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• 1141. [Article] Virulence factors of Aeromonas salmonicida and their interaction with the salmonid host

  Selected secreted and cellular virulence factors of Aeromonas salmonicida were examined. A protocol was developed for the separation of two secreted proteases (P1 and P2 protease), and a trout erythrocyte ...

  Citation × Citation Citation Abstract Copy Title: Virulence factors of Aeromonas salmonicida and their interaction with the salmonid host Author: Rockey, Daniel D. Selected secreted and cellular virulence factors of Aeromonas salmonicida were examined. A protocol was developed for the separation of two secreted proteases (P1 and P2 protease), and a trout erythrocyte specific hemolysin (T-lysin) from supernatants of cultures of the bacterium. Distinctions between the proteases were demonstrated using molecular weight determinations, substrate specificities, sensitivity to chemical protease inhibitor sensitivities, and polyacrylamide gel electrophoresis using gels containing protease substrates (G-PAGE). P1, but not P2, protease was detected in G-PAGE analyses of protease from lesions of coho salmon (Oncorhynchus kisutch) infected by injection. Other proteases of apparent host origin were also detected in these assays. Analysis of the T-lysin demonstrated that although the bacterium produced high titers of the enzyme in vitro, no hemolytic activity was detected in vivo nor in cultures grown in salmonid sera. Subsequent experiments demonstrated that salmonid sera possess an inhibitor of hemolysis capable of protecting erythrocytes from enzymatic or chemical lysis. The inhibitor was partially purified using molecular sieve chromatography and preparative isoelectric focusing. Analysis of P1 protease, P2 protease, and T-lysin production was continued by examining their production in the presence of salmonid sera and in the presence of high concentrations of selected salts added to brain heart infusion broth (BHI). The spectrum of proteases produced in serum was similar to the spectrum produced in BHI. However, a larger phenylmethylsufonyl fluoride sensitive fraction was detected in supernatants from bacterial cells grown in serum. Analysis of supernatants from the cultures grown in high salts indicated that P1 protease and T-lysin production were inhibited by these salts but P2 protease production was not. Growth in high concentrations of magnesium salts also affected the cellular morphology of the bacterium and this effect was associated with the presence of an outer membrane protein layer, the A layer. Four monoclonal antibodies (Mabs) were produced with specificity towards A. salmonicida lipopolysaccharide (LPS). These Mabs were used to identify two distinct epitopes on LPS and to show that the presence of each epitope varied among different strains. The antibodies were also used to demonstrate the difference in the host response of rabbits and rainbow trout (Oncorhynchus mykiss) to A. salmonicida. Title: Virulence factors of Aeromonas salmonicida and their interaction with the salmonid host Author: Rockey, Daniel D. Selected secreted and cellular virulence factors of Aeromonas salmonicida were examined. A protocol was developed for the separation of two secreted proteases (P1 and P2 protease), and a trout erythrocyte specific hemolysin (T-lysin) from supernatants of cultures of the bacterium. Distinctions between the proteases were demonstrated using molecular weight determinations, substrate specificities, sensitivity to chemical protease inhibitor sensitivities, and polyacrylamide gel electrophoresis using gels containing protease substrates (G-PAGE). P1, but not P2, protease was detected in G-PAGE analyses of protease from lesions of coho salmon (Oncorhynchus kisutch) infected by injection. Other proteases of apparent host origin were also detected in these assays. Analysis of the T-lysin demonstrated that although the bacterium produced high titers of the enzyme in vitro, no hemolytic activity was detected in vivo nor in cultures grown in salmonid sera. Subsequent experiments demonstrated that salmonid sera possess an inhibitor of hemolysis capable of protecting erythrocytes from enzymatic or chemical lysis. The inhibitor was partially purified using molecular sieve chromatography and preparative isoelectric focusing. Analysis of P1 protease, P2 protease, and T-lysin production was continued by examining their production in the presence of salmonid sera and in the presence of high concentrations of selected salts added to brain heart infusion broth (BHI). The spectrum of proteases produced in serum was similar to the spectrum produced in BHI. However, a larger phenylmethylsufonyl fluoride sensitive fraction was detected in supernatants from bacterial cells grown in serum. Analysis of supernatants from the cultures grown in high salts indicated that P1 protease and T-lysin production were inhibited by these salts but P2 protease production was not. Growth in high concentrations of magnesium salts also affected the cellular morphology of the bacterium and this effect was associated with the presence of an outer membrane protein layer, the A layer. Four monoclonal antibodies (Mabs) were produced with specificity towards A. salmonicida lipopolysaccharide (LPS). These Mabs were used to identify two distinct epitopes on LPS and to show that the presence of each epitope varied among different strains. The antibodies were also used to demonstrate the difference in the host response of rabbits and rainbow trout (Oncorhynchus mykiss) to A. salmonicida. Close

• 1142. [Article] Oregon coastal community water supply assessment

  On the Oregon coast, however, the issue of water supply has become paramount, especially given the need to restore instream flows in order to restore coastal salmon runs and meet water quality standards. ...

  Citation × Citation Citation Abstract Copy Title: Oregon coastal community water supply assessment Author: Achterman, Gail, Rolston, Irene, Davis-Born, Renee, Institute for Natural Resources, Gaines, Lisa On the Oregon coast, however, the issue of water supply has become paramount, especially given the need to restore instream flows in order to restore coastal salmon runs and meet water quality standards. With the ebb and flow of population and the economic growth of Oregon coastal communities, three hypotheses have been generated about the ability of these communities to meet future water supply needs. The purpose of this project was to better understand the challenges and opportunities facing coastal community water suppliers as a whole and to ultimately improve the prospects for meeting future water needs. Findings show that contrary to the first hypothesis, most of those interviewed do not think that economic development is constrained by waters supply. However, it does appear that it would be difficult for state economic development officials to match businesses and industries interested in relocating to the Oregon coast with community water supply availability and reliability. Findings also show that the major problem facing community water suppliers in preparing water management and conservation plans cited by interviewees is financial. Though Oregon’s coastal communities face several planning, management, physical, economic, and regulatory challenges in preparing for future water supply needs, numerous partnership, conservation, and research and training opportunities exist. What is needed is an opportunity for a facilitated process of restructuring water supply systems. Title: Oregon coastal community water supply assessment Author: Achterman, Gail, Rolston, Irene, Davis-Born, Renee, Institute for Natural Resources, Gaines, Lisa On the Oregon coast, however, the issue of water supply has become paramount, especially given the need to restore instream flows in order to restore coastal salmon runs and meet water quality standards. With the ebb and flow of population and the economic growth of Oregon coastal communities, three hypotheses have been generated about the ability of these communities to meet future water supply needs. The purpose of this project was to better understand the challenges and opportunities facing coastal community water suppliers as a whole and to ultimately improve the prospects for meeting future water needs. Findings show that contrary to the first hypothesis, most of those interviewed do not think that economic development is constrained by waters supply. However, it does appear that it would be difficult for state economic development officials to match businesses and industries interested in relocating to the Oregon coast with community water supply availability and reliability. Findings also show that the major problem facing community water suppliers in preparing water management and conservation plans cited by interviewees is financial. Though Oregon’s coastal communities face several planning, management, physical, economic, and regulatory challenges in preparing for future water supply needs, numerous partnership, conservation, and research and training opportunities exist. What is needed is an opportunity for a facilitated process of restructuring water supply systems. Close

• 1143. [Article] Molecular Analysis of Environmental Water Samples as a Monitoring Method for the Fish Parasite Ichthyophthirius multifiliis

  Parasites are ubiquitous members of ecological communities, capable of contributing to the decline of vulnerable populations. Therefore, monitoring parasite level is a critical component for host management. ...

  Citation × Citation Citation Abstract Copy Title: Molecular Analysis of Environmental Water Samples as a Monitoring Method for the Fish Parasite Ichthyophthirius multifiliis Author: Howell, Claire K. Parasites are ubiquitous members of ecological communities, capable of contributing to the decline of vulnerable populations. Therefore, monitoring parasite level is a critical component for host management. Molecular tools, such as quantitative polymerase chain reaction (qPCR), can be valuable additions to monitoring protocols that assess parasitic disease risk to hosts. To be successful, monitoring protocols must capture biologically relevant environmental data, and relate that data to disease risk. This project assesses the application of molecular analysis of environmental water samples for monitoring the ciliate protozoan Ichthyophthirius multifiliis (Ich) in the Klamath River, CA. Ich is an economically and ecologically significant parasite of freshwater fishes, and has contributed to mortality of pre-spawning adult salmon throughout the Pacific Northwest, including in the Klamath River. Chapter 1 introduces the study site (the lower Klamath River, CA), host population of concern (Klamath River salmonids), parasite of interest (Ich), and primary molecular technique (qPCR). Chapter 2 describes the development and validation of a qPCR assay targeting the SSU rDNA of Ich, as well as the initial application of the assay to environmental water samples. Chapter 3 presents a field application of the sampling method. Chapters 2 and 3 demonstrate the assay’s potential to inform the management of Ich infections in the Klamath River. Chapter 4 compares the genetic variation of Ich isolates published in GenBank, and those collected from pet shops (OR) and natural rivers (CA) (primarily the Klamath River) at the cox1 and SSU gene loci. This research indicates that qPCR analysis of environmental water samples could be a valuable monitoring tool for waterborne Ich in the Klamath River. Title: Molecular Analysis of Environmental Water Samples as a Monitoring Method for the Fish Parasite Ichthyophthirius multifiliis Author: Howell, Claire K. Parasites are ubiquitous members of ecological communities, capable of contributing to the decline of vulnerable populations. Therefore, monitoring parasite level is a critical component for host management. Molecular tools, such as quantitative polymerase chain reaction (qPCR), can be valuable additions to monitoring protocols that assess parasitic disease risk to hosts. To be successful, monitoring protocols must capture biologically relevant environmental data, and relate that data to disease risk. This project assesses the application of molecular analysis of environmental water samples for monitoring the ciliate protozoan Ichthyophthirius multifiliis (Ich) in the Klamath River, CA. Ich is an economically and ecologically significant parasite of freshwater fishes, and has contributed to mortality of pre-spawning adult salmon throughout the Pacific Northwest, including in the Klamath River. Chapter 1 introduces the study site (the lower Klamath River, CA), host population of concern (Klamath River salmonids), parasite of interest (Ich), and primary molecular technique (qPCR). Chapter 2 describes the development and validation of a qPCR assay targeting the SSU rDNA of Ich, as well as the initial application of the assay to environmental water samples. Chapter 3 presents a field application of the sampling method. Chapters 2 and 3 demonstrate the assay’s potential to inform the management of Ich infections in the Klamath River. Chapter 4 compares the genetic variation of Ich isolates published in GenBank, and those collected from pet shops (OR) and natural rivers (CA) (primarily the Klamath River) at the cox1 and SSU gene loci. This research indicates that qPCR analysis of environmental water samples could be a valuable monitoring tool for waterborne Ich in the Klamath River. Close

• 1144. [Article] Ecosystem Service Values and the Klamath River Dam Removal

  In February 2010, two agreements were finalized by Federal, State, and Tribal governments and PacifiCorp, a utility company that owns dams on the Klamath River: the Klamath Basin Restoration Agreement ...

  Citation × Citation Citation Abstract Copy Title: Ecosystem Service Values and the Klamath River Dam Removal Author: Kosaka, Rosemary In February 2010, two agreements were finalized by Federal, State, and Tribal governments and PacifiCorp, a utility company that owns dams on the Klamath River: the Klamath Basin Restoration Agreement (KBRA) and the Klamath Hydroelectric Settlement Agreement (Settlement Agreement). These agreements included provisions that would affect the Klamath River Basin such as removing four dams on the Klamath River, habitat restoration projects, and water allocation schedules for water users. To determine whether implementing these agreements would provide environmental benefits that outweighed the costs, an extensive benefit-cost analysis was undertaken, a collaboration between agencies within the Department of Interior and the Department of Commerce’s National Oceanic and Atmospheric Administration. Ecosystem service benefits such as the restoration of salmonid fisheries, improvements to irrigated agriculture, and increased recreational opportunities were evaluated against ecosystem service costs such as dam removal, forgone hydropower, and habitat restoration activities. When considering these and other use values, the net benefit of implementing the KBRA and Settlement Agreement was negative (-US$1.6 billion). When including non-use values such as public willingness-to-pay to reduce the extinction risk of Coho salmon, the net benefit of implementing these Agreements was positive (+US$14.1 billion). The addition of these non-use ecosystem service values tipped the scales in favor of the preferred outcome: removing the four Klamath Dams and implementing the other provisions of the Agreements. This talk will discuss the range of ecosystem service values that were evaluated, the controversial nature of the benefit-cost analysis, and the underlying politics and historical context surrounding the Agreements.  Title: Ecosystem Service Values and the Klamath River Dam Removal Author: Kosaka, Rosemary In February 2010, two agreements were finalized by Federal, State, and Tribal governments and PacifiCorp, a utility company that owns dams on the Klamath River: the Klamath Basin Restoration Agreement (KBRA) and the Klamath Hydroelectric Settlement Agreement (Settlement Agreement). These agreements included provisions that would affect the Klamath River Basin such as removing four dams on the Klamath River, habitat restoration projects, and water allocation schedules for water users. To determine whether implementing these agreements would provide environmental benefits that outweighed the costs, an extensive benefit-cost analysis was undertaken, a collaboration between agencies within the Department of Interior and the Department of Commerce’s National Oceanic and Atmospheric Administration. Ecosystem service benefits such as the restoration of salmonid fisheries, improvements to irrigated agriculture, and increased recreational opportunities were evaluated against ecosystem service costs such as dam removal, forgone hydropower, and habitat restoration activities. When considering these and other use values, the net benefit of implementing the KBRA and Settlement Agreement was negative (-US$1.6 billion). When including non-use values such as public willingness-to-pay to reduce the extinction risk of Coho salmon, the net benefit of implementing these Agreements was positive (+US$14.1 billion). The addition of these non-use ecosystem service values tipped the scales in favor of the preferred outcome: removing the four Klamath Dams and implementing the other provisions of the Agreements. This talk will discuss the range of ecosystem service values that were evaluated, the controversial nature of the benefit-cost analysis, and the underlying politics and historical context surrounding the Agreements.  Close

• 1145. [Article] Performance of the European-EU Seafood Sector - Veiwed through Aquaculture and Sea Bass & Sea Bream

  Suggested Bibliographic Reference: Challenging New Frontiers in the Global Seafood Sector: Proceedings of the Eighteenth Biennial Conference of the International Institute of Fisheries Economics and Trade, ...

  Citation × Citation Citation Abstract Copy Title: Performance of the European-EU Seafood Sector - Veiwed through Aquaculture and Sea Bass & Sea Bream Author: Valle, Paul S., Analyse, Kontali Year: 2016 Suggested Bibliographic Reference: Challenging New Frontiers in the Global Seafood Sector: Proceedings of the Eighteenth Biennial Conference of the International Institute of Fisheries Economics and Trade, July 11-15, 2016. Compiled by Stefani J. Evers and Ann L. Shriver. International Institute of Fisheries Economics and Trade (IIFET), Corvallis, 2016. Title: Performance of the European-EU Seafood Sector - Veiwed through Aquaculture and Sea Bass & Sea Bream Author: Valle, Paul S., Analyse, Kontali Year: 2016 Suggested Bibliographic Reference: Challenging New Frontiers in the Global Seafood Sector: Proceedings of the Eighteenth Biennial Conference of the International Institute of Fisheries Economics and Trade, July 11-15, 2016. Compiled by Stefani J. Evers and Ann L. Shriver. International Institute of Fisheries Economics and Trade (IIFET), Corvallis, 2016. Close

• 1146. [Article] Characterization of a new Lactobacillus species infectious for salmonid fish

  A new Lactobacillus species is proposed to include 17 strains of a bacterium from rainbow (Salmo gairdneri) and cutthroat trout (Salmo clarki), and chinook salmon (Oncorhynchus tshawytscha). The bacterium ...

  Citation × Citation Citation Abstract Copy Title: Characterization of a new Lactobacillus species infectious for salmonid fish Author: Hiu, Stephen Fooklen A new Lactobacillus species is proposed to include 17 strains of a bacterium from rainbow (Salmo gairdneri) and cutthroat trout (Salmo clarki), and chinook salmon (Oncorhynchus tshawytscha). The bacterium was isolated most frequently from fish stressed by handling or spawn ing. Phenotypically, the strains belong to the family Lactobacillaceae and can be distinguished from other species of Lactobacil1 us by their morphology and physiological characteristics. Growth occurred between 6 and 40°C. DL-lactic acid was produced homofermentatively from glucose. Diaminopimelic acid was present in the cell wall peptidoglycan. The 17 isolates were closely related gene tically, as demonstrated by similar percent guanine plus cytosine content (35 mol%) and high DNA reassociation values, both characteristics of a single species. Isolates exhibited less than 10% DNA reassoci ati on to other reference Lactobacillus strains with similar mol% G+C. The bacterium was pathogenic for rainbow trout maintained at 18 or 21°C. A 73 % mortality after 18 days was achieved at each water temperature after the fish were injected intraperitoneally with 3.3 x 10⁸ cells. The mean time from infection to death was 4 days for fish held at 18°C and 3 days for fish held at 21°C. The 50% lethal dose (LD50) for rainbow trout injected intraperitoneally and maintained in 18°C water was 5.4 x 10⁷. Histopathological examination of experimentally in fected fish showed that the bacterium was localized in the visceral adipose tissue, the peritoneal membrane, the loose connective tissue surrounding the liver, esophagus and spleen, and in the cardiac muscle and muscularis of the esophagus. Necrosis of the spleen, liver, or kidney was not observed. Gross pathology included ascites fluid accumulation and hemorrhaging of the visceral adipose tissue and lower intestine. The isolates from fish best match the description of the genus Lactobacillus but differ from other members of the genus genetically, in their fermentation patterns, and by their association with disease in fish and should be recognized as a new species for which the name Lactobacil! us piscicol us is proposed. Strain B270, isolated from diseased cutthroat trout at Bandon Hatchery, Coos County, Oregon, U.S.A., is designated the type strain. Title: Characterization of a new Lactobacillus species infectious for salmonid fish Author: Hiu, Stephen Fooklen A new Lactobacillus species is proposed to include 17 strains of a bacterium from rainbow (Salmo gairdneri) and cutthroat trout (Salmo clarki), and chinook salmon (Oncorhynchus tshawytscha). The bacterium was isolated most frequently from fish stressed by handling or spawn ing. Phenotypically, the strains belong to the family Lactobacillaceae and can be distinguished from other species of Lactobacil1 us by their morphology and physiological characteristics. Growth occurred between 6 and 40°C. DL-lactic acid was produced homofermentatively from glucose. Diaminopimelic acid was present in the cell wall peptidoglycan. The 17 isolates were closely related gene tically, as demonstrated by similar percent guanine plus cytosine content (35 mol%) and high DNA reassociation values, both characteristics of a single species. Isolates exhibited less than 10% DNA reassoci ati on to other reference Lactobacillus strains with similar mol% G+C. The bacterium was pathogenic for rainbow trout maintained at 18 or 21°C. A 73 % mortality after 18 days was achieved at each water temperature after the fish were injected intraperitoneally with 3.3 x 10⁸ cells. The mean time from infection to death was 4 days for fish held at 18°C and 3 days for fish held at 21°C. The 50% lethal dose (LD50) for rainbow trout injected intraperitoneally and maintained in 18°C water was 5.4 x 10⁷. Histopathological examination of experimentally in fected fish showed that the bacterium was localized in the visceral adipose tissue, the peritoneal membrane, the loose connective tissue surrounding the liver, esophagus and spleen, and in the cardiac muscle and muscularis of the esophagus. Necrosis of the spleen, liver, or kidney was not observed. Gross pathology included ascites fluid accumulation and hemorrhaging of the visceral adipose tissue and lower intestine. The isolates from fish best match the description of the genus Lactobacillus but differ from other members of the genus genetically, in their fermentation patterns, and by their association with disease in fish and should be recognized as a new species for which the name Lactobacil! us piscicol us is proposed. Strain B270, isolated from diseased cutthroat trout at Bandon Hatchery, Coos County, Oregon, U.S.A., is designated the type strain. Close

• 1147. [Article] A provenance study of crypto-crystalline silicates at the Cooper's Ferry site : a geochemical approach

  A provenance study of crypto-crystalline silicates was performed at the Cooper's Ferry archaeological site in west-central Idaho on the Columbia Plateau. In this research, the author used instrumental ...

  Citation × Citation Citation Abstract Copy Title: A provenance study of crypto-crystalline silicates at the Cooper's Ferry site : a geochemical approach Author: Nyers, Alexander John A provenance study of crypto-crystalline silicates was performed at the Cooper's Ferry archaeological site in west-central Idaho on the Columbia Plateau. In this research, the author used instrumental neutron activation analysis as well as portable x-ray fluorescence to examine and characterize the geochemistry of 300 geologic samples of crypto-crystalline silicates from six different sources in the region surrounding Cooper's Ferry. The author then examined approximately 600 archaeological artifacts from Cooper's Ferry using portable x-ray fluorescence and attempted to correlate archaeological artifacts to examined geologic sources using a multivariate statistical approach. This research finds that the tool stone of approximately 24 percent of artifacts examined originated from a sampled local chert source. This research also examined the ratio of possible chert sources scene in the archaeological record by using multiple cluster analysis techniques and finds that no observable founder effect is seen at Cooper's Ferry. Furthermore, there seems to be a long standing transfer of crypto-crystalline silicate source knowledge at Cooper's Ferry, indicating an extended period of cultural stability at the site. This stability can be extrapolated as a single cultural group residing at the site throughout its occupation history - approximately 11,000 to 8,000 RCYBP. Title: A provenance study of crypto-crystalline silicates at the Cooper's Ferry site : a geochemical approach Author: Nyers, Alexander John A provenance study of crypto-crystalline silicates was performed at the Cooper's Ferry archaeological site in west-central Idaho on the Columbia Plateau. In this research, the author used instrumental neutron activation analysis as well as portable x-ray fluorescence to examine and characterize the geochemistry of 300 geologic samples of crypto-crystalline silicates from six different sources in the region surrounding Cooper's Ferry. The author then examined approximately 600 archaeological artifacts from Cooper's Ferry using portable x-ray fluorescence and attempted to correlate archaeological artifacts to examined geologic sources using a multivariate statistical approach. This research finds that the tool stone of approximately 24 percent of artifacts examined originated from a sampled local chert source. This research also examined the ratio of possible chert sources scene in the archaeological record by using multiple cluster analysis techniques and finds that no observable founder effect is seen at Cooper's Ferry. Furthermore, there seems to be a long standing transfer of crypto-crystalline silicate source knowledge at Cooper's Ferry, indicating an extended period of cultural stability at the site. This stability can be extrapolated as a single cultural group residing at the site throughout its occupation history - approximately 11,000 to 8,000 RCYBP. Close

• 1148. [Article] Bayesian parentage analysis with systematic accountability of genotyping error, missing data, and false matching

  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://bioinformatics.oxfordjourna...

  Citation × Citation Citation Abstract Copy Title: Bayesian parentage analysis with systematic accountability of genotyping error, missing data, and false matching Author: Christie, Mark R., Tennessen, Jacob A., Blouin, Michael S. 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://bioinformatics.oxfordjournals.org/. Title: Bayesian parentage analysis with systematic accountability of genotyping error, missing data, and false matching Author: Christie, Mark R., Tennessen, Jacob A., Blouin, Michael S. 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://bioinformatics.oxfordjournals.org/. Close

• 1149. [Article] An integrated epidemiological-economic model of sea lice control in aquaculture: A system dynamics approach

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  Citation × Citation Citation Abstract Copy Title: An integrated epidemiological-economic model of sea lice control in aquaculture: A system dynamics approach Author: Hamza, Kanar Abstract Only Title: An integrated epidemiological-economic model of sea lice control in aquaculture: A system dynamics approach Author: Hamza, Kanar Abstract Only Close

• 1150. [Article] Bluefin Tuna Full Life Cycle: Review and Prospects over the Next Thirty Years

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  Citation × Citation Citation Abstract Copy Title: Bluefin Tuna Full Life Cycle: Review and Prospects over the Next Thirty Years Author: McElroy, Seamus Abstract Only Title: Bluefin Tuna Full Life Cycle: Review and Prospects over the Next Thirty Years Author: McElroy, Seamus Abstract Only Close