times higher in catchments with roads compared to roadless catchments and 1.4 times higher in catchments with road-stream intersections compared to those that were unconnected. Infestation was twice as likely in catchments with both harvest and road presence than road presence alone. Single-variable logistic regression showed that a one percent increase in harvest density increased infestation odds 25% and a one-unit (km/km²) increase in road density increased infestation odds 80%. Road and stream network configuration was also important to pathogen distribution: 1) uninfested catchments are most likely to be spatially removed from infested, roaded catchments, 2) only 11% of 287 roaded catchments downstream of infested, roaded catchments were uninfested, and 3) only 12% of 319 catchments downstream of infested catchments were uninfested. Road networks and timber harvest patchworks appear to reduce landscape heterogeneity by providing up-catchment and down-catchment access to host populations by linking pathogenic materials to the stream network. Timber harvest data suggest that while infestation risk to Port-Orford-cedar populations remains high, management policies may have curbed infestation risk in timber-harvested catchments; if this is a result of specific P. lateralis mitigation policies adopted in the late 1980's or broader, region-wide conservation policies (i.e. the Northwest Forest Plan) is yet unclear. Close

• 1895. [Article] The physiology of seasonal growth in tall fescue varieties (Festuca arundinacea Schreb.)

  The winter and summer growth of varieties of tall fescue (Festuca arundinacea Schreb.) that had originated from the Mediterranean region (Oregon 1000 and Tunisia) and northern Europe (Alta) were studied ...

  Citation × Citation Citation Abstract Copy Title: The physiology of seasonal growth in tall fescue varieties (Festuca arundinacea Schreb.) Author: Blacklow, Warren Marcus The winter and summer growth of varieties of tall fescue (Festuca arundinacea Schreb.) that had originated from the Mediterranean region (Oregon 1000 and Tunisia) and northern Europe (Alta) were studied outdoors in the Mediterranean climate of western Oregon, and in greenhouses and controlled environment chambers. Treatments of temperature, photoperiod and gibberellic acid (GA) were imposed in order to establish the limitations to winter and summer forage production. Measurements of photosynthesis and the distribution of assimilates were made by growth analysis and the level and nature of reserve carbohydrates by the copper-iodometric method. In western Oregon, the varieties that had originated from the Mediterranean region made more foliar growth during the winter but less during the summer than Alta. These two different patterns of seasonal growth were interpreted as ecotypic variation that had enabled the species to survive seasons of stress in the regions of origin--freezing winters of northern Europe and summer droughts of the Mediterranean. Cubes of sod taken during the winter months from swards of Alta and Tunisia showed that Alta had a greater density of tillers and buds, and a higher level of reserve carbohydrates than Tunisia. This result suggested that Tunisia utilized photosynthate during the winter for the production of leaves rather than storing it as carbohydrates. During the winter of 1967 the foliar growth of both Alta and Oregon 1000 was increased by a temperature of 15 to 20C, a foliar spray of 0.1% GA, and possibly by a long photoperiod. The suggestion was that winter growth was limited more by the internal growth regulator balance than the external weather, and that relative rather than true dormancy was involved. Although the chlorophyll concentration in the foliage was reduced by GA the total chlorophyll was actually increased by 10 to 30% and, consequently, the chlorosis may not be deleterious to pasture production. The rate of regrowth of Tunisia was greater at 7/3C than Alta but this difference was eliminated by GA. Rate of regrowth may be an important determinant of winter growth of ecotypes of forages grasses and GA may promote the mobilization, or utilization, or both, of reserve carbohydrate--reserves that were found to be higher in Alta than Tunisia. At the end of a prolonged exposure of 18 weeks in a simulated winter environment of 7/3C and 19 ly/day (400 to 750 nm) the total weight of Tunisia was greater than Alta and proportionately more dry weight was present in the leaves than roots. The total available carbohydrates (TAG) extracted with 0.2N H₂SO₄ was similar for Alta and Tunisia; it was 20% of the dry weight of stems. Gibberellic acid increased the concentration of TAC 6% in Alta and 4% in Tunisia. The total water soluble carbohydrates (WSC) were 14 and 9% of the stems of Tunisia and Alta respectively, and 6% of the leaves and 5% of the roots of both varieties. Fructosans were the main component of WSC, and sucrose and reducing sugars were of lesser concentrations. The WSC were increased by GA in all parts of the plants and the increase was greatest in Alta; sucrose showed the greatest increase. Subtraction of WSC from TAG gave an estimation of starch; it was unexpectedly high with concentrations as high as fructosans and indicated that 0.2N H₂SO₄ may have extracted structural carbohydrates. The superior growth rate of Alta in the summer was established in June. At the end of June 1968 the relative growth rate of both Alta and Tunisia was increased by GA due to a stimulation of net assimilation rates. The WSC were highest in the stems and were 14 and 9% of the stems of Alta and Tunisia respectively. Fructosans were the main WSC and the higher level of WSC in Alta was due to a higher level of fructosans. Gibberellic acid increased the WSC by 1% of the dry weight during the treatment time of 8 days. The measurement of photosynthesis of leaf segments of tall fescue by manometry was unreliable. The activity of isolated chloroplasts was also unreliable although some improvement was obtained by isolating in the presence of polyvinylpyrrolidone. The concept developed in this thesis was that when an ecotype is introduced to a new environment, or used as a basis for a new variety, the production and utilization of photosynthate may be controlled by an internal growth regulator balance which is not well coordinated with the weather. In such a circumstance, the possibility exists that the growth regulator balance may be adjusted by a timely application of the appropriate growth regulators in order that the variety may grow to the limit of its genetic capacity during periods of favorable weather. Title: The physiology of seasonal growth in tall fescue varieties (Festuca arundinacea Schreb.) Author: Blacklow, Warren Marcus The winter and summer growth of varieties of tall fescue (Festuca arundinacea Schreb.) that had originated from the Mediterranean region (Oregon 1000 and Tunisia) and northern Europe (Alta) were studied outdoors in the Mediterranean climate of western Oregon, and in greenhouses and controlled environment chambers. Treatments of temperature, photoperiod and gibberellic acid (GA) were imposed in order to establish the limitations to winter and summer forage production. Measurements of photosynthesis and the distribution of assimilates were made by growth analysis and the level and nature of reserve carbohydrates by the copper-iodometric method. In western Oregon, the varieties that had originated from the Mediterranean region made more foliar growth during the winter but less during the summer than Alta. These two different patterns of seasonal growth were interpreted as ecotypic variation that had enabled the species to survive seasons of stress in the regions of origin--freezing winters of northern Europe and summer droughts of the Mediterranean. Cubes of sod taken during the winter months from swards of Alta and Tunisia showed that Alta had a greater density of tillers and buds, and a higher level of reserve carbohydrates than Tunisia. This result suggested that Tunisia utilized photosynthate during the winter for the production of leaves rather than storing it as carbohydrates. During the winter of 1967 the foliar growth of both Alta and Oregon 1000 was increased by a temperature of 15 to 20C, a foliar spray of 0.1% GA, and possibly by a long photoperiod. The suggestion was that winter growth was limited more by the internal growth regulator balance than the external weather, and that relative rather than true dormancy was involved. Although the chlorophyll concentration in the foliage was reduced by GA the total chlorophyll was actually increased by 10 to 30% and, consequently, the chlorosis may not be deleterious to pasture production. The rate of regrowth of Tunisia was greater at 7/3C than Alta but this difference was eliminated by GA. Rate of regrowth may be an important determinant of winter growth of ecotypes of forages grasses and GA may promote the mobilization, or utilization, or both, of reserve carbohydrate--reserves that were found to be higher in Alta than Tunisia. At the end of a prolonged exposure of 18 weeks in a simulated winter environment of 7/3C and 19 ly/day (400 to 750 nm) the total weight of Tunisia was greater than Alta and proportionately more dry weight was present in the leaves than roots. The total available carbohydrates (TAG) extracted with 0.2N H₂SO₄ was similar for Alta and Tunisia; it was 20% of the dry weight of stems. Gibberellic acid increased the concentration of TAC 6% in Alta and 4% in Tunisia. The total water soluble carbohydrates (WSC) were 14 and 9% of the stems of Tunisia and Alta respectively, and 6% of the leaves and 5% of the roots of both varieties. Fructosans were the main component of WSC, and sucrose and reducing sugars were of lesser concentrations. The WSC were increased by GA in all parts of the plants and the increase was greatest in Alta; sucrose showed the greatest increase. Subtraction of WSC from TAG gave an estimation of starch; it was unexpectedly high with concentrations as high as fructosans and indicated that 0.2N H₂SO₄ may have extracted structural carbohydrates. The superior growth rate of Alta in the summer was established in June. At the end of June 1968 the relative growth rate of both Alta and Tunisia was increased by GA due to a stimulation of net assimilation rates. The WSC were highest in the stems and were 14 and 9% of the stems of Alta and Tunisia respectively. Fructosans were the main WSC and the higher level of WSC in Alta was due to a higher level of fructosans. Gibberellic acid increased the WSC by 1% of the dry weight during the treatment time of 8 days. The measurement of photosynthesis of leaf segments of tall fescue by manometry was unreliable. The activity of isolated chloroplasts was also unreliable although some improvement was obtained by isolating in the presence of polyvinylpyrrolidone. The concept developed in this thesis was that when an ecotype is introduced to a new environment, or used as a basis for a new variety, the production and utilization of photosynthate may be controlled by an internal growth regulator balance which is not well coordinated with the weather. In such a circumstance, the possibility exists that the growth regulator balance may be adjusted by a timely application of the appropriate growth regulators in order that the variety may grow to the limit of its genetic capacity during periods of favorable weather. Close

• 1896. [Article] Energy recovery from biodiesel waste : performance of microbial electrochemical systems on glycerol

  Pure glycerol and the crude waste glycerin byproduct of biodiesel production were tested as substrates for electricity production in single-chamber, air-cathode microbial fuel cells (MFCs) and in single-chamber ...

  Citation × Citation Citation Abstract Copy Title: Energy recovery from biodiesel waste : performance of microbial electrochemical systems on glycerol Author: Chignell, Jeremy Pure glycerol and the crude waste glycerin byproduct of biodiesel production were tested as substrates for electricity production in single-chamber, air-cathode microbial fuel cells (MFCs) and in single-chamber microbial electrolysis cells (MECs), using pure and mixed microbial cultures as anode biocatalyst. Current densities of 0.40 A/m² and 0.13 A/m² were generated on 50 mM glycerol in aircathode MFCs by pure cultures of Shewanella oneidensis MR-1 and Rhodopseudomonas palustris ATCC 17001, respectively, after aerobic flask culture. A mixed culture of bacteria originally derived from wastewater generated higher current and power densities than any of the pure cultures and, at 10 mM glycerol, achieved an average maximum power density of 2.70 ± 0.15 W/m² anode surface area (47.8 ± 2.6 W/m³ reactor volume) at a current density of 7.66 ± 0.21 A/m² anode surface area. At an optimal fixed external resistance of 210 Ω the mixed culture MFC followed Michaelis-Menten saturation kinetics, resulting in a Km of 2.92 mM glycerol and a theoretical Vmax of 0.437 volts. Coulombic efficiencies decreased linearly with increased glycerol concentration. Power was generated by mixed culture MFCs from raw waste glycerin byproduct of biodiesel manufacture both with and without methanol, and with and without potassium salts and soaps. Maximum volumetric current and power densities achieved on waste glycerin (147.7 A/m³ and 56.8 W/m³) were greater than those reported in previous studies, but CE values (10-17.6%) were significantly lower, likely due to losses from aerobic respiration in the micro-aerobic environment of an MFC. Decreases in maximum current density of 43.4% and 65.1% were observed over successive batches of waste glycerin with and without methanol, respectively. Decreases in performance were attributed primarily to the presence of potassium salts, soaps, FFAs, and residual catalyst in the waste glycerin, rather than to methanol. MFCs operating on waste glycerin from which these salts and soaps had been precipitated did not show the same pattern of decreasing maximum current density over multiple batches. Cathode potentiometry indicated a decrease in cathode performance after development of a thick biofilm on the cathode surface during batches of glycerol and glycerin. The best fit lines of cathode potential vs. current density before and after cathode biofilm development during batches of glycerol were used to predict a 30.2% decrease in power density, a result that corresponded well to the 25.7% decrease in power density that was actually observed. Single chamber, membrane-free mixed culture MECs were able to produce hydrogen successfully from both pure glycerol and waste glycerin byproduct from biodiesel manufacture. At an applied voltage of 0.6 V, a maximum current density of 7.5 ± 0.4 A/m² (238.6 ± 12.7 A/m³) was observed, the highest reported current density for a MEC operating on glycerol. Maximum current densities on 0.5% waste glycerin with and without methanol were 0.1-0.2 A/m² less than previously reported values. Maximum hydrogen yields from the mixed culture MEC on 50 mM glycerol were 1.8 ± 0.1 mol hydrogen/mol glycerol, at an energy efficiency of 117.7%. Hydrogen yields on waste glycerin were an order of magnitude lower, though energy efficiencies were greater than those for pure glycerol. Hydrogen production rates were highest at 50 mM glycerol, reaching 1.3 ± 0.1 m³/day/m³. Methane formation reduced hydrogen recoveries by 30.4% and 36.8% for 50 mM and 10 mM glycerol, respectively, assuming cathodic losses of electrons went to methane formation. A culture dominated by a member of the genus Citrobacter produced high current densities of ~2.0 A/m² in MECs on 50 mM glycerol, at yields of 0.93 ± 0.05 mol hydrogen/mol glycerol, energy efficiency greater than 100%, and hydrogen production rate greater than that of fermentative hydrogen production from glycerol by this species and by a genetically altered E. coli strain. The results of this study suggest that, ideally with removal of potassium salts, soaps, and catalyst, and with some method to minimize biofilm formation on the surface of MFC air-cathodes, MFCs and MECs represent promising treatment methods to generate electricity or hydrogen gas while treating the waste products of biodiesel manufacture. These results represent an important step in improving the economic viability of the ever-growing biodiesel industry as the world energy economy continues to shift from fossil fuels to renewable energy sources. Title: Energy recovery from biodiesel waste : performance of microbial electrochemical systems on glycerol Author: Chignell, Jeremy Pure glycerol and the crude waste glycerin byproduct of biodiesel production were tested as substrates for electricity production in single-chamber, air-cathode microbial fuel cells (MFCs) and in single-chamber microbial electrolysis cells (MECs), using pure and mixed microbial cultures as anode biocatalyst. Current densities of 0.40 A/m² and 0.13 A/m² were generated on 50 mM glycerol in aircathode MFCs by pure cultures of Shewanella oneidensis MR-1 and Rhodopseudomonas palustris ATCC 17001, respectively, after aerobic flask culture. A mixed culture of bacteria originally derived from wastewater generated higher current and power densities than any of the pure cultures and, at 10 mM glycerol, achieved an average maximum power density of 2.70 ± 0.15 W/m² anode surface area (47.8 ± 2.6 W/m³ reactor volume) at a current density of 7.66 ± 0.21 A/m² anode surface area. At an optimal fixed external resistance of 210 Ω the mixed culture MFC followed Michaelis-Menten saturation kinetics, resulting in a Km of 2.92 mM glycerol and a theoretical Vmax of 0.437 volts. Coulombic efficiencies decreased linearly with increased glycerol concentration. Power was generated by mixed culture MFCs from raw waste glycerin byproduct of biodiesel manufacture both with and without methanol, and with and without potassium salts and soaps. Maximum volumetric current and power densities achieved on waste glycerin (147.7 A/m³ and 56.8 W/m³) were greater than those reported in previous studies, but CE values (10-17.6%) were significantly lower, likely due to losses from aerobic respiration in the micro-aerobic environment of an MFC. Decreases in maximum current density of 43.4% and 65.1% were observed over successive batches of waste glycerin with and without methanol, respectively. Decreases in performance were attributed primarily to the presence of potassium salts, soaps, FFAs, and residual catalyst in the waste glycerin, rather than to methanol. MFCs operating on waste glycerin from which these salts and soaps had been precipitated did not show the same pattern of decreasing maximum current density over multiple batches. Cathode potentiometry indicated a decrease in cathode performance after development of a thick biofilm on the cathode surface during batches of glycerol and glycerin. The best fit lines of cathode potential vs. current density before and after cathode biofilm development during batches of glycerol were used to predict a 30.2% decrease in power density, a result that corresponded well to the 25.7% decrease in power density that was actually observed. Single chamber, membrane-free mixed culture MECs were able to produce hydrogen successfully from both pure glycerol and waste glycerin byproduct from biodiesel manufacture. At an applied voltage of 0.6 V, a maximum current density of 7.5 ± 0.4 A/m² (238.6 ± 12.7 A/m³) was observed, the highest reported current density for a MEC operating on glycerol. Maximum current densities on 0.5% waste glycerin with and without methanol were 0.1-0.2 A/m² less than previously reported values. Maximum hydrogen yields from the mixed culture MEC on 50 mM glycerol were 1.8 ± 0.1 mol hydrogen/mol glycerol, at an energy efficiency of 117.7%. Hydrogen yields on waste glycerin were an order of magnitude lower, though energy efficiencies were greater than those for pure glycerol. Hydrogen production rates were highest at 50 mM glycerol, reaching 1.3 ± 0.1 m³/day/m³. Methane formation reduced hydrogen recoveries by 30.4% and 36.8% for 50 mM and 10 mM glycerol, respectively, assuming cathodic losses of electrons went to methane formation. A culture dominated by a member of the genus Citrobacter produced high current densities of ~2.0 A/m² in MECs on 50 mM glycerol, at yields of 0.93 ± 0.05 mol hydrogen/mol glycerol, energy efficiency greater than 100%, and hydrogen production rate greater than that of fermentative hydrogen production from glycerol by this species and by a genetically altered E. coli strain. The results of this study suggest that, ideally with removal of potassium salts, soaps, and catalyst, and with some method to minimize biofilm formation on the surface of MFC air-cathodes, MFCs and MECs represent promising treatment methods to generate electricity or hydrogen gas while treating the waste products of biodiesel manufacture. These results represent an important step in improving the economic viability of the ever-growing biodiesel industry as the world energy economy continues to shift from fossil fuels to renewable energy sources. Close

• 1897. [Article] Effects of medicinal herbs on contraction rate of cultured cardiomyocyte. Possible mechanisms involved in the chronotropic effects of hawthorn and berberine in neonatal murine cardiomyocyte

  Herbs have been used for many centuries in diverse civilizations for the treatment of heart disease. Only a few natural supplements claim to have direct cardiovascular actions including hawthorn (Crataegus ...

  Citation × Citation Citation Abstract Copy Title: Effects of medicinal herbs on contraction rate of cultured cardiomyocyte. Possible mechanisms involved in the chronotropic effects of hawthorn and berberine in neonatal murine cardiomyocyte Author: Salehi, Satin Herbs have been used for many centuries in diverse civilizations for the treatment of heart disease. Only a few natural supplements claim to have direct cardiovascular actions including hawthorn (Crataegus spp.) and berberine derived from the Berberidaceae family. Several different studies indicate important cardiovascular effects of hawthorn and berberine. For example, both exert positive inotropic effects and have been used in the treatment of congestive heart failure. Recently, it was shown that hawthorn extract preparations cause negative chronotropic effects in a cultured neonatal murine cardiomyocyte assay independent of beta-adrenergic receptor blockade. The aim of this study was to further characterize the effect of hawthorn extract to decrease the contraction rate of cultured cardiomyocytes. We hypothesized that hawthorn extract may be acting through muscarinic receptors to decrease contraction rate of cardiomyocytes. Atrial and ventricular cardiomyocytes were treated with hawthorn extract in the presence of atropine or himbacine. Changes in the contraction rate of cultured cardiomyocytes revealed that both muscarinic antagonists significantly attenuated the negative chronotropic activity of hawthorn extract. Using quinuclidinyl benzilate, L-[benzylic-4,4'-3H] ([³H]-QNB) as a radioligand antagonist, the effect of a partially purified hawthorn extract fraction to inhibit muscarinic receptor binding was quantified. Hawthorn extract fraction 3 dose-dependently inhibited [³H]-QNB binding to mouse heart membranes. These findings suggest that muscarinic receptors may be involved in the negative chronotropic effect of hawthorn extracts in neonatal murine cardiomyocytes. Berberine exhibits variable positive and negative chronotropic effects in different species. Our first aim was to examine the effect of berberine in a cultured neonatal murine cardiomyocyte assay. Our study demonstrates that berberine has significant negative chronotropic actions on cardiomyocytes which is not an effect of beta-adrenergic receptor blockade. Pertussis toxin (PTX), a Gi/o protein inhibitor, blocked the negative chronotropic activity of berberine. Muscarinic, adenosine, opioid, and α₂ receptors are coupled through a G-protein (Gi/o) to adenylyl cyclase in an inhibitory fashion. Activation of these receptors are primarily responsible for PTX-sensitive negative chronotropic effects in heart. We hypothesized that berberine may be acting through one of these receptor type to decrease contraction rate of cardiomyocytes. For this purpose, we studied the effects of the muscarinic-receptor antagonists, atropine, himbacine, or AF- DX 116 on the negative chronotropic activity of berberine. Muscarinic antagonists completely blocked the effect of berberine on contraction rate of cardiomyocytes, whereas the bradycardic effect of berberine was not inhibited by the opioid, adenosine, or α2 receptor antagonists naloxone, CGS 15943, or phentolamine, respectively. Using [³H]QNB as a radioligand, we demonstrated that berberine bound to muscarinic receptors of adult mouse heart membranes with relatively high affinity. Furthermore, berberine dose-dependently inhibited [³H]QNB binding to muscarinic M2 receptors exogenously expressed in HEK 293 cells. Therefore, the findings of the present study suggest that berberine has muscarinic agonist effects in cultured neonatal murine cardiomyocytes, potentially explaining reported physiological effects of berberine. Cardiac hypertrophy represents the most important factor in the development of congestive heart failure. We investigated the inhibitory effect of berberine on hypertrophy of H9c2 cells. In rat heart-derived H9c2 myoblast cells treated with different hypertrophic agonists such as insulin growth factor II (IGF-II), arginine vasopressin (AVP), phenylephrine, and isoproterenol, protein content and size of cells were significantly increased compared to control group. However, the number of H9c2 cells after treatment with hypertrophic agonists did not differ significantly compared to control. The increases in area of cells and protein content induced by the hypertrophic agonists were inhibited by treatment with berberine in a concentration-dependent manner. Our findings have provided the first scientific evidence that berberine may have an inhibitory effect on hypertrophy of heart-derived cells, and provide a rationale for further studies to evaluate berberine's cardiac activity. Title: Effects of medicinal herbs on contraction rate of cultured cardiomyocyte. Possible mechanisms involved in the chronotropic effects of hawthorn and berberine in neonatal murine cardiomyocyte Author: Salehi, Satin Herbs have been used for many centuries in diverse civilizations for the treatment of heart disease. Only a few natural supplements claim to have direct cardiovascular actions including hawthorn (Crataegus spp.) and berberine derived from the Berberidaceae family. Several different studies indicate important cardiovascular effects of hawthorn and berberine. For example, both exert positive inotropic effects and have been used in the treatment of congestive heart failure. Recently, it was shown that hawthorn extract preparations cause negative chronotropic effects in a cultured neonatal murine cardiomyocyte assay independent of beta-adrenergic receptor blockade. The aim of this study was to further characterize the effect of hawthorn extract to decrease the contraction rate of cultured cardiomyocytes. We hypothesized that hawthorn extract may be acting through muscarinic receptors to decrease contraction rate of cardiomyocytes. Atrial and ventricular cardiomyocytes were treated with hawthorn extract in the presence of atropine or himbacine. Changes in the contraction rate of cultured cardiomyocytes revealed that both muscarinic antagonists significantly attenuated the negative chronotropic activity of hawthorn extract. Using quinuclidinyl benzilate, L-[benzylic-4,4'-3H] ([³H]-QNB) as a radioligand antagonist, the effect of a partially purified hawthorn extract fraction to inhibit muscarinic receptor binding was quantified. Hawthorn extract fraction 3 dose-dependently inhibited [³H]-QNB binding to mouse heart membranes. These findings suggest that muscarinic receptors may be involved in the negative chronotropic effect of hawthorn extracts in neonatal murine cardiomyocytes. Berberine exhibits variable positive and negative chronotropic effects in different species. Our first aim was to examine the effect of berberine in a cultured neonatal murine cardiomyocyte assay. Our study demonstrates that berberine has significant negative chronotropic actions on cardiomyocytes which is not an effect of beta-adrenergic receptor blockade. Pertussis toxin (PTX), a Gi/o protein inhibitor, blocked the negative chronotropic activity of berberine. Muscarinic, adenosine, opioid, and α₂ receptors are coupled through a G-protein (Gi/o) to adenylyl cyclase in an inhibitory fashion. Activation of these receptors are primarily responsible for PTX-sensitive negative chronotropic effects in heart. We hypothesized that berberine may be acting through one of these receptor type to decrease contraction rate of cardiomyocytes. For this purpose, we studied the effects of the muscarinic-receptor antagonists, atropine, himbacine, or AF- DX 116 on the negative chronotropic activity of berberine. Muscarinic antagonists completely blocked the effect of berberine on contraction rate of cardiomyocytes, whereas the bradycardic effect of berberine was not inhibited by the opioid, adenosine, or α2 receptor antagonists naloxone, CGS 15943, or phentolamine, respectively. Using [³H]QNB as a radioligand, we demonstrated that berberine bound to muscarinic receptors of adult mouse heart membranes with relatively high affinity. Furthermore, berberine dose-dependently inhibited [³H]QNB binding to muscarinic M2 receptors exogenously expressed in HEK 293 cells. Therefore, the findings of the present study suggest that berberine has muscarinic agonist effects in cultured neonatal murine cardiomyocytes, potentially explaining reported physiological effects of berberine. Cardiac hypertrophy represents the most important factor in the development of congestive heart failure. We investigated the inhibitory effect of berberine on hypertrophy of H9c2 cells. In rat heart-derived H9c2 myoblast cells treated with different hypertrophic agonists such as insulin growth factor II (IGF-II), arginine vasopressin (AVP), phenylephrine, and isoproterenol, protein content and size of cells were significantly increased compared to control group. However, the number of H9c2 cells after treatment with hypertrophic agonists did not differ significantly compared to control. The increases in area of cells and protein content induced by the hypertrophic agonists were inhibited by treatment with berberine in a concentration-dependent manner. Our findings have provided the first scientific evidence that berberine may have an inhibitory effect on hypertrophy of heart-derived cells, and provide a rationale for further studies to evaluate berberine's cardiac activity. Close

• 1898. [Article] A computer simulation study of the relative efficiency of several forest sampling techniques as influenced by the spatial distribution of trees found in five major forest types of the Pacific Northwest

  This study was initiated to determine the relative efficiency of systematic, stratified and simple random sampling for crown area and tree frequency estimation of five of the major forest types found in ...

  Citation × Citation Citation Abstract Copy Title: A computer simulation study of the relative efficiency of several forest sampling techniques as influenced by the spatial distribution of trees found in five major forest types of the Pacific Northwest Author: Payandeh, Bijan This study was initiated to determine the relative efficiency of systematic, stratified and simple random sampling for crown area and tree frequency estimation of five of the major forest types found in the Pacific Northwest. Several of the more common methods of estimating spatial distribution coefficients were evaluated. Finally the effect of spatial distribution of trees in these forest types on the relative efficiency of two-dimensional systematic sampling was analyzed. Crown maps of five 48-acre tracts of the following types were made from large scale (1:2500) aerial photographs and photographically enlarged to the scale of 1:624: 1.Typical ponderosa-pine of Eastern Oregon 2.Mixed species of Oregon’s Coastal type 3.Mixed pine stands of Northeastern Oregon 4.Even aged Douglas-fir stands common to the Pacific Northwest 5.Typical old growth Douglas-fir of the Pacific Northwest. The basic data consisted of the location (by grid coordinates) and size of each tree crown as obtained from crown maps. These data were committed to the memory of the CDC 3300 computer and the entire analyses executed through computer simulation techniques as follows: Exhaustive two-dimensional systematic sampling was taken using one quarter acre sampling units, Sample mean variances were computed for the three sampling schemes using analysis of variance principles. Relative efficiency of systematic and stratified sampling was also computed. The same parameters were also estimated by variable plot sampling based on 24 points systematically located at the middle 24 acre of each type. The same principles were used to compute variances as close approximations. Eight of the more common non-randomness measures were compared. To evaluate these methods and obtain the required data for examining the effect of spatial variation on relative efficiency of systematic sampling, four new populations were generated from each forest type. These newly computer generated populations were sampled in the same way as for the original forest types. Spatial distribution coefficients of these populations were also computed. Multiple regression analysis was employed using stepwise computer program to establish relationships between the relative efficiency of systematic sampling and the coefficients of randomization. Logarithmic transformation was used to satisfy equality of variances in establishing regression equations. The results of this study indicated that the relative efficiency of two-dimensional systematic sampling may vary greatly depending on the parameter being estimated. For tree frequency estimation (a discrete variable) of the original forest types the gain in precision of systematic sampling varied from 20 to 167 percent. In estimating crown area (a continuous variable) systematic sampling was less precise than simple random sampling on one forest type, while yielding gains in precision ranging from 10 to 179 percent for the other original forest types. There were no significant differences in precision obtained by the three sampling schemes for estimating both parameters when applied to completely randomly dispersed populations. Systematic sampling was less precise than both stratified and random sampling when applied to uniformly spaced populations. The loss in precision in this case ranged from 15 to about 79 percent. Of the eight non-randomness measures (measures of spatial distribution) the point method proved to be best. Grosenbaugh' s Q-factor which is considered to be the most practical method was rejected as being invalid. All original forest types were found to be clustered. Regression equations of relative efficiency on the coefficient of randomization for crown area estimation of the five forest types were mostly non-linear. Since these predicting models produced low correlations and were obviously different from each other, no attempt was made to establish a generalized model. Relative efficiency of systematic sampling for tree frequency estimation was highly correlated with the coefficient of randomization. Of the five equations established, four were not significantly different from each other, thus they were pooled and a generalized model developed which turned out to be y = 1.402x with simple correlation coefficient of r=0.81 where: y = common log of relative efficiency of systematic sampling x = common log of spatial distribution coefficient measured by the point method. Therefore, when an estimate of spatial distribution of trees in a forest is known, the relative efficiency of systematic plot sampling can be predicted with a high degree of accuracy. Such relationships could also be applied as adjustment factors to systematic sampling variance when being treated as simple random samples. Title: A computer simulation study of the relative efficiency of several forest sampling techniques as influenced by the spatial distribution of trees found in five major forest types of the Pacific Northwest Author: Payandeh, Bijan This study was initiated to determine the relative efficiency of systematic, stratified and simple random sampling for crown area and tree frequency estimation of five of the major forest types found in the Pacific Northwest. Several of the more common methods of estimating spatial distribution coefficients were evaluated. Finally the effect of spatial distribution of trees in these forest types on the relative efficiency of two-dimensional systematic sampling was analyzed. Crown maps of five 48-acre tracts of the following types were made from large scale (1:2500) aerial photographs and photographically enlarged to the scale of 1:624: 1.Typical ponderosa-pine of Eastern Oregon 2.Mixed species of Oregon’s Coastal type 3.Mixed pine stands of Northeastern Oregon 4.Even aged Douglas-fir stands common to the Pacific Northwest 5.Typical old growth Douglas-fir of the Pacific Northwest. The basic data consisted of the location (by grid coordinates) and size of each tree crown as obtained from crown maps. These data were committed to the memory of the CDC 3300 computer and the entire analyses executed through computer simulation techniques as follows: Exhaustive two-dimensional systematic sampling was taken using one quarter acre sampling units, Sample mean variances were computed for the three sampling schemes using analysis of variance principles. Relative efficiency of systematic and stratified sampling was also computed. The same parameters were also estimated by variable plot sampling based on 24 points systematically located at the middle 24 acre of each type. The same principles were used to compute variances as close approximations. Eight of the more common non-randomness measures were compared. To evaluate these methods and obtain the required data for examining the effect of spatial variation on relative efficiency of systematic sampling, four new populations were generated from each forest type. These newly computer generated populations were sampled in the same way as for the original forest types. Spatial distribution coefficients of these populations were also computed. Multiple regression analysis was employed using stepwise computer program to establish relationships between the relative efficiency of systematic sampling and the coefficients of randomization. Logarithmic transformation was used to satisfy equality of variances in establishing regression equations. The results of this study indicated that the relative efficiency of two-dimensional systematic sampling may vary greatly depending on the parameter being estimated. For tree frequency estimation (a discrete variable) of the original forest types the gain in precision of systematic sampling varied from 20 to 167 percent. In estimating crown area (a continuous variable) systematic sampling was less precise than simple random sampling on one forest type, while yielding gains in precision ranging from 10 to 179 percent for the other original forest types. There were no significant differences in precision obtained by the three sampling schemes for estimating both parameters when applied to completely randomly dispersed populations. Systematic sampling was less precise than both stratified and random sampling when applied to uniformly spaced populations. The loss in precision in this case ranged from 15 to about 79 percent. Of the eight non-randomness measures (measures of spatial distribution) the point method proved to be best. Grosenbaugh' s Q-factor which is considered to be the most practical method was rejected as being invalid. All original forest types were found to be clustered. Regression equations of relative efficiency on the coefficient of randomization for crown area estimation of the five forest types were mostly non-linear. Since these predicting models produced low correlations and were obviously different from each other, no attempt was made to establish a generalized model. Relative efficiency of systematic sampling for tree frequency estimation was highly correlated with the coefficient of randomization. Of the five equations established, four were not significantly different from each other, thus they were pooled and a generalized model developed which turned out to be y = 1.402x with simple correlation coefficient of r=0.81 where: y = common log of relative efficiency of systematic sampling x = common log of spatial distribution coefficient measured by the point method. Therefore, when an estimate of spatial distribution of trees in a forest is known, the relative efficiency of systematic plot sampling can be predicted with a high degree of accuracy. Such relationships could also be applied as adjustment factors to systematic sampling variance when being treated as simple random samples. Close

• 1899. [Article] Host range and chemical composition of lactic streptococcal bacteriophages

  Comparisons were made of the abilities of Streptococcus lactis, Streptococcus cremoris and Streptococcus diacetilactis bacteriophages to endure various laboratory isolation and storage treatments. Neutralization ...

  Citation × Citation Citation Abstract Copy Title: Host range and chemical composition of lactic streptococcal bacteriophages Author: Henning, David Ralph Comparisons were made of the abilities of Streptococcus lactis, Streptococcus cremoris and Streptococcus diacetilactis bacteriophages to endure various laboratory isolation and storage treatments. Neutralization of Cottage cheese whey containing phages offered no survival advantage over unneutralized samples, refrigeration of neutral and acid whey samples increased the survival of only the S. diacetilactis phage. About 50 percent of the phages could be recovered from milk coagulated by addition of lactic acid to provide casein-free, clear, phage-containing whey. Sterilization of phage lysates by membrane filtration allowed collection of 92 to 99 percent of the phages; Seitz filtration allowed collection of a maximum of 24 percent. Whey samples containing phages could be concentrated by removing water using polyethylene glycol. Lyophilization decreased phage titers at least 50 percent. Cross reaction patterns of phages for strains of lactic streptococci revealed that similar strains were present in cultures supplied by several companies. For example, phages which were lytic for strains isolated from one brand of commercial mixed strain starter cultures would lyse strains isolated from as many as three different brands of starter cultures. The lytic patterns of 60 bacteriophage races toward 100 single lactic streptococcal strains allowed the establishment of eight phage groups, A through H. The phages within a particular group were generally species specific. However several exceptions were noted. Group A phages attacked primarily strains of S. diacetilactis. Groups B through H phages mainly attacked strains of S. lactis and S. cremoris. Groups G and H consisted of one phage that attacked only the homologous host. Lytic reactions determined by multiple printing of phages on lawns seeded with possible hosts were employed for selecting strains to be used in mixed-strain starter cultures. A computer was used in selecting strains for blending into mixed-strain cultures with resulting maximum protection against phage. The strains selected by the computer were arranged in a sequence or rotation system suitable for use in dairy plant fermentations. Protection from phage infection as determined by a resistance index remained high for six successive cultures, but the addition of the seventh culture to the rotation system increased the likelihood of phage attack significantly. Neutralization of representatives of each host range phage group by standardized rabbit antisera prepared against four different phages revealed similarity among several groups. However the neutralization of phages was not constant within each group. Electron photomicrographs of a phage for S. diacetilactis revealed a tadpole-shaped particle. The head width and length were each about 60 mμ , the tail width was about 10mμ and the tail length was about 170 mμ . There also were suggestions for a polyhedral head structure in enlarged (84,000X) pictures of the viruses. Chemical compositional studies of the phage studied by electron microscopy revealed that phosphorus represented 4.45 percent of the phage dry weight. Nitrogen was found to constitute 12.8 percent of the phage protein. A ratio of phage phosphorus to phage protein nitrogen of 2.7 was determined. Bacteriophages prepared in broth medium were recovered by differential centrifugation and purified in cesium chloride density gradients. An amino acid analysis revealed the following mole percentages for the amino acids quantitated: lysine, 8.1; histidine, 1.7; arginine, 3.8; aspartic acid and asparagine, 10.0; threonine, 7.5; serine, 6.8; glutamic acid and glutamine, 12.1; proline, 3.4; glycine, 9.0; alanine, 9.5; valine, 8.7; methionine, 1.1; isoleucine, 7.9; tyrosine, 2.2 and phenylalanine, 2.8. The nucleic acid of the phage was determined to be double-stranded DNA with a thermal melting point of 84.3°C, indicating an average base composition of 35.7 percent guanine plus cytosine. Calculated values for percentage DNA and protein composition of the phage were 44 and 56 percent respectively. The density of the phage was calculated to be 1.47g/cc. Title: Host range and chemical composition of lactic streptococcal bacteriophages Author: Henning, David Ralph Comparisons were made of the abilities of Streptococcus lactis, Streptococcus cremoris and Streptococcus diacetilactis bacteriophages to endure various laboratory isolation and storage treatments. Neutralization of Cottage cheese whey containing phages offered no survival advantage over unneutralized samples, refrigeration of neutral and acid whey samples increased the survival of only the S. diacetilactis phage. About 50 percent of the phages could be recovered from milk coagulated by addition of lactic acid to provide casein-free, clear, phage-containing whey. Sterilization of phage lysates by membrane filtration allowed collection of 92 to 99 percent of the phages; Seitz filtration allowed collection of a maximum of 24 percent. Whey samples containing phages could be concentrated by removing water using polyethylene glycol. Lyophilization decreased phage titers at least 50 percent. Cross reaction patterns of phages for strains of lactic streptococci revealed that similar strains were present in cultures supplied by several companies. For example, phages which were lytic for strains isolated from one brand of commercial mixed strain starter cultures would lyse strains isolated from as many as three different brands of starter cultures. The lytic patterns of 60 bacteriophage races toward 100 single lactic streptococcal strains allowed the establishment of eight phage groups, A through H. The phages within a particular group were generally species specific. However several exceptions were noted. Group A phages attacked primarily strains of S. diacetilactis. Groups B through H phages mainly attacked strains of S. lactis and S. cremoris. Groups G and H consisted of one phage that attacked only the homologous host. Lytic reactions determined by multiple printing of phages on lawns seeded with possible hosts were employed for selecting strains to be used in mixed-strain starter cultures. A computer was used in selecting strains for blending into mixed-strain cultures with resulting maximum protection against phage. The strains selected by the computer were arranged in a sequence or rotation system suitable for use in dairy plant fermentations. Protection from phage infection as determined by a resistance index remained high for six successive cultures, but the addition of the seventh culture to the rotation system increased the likelihood of phage attack significantly. Neutralization of representatives of each host range phage group by standardized rabbit antisera prepared against four different phages revealed similarity among several groups. However the neutralization of phages was not constant within each group. Electron photomicrographs of a phage for S. diacetilactis revealed a tadpole-shaped particle. The head width and length were each about 60 mμ , the tail width was about 10mμ and the tail length was about 170 mμ . There also were suggestions for a polyhedral head structure in enlarged (84,000X) pictures of the viruses. Chemical compositional studies of the phage studied by electron microscopy revealed that phosphorus represented 4.45 percent of the phage dry weight. Nitrogen was found to constitute 12.8 percent of the phage protein. A ratio of phage phosphorus to phage protein nitrogen of 2.7 was determined. Bacteriophages prepared in broth medium were recovered by differential centrifugation and purified in cesium chloride density gradients. An amino acid analysis revealed the following mole percentages for the amino acids quantitated: lysine, 8.1; histidine, 1.7; arginine, 3.8; aspartic acid and asparagine, 10.0; threonine, 7.5; serine, 6.8; glutamic acid and glutamine, 12.1; proline, 3.4; glycine, 9.0; alanine, 9.5; valine, 8.7; methionine, 1.1; isoleucine, 7.9; tyrosine, 2.2 and phenylalanine, 2.8. The nucleic acid of the phage was determined to be double-stranded DNA with a thermal melting point of 84.3°C, indicating an average base composition of 35.7 percent guanine plus cytosine. Calculated values for percentage DNA and protein composition of the phage were 44 and 56 percent respectively. The density of the phage was calculated to be 1.47g/cc. Close

• 1900. [Article] Effects of pollen collected by honey bees from pollination dependent agricultural cropping systems on honey bee nutrition

  Managed honey bee (Apis mellifera L.) colonies are important pollinators of many cultivated crops. Honey bee colony declines averaging 30% annually in the United States for the past 7 years have caused ...

  Citation × Citation Citation Abstract Copy Title: Effects of pollen collected by honey bees from pollination dependent agricultural cropping systems on honey bee nutrition Author: Topitzhofer, Ellen Managed honey bee (Apis mellifera L.) colonies are important pollinators of many cultivated crops. Honey bee colony declines averaging 30% annually in the United States for the past 7 years have caused significant concern and hence have been a topic of intensive investigation. These declines are reportedly due to multiple factors. Poor nutrition, which may be a result of current migratory pollination practices, is one such factor. Migratory pollination is a common practice of beekeepers from the Pacific Northwest and involves the placement of managed honey bee colonies within a series of cropping systems. There is a gap in knowledge on how migratory pollination practices impact honey bee nutrition. To understand the potential impacts of migratory pollination on honey bee nutrition, it is critical to assess the diversity of pollen collected by bees when colonies are placed adjacent to these cropping systems. In this study, we describe the diversity of pollen collected by honey bee colonies managed by beekeepers in the Pacific Northwest region of the United States when placed in seven major cropping systems. We quantified the percent of target crop pollen and overall diversity of pollen collected by honey bees when colonies were placed in these cropping systems. We collected and identified pollen in almond (Prunus dulcis (Mill.)), cherry (Prunus avium L.), highbush blueberry (Vaccinium corymbosum L.), meadowfoam (Limnanthes alba Benth.), white clover (Trifolium repens L.), radish (Raphanus sativus L.), and carrot (Daucus carota (Hoffm.)) cropping systems. We found that pollen collected from colonies placed in almond cropping systems was predominately Prunus sp., and hence, low in pollen diversity. At the other end of the spectrum, pollen collected from colonies placed adjacent to blueberry cropping systems did not yield any target pollen types (Highbush blueberry, Vaccinium corymbosum L.), but was high in overall pollen diversity. The pollen collected from colonies placed in other cropping systems was largely intermediate in diversity between these two extremes. There were not many plant species in bloom when pollen was collected from colonies placed in almond cropping system, whereas more plants were in bloom when we collected pollen from colonies placed in blueberry cropping system. The results of this study demonstrate that honey bees collected pollen from plants in the surrounding environment and collected different degrees of pollen diversity across different cropping systems in which the colonies were placed. We further determined if pollen diversity influences colony-level protein utilization and biosynthesis of protein in nurse bees by conducting a pollen feeding experiment. Pollen collected from four different cropping systems in the first study was used to formulate four different diets, each varying in pollen diversity. We measured protein consumption in experimental colonies and by sampling nurse bees from each colony to estimate hypopharyngeal gland protein content and proteolytic enzyme activity after five weeks of feeding on the experimental pollen diets. Experimental colonies fed on pollen collected from almond cropping system exhibited a high protein consumption rate. However, low protein content as found in hypopharyngeal glands of nurse bees in these colonies. The nurse bees in these colonies also had low proteolytic enzyme activity, which indicates a lower rate of protein digestion. Overall, these results suggest that the diet representing pollen collected from almond cropping systems had low digestion rate and may have resulted in lower nurse bee hypopharyngeal gland protein. However, we cannot say this with certainty, as there were other confounding factors involved, such as presence of pesticides in the pollen collected from the cropping systems. Title: Effects of pollen collected by honey bees from pollination dependent agricultural cropping systems on honey bee nutrition Author: Topitzhofer, Ellen Managed honey bee (Apis mellifera L.) colonies are important pollinators of many cultivated crops. Honey bee colony declines averaging 30% annually in the United States for the past 7 years have caused significant concern and hence have been a topic of intensive investigation. These declines are reportedly due to multiple factors. Poor nutrition, which may be a result of current migratory pollination practices, is one such factor. Migratory pollination is a common practice of beekeepers from the Pacific Northwest and involves the placement of managed honey bee colonies within a series of cropping systems. There is a gap in knowledge on how migratory pollination practices impact honey bee nutrition. To understand the potential impacts of migratory pollination on honey bee nutrition, it is critical to assess the diversity of pollen collected by bees when colonies are placed adjacent to these cropping systems. In this study, we describe the diversity of pollen collected by honey bee colonies managed by beekeepers in the Pacific Northwest region of the United States when placed in seven major cropping systems. We quantified the percent of target crop pollen and overall diversity of pollen collected by honey bees when colonies were placed in these cropping systems. We collected and identified pollen in almond (Prunus dulcis (Mill.)), cherry (Prunus avium L.), highbush blueberry (Vaccinium corymbosum L.), meadowfoam (Limnanthes alba Benth.), white clover (Trifolium repens L.), radish (Raphanus sativus L.), and carrot (Daucus carota (Hoffm.)) cropping systems. We found that pollen collected from colonies placed in almond cropping systems was predominately Prunus sp., and hence, low in pollen diversity. At the other end of the spectrum, pollen collected from colonies placed adjacent to blueberry cropping systems did not yield any target pollen types (Highbush blueberry, Vaccinium corymbosum L.), but was high in overall pollen diversity. The pollen collected from colonies placed in other cropping systems was largely intermediate in diversity between these two extremes. There were not many plant species in bloom when pollen was collected from colonies placed in almond cropping system, whereas more plants were in bloom when we collected pollen from colonies placed in blueberry cropping system. The results of this study demonstrate that honey bees collected pollen from plants in the surrounding environment and collected different degrees of pollen diversity across different cropping systems in which the colonies were placed. We further determined if pollen diversity influences colony-level protein utilization and biosynthesis of protein in nurse bees by conducting a pollen feeding experiment. Pollen collected from four different cropping systems in the first study was used to formulate four different diets, each varying in pollen diversity. We measured protein consumption in experimental colonies and by sampling nurse bees from each colony to estimate hypopharyngeal gland protein content and proteolytic enzyme activity after five weeks of feeding on the experimental pollen diets. Experimental colonies fed on pollen collected from almond cropping system exhibited a high protein consumption rate. However, low protein content as found in hypopharyngeal glands of nurse bees in these colonies. The nurse bees in these colonies also had low proteolytic enzyme activity, which indicates a lower rate of protein digestion. Overall, these results suggest that the diet representing pollen collected from almond cropping systems had low digestion rate and may have resulted in lower nurse bee hypopharyngeal gland protein. However, we cannot say this with certainty, as there were other confounding factors involved, such as presence of pesticides in the pollen collected from the cropping systems. Close