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• 111. [Article] DNA-based identification of commercially important salmon and trout species (genera Oncorhynchus and Salmo) in North America

  There are seven commercially important species of salmon and trout (genera Oncorhynchus and Salmo) in North America, many of which are closely related but command markedly different prices. The purpose ...

  Citation × Citation Citation Abstract Copy Title: DNA-based identification of commercially important salmon and trout species (genera Oncorhynchus and Salmo) in North America Author: Rasmussen, Rosalee S. There are seven commercially important species of salmon and trout (genera Oncorhynchus and Salmo) in North America, many of which are closely related but command markedly different prices. The purpose of this research was to provide improved and novel methods for the detection of salmon species substitution on the commercial market. This work took place in three parts: first an existing method was optimized and improved upon, then a comprehensive collection of reference salmon sequences was built for use in species identification with DNA barcoding, and finally, based on these sequences, a novel species-specific multiplex polymerase chain reaction (PCR) assay was developed. In the first study, a PCR-restriction fragment length polymorphism (RFLP) method for salmon species identification was optimized for use with U.S. commercial products. The restriction digest was shortened to 1 h rather than overnight and the method was successful with lightly processed products. However, heavily processed samples could not be identified. Next, DNA barcoding was examined as a method for salmon species identification. Sequence information was collected for 924 reference samples from a wide geographic range. Sequences showed low intraspecies divergences (mean 0.26%), and the mean congeneric divergence was 32-fold greater, at 8.22%. The minimum interspecies divergence was always greater than the maximum intraspecies divergence, indicating that these species can be differentiated using DNA barcodes. In the next study, species-specific primers and probes were developed based on DNA barcode sequence information to diagnose salmon species in both real-time and conventional PCR systems. The primers and probes were combined into multiplex assays and tested for specificity against 94-112 reference samples representing 19-25 species. Strong signals were detected for the target species in both systems, and nonspecific amplification was minimal. Both assays showed high sensitivity, with detection levels of 0.05 to 5.0 ng (0.1 to 10% in DNA admixtures). Overall, this study presents a rapid, specific and sensitive method for salmon species identification that can be applied to mixed-species and heavily processed samples in either a conventional or real-time format. Title: DNA-based identification of commercially important salmon and trout species (genera Oncorhynchus and Salmo) in North America Author: Rasmussen, Rosalee S. There are seven commercially important species of salmon and trout (genera Oncorhynchus and Salmo) in North America, many of which are closely related but command markedly different prices. The purpose of this research was to provide improved and novel methods for the detection of salmon species substitution on the commercial market. This work took place in three parts: first an existing method was optimized and improved upon, then a comprehensive collection of reference salmon sequences was built for use in species identification with DNA barcoding, and finally, based on these sequences, a novel species-specific multiplex polymerase chain reaction (PCR) assay was developed. In the first study, a PCR-restriction fragment length polymorphism (RFLP) method for salmon species identification was optimized for use with U.S. commercial products. The restriction digest was shortened to 1 h rather than overnight and the method was successful with lightly processed products. However, heavily processed samples could not be identified. Next, DNA barcoding was examined as a method for salmon species identification. Sequence information was collected for 924 reference samples from a wide geographic range. Sequences showed low intraspecies divergences (mean 0.26%), and the mean congeneric divergence was 32-fold greater, at 8.22%. The minimum interspecies divergence was always greater than the maximum intraspecies divergence, indicating that these species can be differentiated using DNA barcodes. In the next study, species-specific primers and probes were developed based on DNA barcode sequence information to diagnose salmon species in both real-time and conventional PCR systems. The primers and probes were combined into multiplex assays and tested for specificity against 94-112 reference samples representing 19-25 species. Strong signals were detected for the target species in both systems, and nonspecific amplification was minimal. Both assays showed high sensitivity, with detection levels of 0.05 to 5.0 ng (0.1 to 10% in DNA admixtures). Overall, this study presents a rapid, specific and sensitive method for salmon species identification that can be applied to mixed-species and heavily processed samples in either a conventional or real-time format. Close

• 112. [Article] Foraminiferal trends of the central Oregon shelf

  Sediments of a portion of the central Oregon shelf between 17 and 339 m have been examined for modern foraminifera. Eighty-three samples were collected from 33 stations along three traverses located between ...

  Citation × Citation Citation Abstract Copy Title: Foraminiferal trends of the central Oregon shelf Author: Boettcher, Richard Scott Sediments of a portion of the central Oregon shelf between 17 and 339 m have been examined for modern foraminifera. Eighty-three samples were collected from 33 stations along three traverses located between 43° 16'N and 43° 50'N. One hundred fifty-five benthic and nine planktonic species are recognized. Fifty-six benthic species occur with a frequency of more than two percent in at least one sample. Benthic species are grouped into four distinct bathymetric faunas. Elphidiella hannai and Buccella spp. are indicative of Fauna A (17-50 m). Fauna B (50-100 m) is characterized by Buliminella elegantissima and Elphidium magellanicum. In the rocky area off Cape Arago Cassidulina californica, C. limbata, Cibicides fletcheri, and C. lobatulus become dominant. Spiroplectammina biformis, Textularia earlandi, and Trifarina angulosa are important species of Fauna C (100-175 m). Abundant species of Fauna D (175-339 m) include Eggerella advena, Epistominella exigua, and Uvigerina juncea. Species diversity increases offshore to a maximum of about 35 benthic species near 100 m and then decreases slightly with depth. Standing crop is low nearshore, rises to a maximum of approximately 300 specimens per 20 cm³ between 125 and 150 m, and then declines. Total benthic population reaches a maximum of approximately 6000 specimens per sample between 150 and 175 m. Values then decrease to about 2000 specimens at 339 m. A maximum of 15 to 20 percent live benthic specimens occurs near 50 m. Planktonic foraminifera constitute less than ten percent of the total population. Maximum percentages generally occur shoaler than 100 m, while maximum specimens per sample occur at the deepest stations. Porcelaneous specimens do not exceed six percent of the benthic population. Agglutinated foraminifera are more abundant than calcareous specimens deeper than 100 m. The frequency of occurrence of a species may vary by as much as 25 percentage points from samples collected approximately 15 cm apart. Statistical analysis of selected species indicates that sampling density was not too close along any one traverse, although the traverses possibly could have been spaced farther apart. Miscellaneous biofacies trends indicate that: thecamoebians are most abundant between 50 and 125 m; statoliths and otoliths occur most frequently between 75 and 2OO m; highest ostracod values are found between 25 and 150 m; and radiolarians generally exceed foraminifera deeper than 250 m. Title: Foraminiferal trends of the central Oregon shelf Author: Boettcher, Richard Scott Sediments of a portion of the central Oregon shelf between 17 and 339 m have been examined for modern foraminifera. Eighty-three samples were collected from 33 stations along three traverses located between 43° 16'N and 43° 50'N. One hundred fifty-five benthic and nine planktonic species are recognized. Fifty-six benthic species occur with a frequency of more than two percent in at least one sample. Benthic species are grouped into four distinct bathymetric faunas. Elphidiella hannai and Buccella spp. are indicative of Fauna A (17-50 m). Fauna B (50-100 m) is characterized by Buliminella elegantissima and Elphidium magellanicum. In the rocky area off Cape Arago Cassidulina californica, C. limbata, Cibicides fletcheri, and C. lobatulus become dominant. Spiroplectammina biformis, Textularia earlandi, and Trifarina angulosa are important species of Fauna C (100-175 m). Abundant species of Fauna D (175-339 m) include Eggerella advena, Epistominella exigua, and Uvigerina juncea. Species diversity increases offshore to a maximum of about 35 benthic species near 100 m and then decreases slightly with depth. Standing crop is low nearshore, rises to a maximum of approximately 300 specimens per 20 cm³ between 125 and 150 m, and then declines. Total benthic population reaches a maximum of approximately 6000 specimens per sample between 150 and 175 m. Values then decrease to about 2000 specimens at 339 m. A maximum of 15 to 20 percent live benthic specimens occurs near 50 m. Planktonic foraminifera constitute less than ten percent of the total population. Maximum percentages generally occur shoaler than 100 m, while maximum specimens per sample occur at the deepest stations. Porcelaneous specimens do not exceed six percent of the benthic population. Agglutinated foraminifera are more abundant than calcareous specimens deeper than 100 m. The frequency of occurrence of a species may vary by as much as 25 percentage points from samples collected approximately 15 cm apart. Statistical analysis of selected species indicates that sampling density was not too close along any one traverse, although the traverses possibly could have been spaced farther apart. Miscellaneous biofacies trends indicate that: thecamoebians are most abundant between 50 and 125 m; statoliths and otoliths occur most frequently between 75 and 2OO m; highest ostracod values are found between 25 and 150 m; and radiolarians generally exceed foraminifera deeper than 250 m. Close

• 113. [Article] Double-crested Cormorants (Phalacrocorax auritus) and Brandt’s Cormorants (P. penicillatus) Breeding at East Sand Island in the Columbia River Estuary : Foraging Ecology, Colony Connectivity, and Overwinter Dispersal

  Double-crested cormorants (Phalacrocorax auritus) and Brandt’s cormorants (P. penicillatus) nest sympatrically in a large mixed-species colony on East Sand Island (ESI) in the Columbia River estuary. Ecological ...

  Citation × Citation Citation Abstract Copy Title: Double-crested Cormorants (Phalacrocorax auritus) and Brandt’s Cormorants (P. penicillatus) Breeding at East Sand Island in the Columbia River Estuary : Foraging Ecology, Colony Connectivity, and Overwinter Dispersal Author: Peck-Richardson, Adam Double-crested cormorants (Phalacrocorax auritus) and Brandt’s cormorants (P. penicillatus) nest sympatrically in a large mixed-species colony on East Sand Island (ESI) in the Columbia River estuary. Ecological theory predicts that such morphologically similar species will partition prey resources when faced with resource limitations. During the summer of 2014, I investigated local movements, foraging dive behavior, and foraging habitat selection by breeding adults of both cormorant species using GPS tags with integrated temperature and depth data-loggers (GPS-TDlog, Earth & Ocean Technologies). The overall foraging areas and core foraging areas (defined as the 95% and 50% kernel density estimates of dive locations, respectively) of double-crested cormorants were much larger and covered a broader range of estuarine habitats than those of Brandt’s cormorants. Only 26% and 27% of the overall and core foraging areas, respectively, for double-crested cormorants overlapped with those of Brandt’s cormorants. Most of the overall and core foraging areas of Brandt’s cormorants (59% and 89%, respectively) overlapped with those of double-crested cormorants, however. Within areas of overlap, Brandt’s cormorants tended to dive deeper (median depth = 6.48 m) than double-crested cormorants (median depth = 2.67 m), and selected dive locations where the water was deeper. After accounting for local water depth, Brandt’s cormorants utilized a deeper, more benthic portion of the water column than did double-crested cormorants. Our results indicate that species-specific patterns of foraging habitat utilization likely reflect past evolutionary divergence in foraging niche and evolved differences in behavioral and physiological adaptations, resulting in some partitioning of prey resources that would mitigate interspecific competition. Nevertheless, the substantial overlap in foraging habitat between the two cormorant species, particularly for Brandt’s cormorants, suggests that superabundant prey resources allow these two large and productive cormorant colonies to coexist on a single island near the mouth of the Columbia River. Annual consumption of millions of out-migrating juvenile salmonids (Oncorhynchus spp.), including smolts from populations listed under the U.S. Endangered Species Act, by double-crested cormorants nesting at ESI motivated natural resource managers to investigate potential management techniques to reduce cormorant predation by reducing the size of the breeding colony. To better understand potential dispersal of cormorants from the ESI colony due to management to reduce colony size, satellite transmitters were fitted on 83 double-crested cormorants captured on the ESI colony before egg-laying in 2013. Dispersal from ESI immediately following tagging was nearly ubiquitous, but temporary, and provided limited information on where cormorants might prospect for alternative nest sites if prevented from nesting on ESI. During this initial pre-nesting period, tagged cormorants were detected at colonies and roost sites as far from ESI as the Puget Sound region of coastal Washington; nevertheless, all but 4% of tagged cormorants returned to ESI within 2 weeks of being tagged. Following the subsequent breeding season, tagged cormorants staged at several nearby estuaries before migrating both north and south from ESI to overwinter in areas from British Columbia to northwestern Mexico; only 3% overwintered in the Columbia River estuary. Tracking data revealed substantial connectivity between the ESI colony and other colonies and regions within the range of the western North America population, suggesting the potential for widespread dispersal throughout the population’s breeding range if nesting habitat on ESI was reduced or eliminated. Dispersal did not extend across the Cascade-Sierra Divide, however; greater connectivity existed with estuary locations throughout the range and particularly with more proximate estuaries that served as post-breeding staging areas. Surprisingly low regional and colony connectivity was observed with the Oregon Coast, despite numerous active and historical colonies in that region, as well as proximity to the colony at ESI. The strong philopatry to ESI that nearly all tagged cormorants exhibited, however, suggests that few alternative nesting opportunities are as attractive for prospecting double-crested cormorants as the ESI colony site. Title: Double-crested Cormorants (Phalacrocorax auritus) and Brandt’s Cormorants (P. penicillatus) Breeding at East Sand Island in the Columbia River Estuary : Foraging Ecology, Colony Connectivity, and Overwinter Dispersal Author: Peck-Richardson, Adam Double-crested cormorants (Phalacrocorax auritus) and Brandt’s cormorants (P. penicillatus) nest sympatrically in a large mixed-species colony on East Sand Island (ESI) in the Columbia River estuary. Ecological theory predicts that such morphologically similar species will partition prey resources when faced with resource limitations. During the summer of 2014, I investigated local movements, foraging dive behavior, and foraging habitat selection by breeding adults of both cormorant species using GPS tags with integrated temperature and depth data-loggers (GPS-TDlog, Earth & Ocean Technologies). The overall foraging areas and core foraging areas (defined as the 95% and 50% kernel density estimates of dive locations, respectively) of double-crested cormorants were much larger and covered a broader range of estuarine habitats than those of Brandt’s cormorants. Only 26% and 27% of the overall and core foraging areas, respectively, for double-crested cormorants overlapped with those of Brandt’s cormorants. Most of the overall and core foraging areas of Brandt’s cormorants (59% and 89%, respectively) overlapped with those of double-crested cormorants, however. Within areas of overlap, Brandt’s cormorants tended to dive deeper (median depth = 6.48 m) than double-crested cormorants (median depth = 2.67 m), and selected dive locations where the water was deeper. After accounting for local water depth, Brandt’s cormorants utilized a deeper, more benthic portion of the water column than did double-crested cormorants. Our results indicate that species-specific patterns of foraging habitat utilization likely reflect past evolutionary divergence in foraging niche and evolved differences in behavioral and physiological adaptations, resulting in some partitioning of prey resources that would mitigate interspecific competition. Nevertheless, the substantial overlap in foraging habitat between the two cormorant species, particularly for Brandt’s cormorants, suggests that superabundant prey resources allow these two large and productive cormorant colonies to coexist on a single island near the mouth of the Columbia River. Annual consumption of millions of out-migrating juvenile salmonids (Oncorhynchus spp.), including smolts from populations listed under the U.S. Endangered Species Act, by double-crested cormorants nesting at ESI motivated natural resource managers to investigate potential management techniques to reduce cormorant predation by reducing the size of the breeding colony. To better understand potential dispersal of cormorants from the ESI colony due to management to reduce colony size, satellite transmitters were fitted on 83 double-crested cormorants captured on the ESI colony before egg-laying in 2013. Dispersal from ESI immediately following tagging was nearly ubiquitous, but temporary, and provided limited information on where cormorants might prospect for alternative nest sites if prevented from nesting on ESI. During this initial pre-nesting period, tagged cormorants were detected at colonies and roost sites as far from ESI as the Puget Sound region of coastal Washington; nevertheless, all but 4% of tagged cormorants returned to ESI within 2 weeks of being tagged. Following the subsequent breeding season, tagged cormorants staged at several nearby estuaries before migrating both north and south from ESI to overwinter in areas from British Columbia to northwestern Mexico; only 3% overwintered in the Columbia River estuary. Tracking data revealed substantial connectivity between the ESI colony and other colonies and regions within the range of the western North America population, suggesting the potential for widespread dispersal throughout the population’s breeding range if nesting habitat on ESI was reduced or eliminated. Dispersal did not extend across the Cascade-Sierra Divide, however; greater connectivity existed with estuary locations throughout the range and particularly with more proximate estuaries that served as post-breeding staging areas. Surprisingly low regional and colony connectivity was observed with the Oregon Coast, despite numerous active and historical colonies in that region, as well as proximity to the colony at ESI. The strong philopatry to ESI that nearly all tagged cormorants exhibited, however, suggests that few alternative nesting opportunities are as attractive for prospecting double-crested cormorants as the ESI colony site. Close

• 114. [Article] Host-pathogen dynamics in a changing environment : susceptibility of amphibians to an emerging infectious disease

  Infectious diseases are a growing concern for both humans and wildlife. The negative effects of infectious disease have been exemplified by the recent global amphibian population declines associated with ...

  Citation × Citation Citation Abstract Copy Title: Host-pathogen dynamics in a changing environment : susceptibility of amphibians to an emerging infectious disease Author: Searle, Catherine L. Infectious diseases are a growing concern for both humans and wildlife. The negative effects of infectious disease have been exemplified by the recent global amphibian population declines associated with disease outbreaks. Although multiple pathogens and factors play a role in these declines, the aquatic fungal pathogen, Batrachochytrium dendrobatidis (Bd), has received considerable attention due to its substantial contribution to amphibian population declines around the world. Bd prevalence and severity appears to be increasing worldwide, either from recent anthropogenic spread of the pathogen or from changes in the environment that have altered host-pathogen dynamics. This dissertation explores the factors that affect host susceptibility to Bd. I first tested the effects of hormonal stress on susceptibility to Bd (Chapter 2). Using corticosterone, the major chronic stress hormone in amphibians, I was able to mimic the physiological effects of stress without altering other factors that may affect the host-pathogen relationship. I exposed three species of larval amphibians to corticosterone for two weeks to induce chronic stress before challenging them with exposure to Bd. I found that exposure to corticosterone did not alter infection prevalence or severity in any species, indicating that chronically elevated levels of corticosterone do not affect susceptibility to Bd. I next examined the interactive effects of the ubiquitous stressor, ultraviolet-B radiation (UVB), and host infection by Bd (Chapter 3). UVB can cause lethal and sublethal effects in amphibians, including increased susceptibility to pathogens. In outdoor mesocosms, I used ambient levels of UVB to stress larval amphibians while simultaneously exposing them to Bd. Although exposure to UVB increased mortality, it did not alter infection. To investigate the effects of community structure on infection prevalence and severity, I studied how six anuran species (frogs and toads) differed in susceptibility to Bd (Chapter 4). I experimentally exposed post-metamorphic amphibians native to North America to Bd under identical laboratory conditions. All species tested had higher rates of mortality when exposed to Bd compared to unexposed controls. However, the species differed widely in their rates of Bd-associated mortality, even though there was no difference in infection levels among species. I also found that within species, the relationship between body size and infection varied, indicating physiological differences in the way that amphibian species respond to pathogen infection. Finally, I studied the effects of the amphibian host community on infection. I experimentally exposed larval amphibians to Bd after manipulating host density and species richness in the laboratory (Chapter 5). I recorded five measures of disease risk and found a dilution effect where greater species richness decreased disease risk, even after taking into account changes in density. Together with Chapter 4, this study emphasizes the need to understand the effects of the community on host-pathogen dynamics. This dissertation provides insight into the effects of stress and community structure on disease dynamics. Although there has been a great effort to understand Bd since it was discovered, the ecology of Bd remains relatively unknown. My research represents an important step in understanding the host-pathogen relationship in a changing environment. Title: Host-pathogen dynamics in a changing environment : susceptibility of amphibians to an emerging infectious disease Author: Searle, Catherine L. Infectious diseases are a growing concern for both humans and wildlife. The negative effects of infectious disease have been exemplified by the recent global amphibian population declines associated with disease outbreaks. Although multiple pathogens and factors play a role in these declines, the aquatic fungal pathogen, Batrachochytrium dendrobatidis (Bd), has received considerable attention due to its substantial contribution to amphibian population declines around the world. Bd prevalence and severity appears to be increasing worldwide, either from recent anthropogenic spread of the pathogen or from changes in the environment that have altered host-pathogen dynamics. This dissertation explores the factors that affect host susceptibility to Bd. I first tested the effects of hormonal stress on susceptibility to Bd (Chapter 2). Using corticosterone, the major chronic stress hormone in amphibians, I was able to mimic the physiological effects of stress without altering other factors that may affect the host-pathogen relationship. I exposed three species of larval amphibians to corticosterone for two weeks to induce chronic stress before challenging them with exposure to Bd. I found that exposure to corticosterone did not alter infection prevalence or severity in any species, indicating that chronically elevated levels of corticosterone do not affect susceptibility to Bd. I next examined the interactive effects of the ubiquitous stressor, ultraviolet-B radiation (UVB), and host infection by Bd (Chapter 3). UVB can cause lethal and sublethal effects in amphibians, including increased susceptibility to pathogens. In outdoor mesocosms, I used ambient levels of UVB to stress larval amphibians while simultaneously exposing them to Bd. Although exposure to UVB increased mortality, it did not alter infection. To investigate the effects of community structure on infection prevalence and severity, I studied how six anuran species (frogs and toads) differed in susceptibility to Bd (Chapter 4). I experimentally exposed post-metamorphic amphibians native to North America to Bd under identical laboratory conditions. All species tested had higher rates of mortality when exposed to Bd compared to unexposed controls. However, the species differed widely in their rates of Bd-associated mortality, even though there was no difference in infection levels among species. I also found that within species, the relationship between body size and infection varied, indicating physiological differences in the way that amphibian species respond to pathogen infection. Finally, I studied the effects of the amphibian host community on infection. I experimentally exposed larval amphibians to Bd after manipulating host density and species richness in the laboratory (Chapter 5). I recorded five measures of disease risk and found a dilution effect where greater species richness decreased disease risk, even after taking into account changes in density. Together with Chapter 4, this study emphasizes the need to understand the effects of the community on host-pathogen dynamics. This dissertation provides insight into the effects of stress and community structure on disease dynamics. Although there has been a great effort to understand Bd since it was discovered, the ecology of Bd remains relatively unknown. My research represents an important step in understanding the host-pathogen relationship in a changing environment. Close

• 115. [Article] Fungal colonization of Douglas-fir sapwood

  The fungi that cause mold and stain of freshly sawn lumber result in millions of dollars in losses to the forest products industry. Stain and mold are typically prevented by either kiln drying or by application ...

  Citation × Citation Citation Abstract Copy Title: Fungal colonization of Douglas-fir sapwood Author: Kang, Sung-Mo The fungi that cause mold and stain of freshly sawn lumber result in millions of dollars in losses to the forest products industry. Stain and mold are typically prevented by either kiln drying or by application of a topical fungicide. While these treatments are effective, kiln drying is costly and many mills object to use of chemicals. One alternative to conventional stain prevention is biological control. One problem with this approach on western wood species such as Douglas-fir is the lack of information on the target stain and mold fungi that colonize the sapwood of this species. The fungi colonizing freshly sawn Douglas-fir sapwood were isolated and identified by culturing lumber obtained from 4 different locations in the Willamette Valley in western Oregon using regular, streptomycin amended or streptomycin/cycloheximide amended malt extract agar. The ability of each taxa to cause discoloration was evaluated in a laboratory discoloration test. A total of 547 fungi were isolated from Douglas-fir sapwood, representing 24 genera and 45 species. Graphium species were the most frequently isolated fungi, representing 17.4 percent of all isolates. Most of these isolates were considered as anamorphs of Ophiostoma piceae. Other frequently isolated sapstaining fungi included Cephaloascus fragrans, Aureobasidium pullulans, Rhinocladiella cellaris, Cladosporium cladosporioides and Scytalidium lignicola. Molds, primary Penicillium and Trichoderma species, were frequently isolated, and may represent potential biological control organisms or competitors of biological control organisms because of their antagonistic characteristics. Many fungal species of unknown biological significance were also isolated from Douglas-fir sapwood, and their roles in the stain development merit further study. Media and lumber source both affected the fiingal flora isolated. Among stain fungi, Graphium species exclusively occurred on cycloheximide amended media. There was also close relationship between the degree of fungal colonization and the length of time after the lumber was cut. The degree of discoloration exceeded 70 percent in all Graphium species. Cephaloascus fragrans, Aureobasidium pullulans, Rhinocladiella cellaris, Cladosporium cladosporioides, Scytalidium lignicola and Thysanophora penicillioides also produced extensive staining of Douglas-fir sapwood. Mold isolates also caused discoloration of Douglas-fir sapwood wafers, although their discoloration could be easily removed. All Penicillium species produced over 90 percent discoloration, while Trichoderma species produced 80 to 86 percent discoloration. The results indicate that Graphium species are the primary stain fungi on Douglas-fir sapwood, however, other species were also capable of colonizing this material. Title: Fungal colonization of Douglas-fir sapwood Author: Kang, Sung-Mo The fungi that cause mold and stain of freshly sawn lumber result in millions of dollars in losses to the forest products industry. Stain and mold are typically prevented by either kiln drying or by application of a topical fungicide. While these treatments are effective, kiln drying is costly and many mills object to use of chemicals. One alternative to conventional stain prevention is biological control. One problem with this approach on western wood species such as Douglas-fir is the lack of information on the target stain and mold fungi that colonize the sapwood of this species. The fungi colonizing freshly sawn Douglas-fir sapwood were isolated and identified by culturing lumber obtained from 4 different locations in the Willamette Valley in western Oregon using regular, streptomycin amended or streptomycin/cycloheximide amended malt extract agar. The ability of each taxa to cause discoloration was evaluated in a laboratory discoloration test. A total of 547 fungi were isolated from Douglas-fir sapwood, representing 24 genera and 45 species. Graphium species were the most frequently isolated fungi, representing 17.4 percent of all isolates. Most of these isolates were considered as anamorphs of Ophiostoma piceae. Other frequently isolated sapstaining fungi included Cephaloascus fragrans, Aureobasidium pullulans, Rhinocladiella cellaris, Cladosporium cladosporioides and Scytalidium lignicola. Molds, primary Penicillium and Trichoderma species, were frequently isolated, and may represent potential biological control organisms or competitors of biological control organisms because of their antagonistic characteristics. Many fungal species of unknown biological significance were also isolated from Douglas-fir sapwood, and their roles in the stain development merit further study. Media and lumber source both affected the fiingal flora isolated. Among stain fungi, Graphium species exclusively occurred on cycloheximide amended media. There was also close relationship between the degree of fungal colonization and the length of time after the lumber was cut. The degree of discoloration exceeded 70 percent in all Graphium species. Cephaloascus fragrans, Aureobasidium pullulans, Rhinocladiella cellaris, Cladosporium cladosporioides, Scytalidium lignicola and Thysanophora penicillioides also produced extensive staining of Douglas-fir sapwood. Mold isolates also caused discoloration of Douglas-fir sapwood wafers, although their discoloration could be easily removed. All Penicillium species produced over 90 percent discoloration, while Trichoderma species produced 80 to 86 percent discoloration. The results indicate that Graphium species are the primary stain fungi on Douglas-fir sapwood, however, other species were also capable of colonizing this material. Close

• 116. [Article] Biomass production and water use of common plant species in Owens Valley, California, USA

  This study evaluated biomass production, water-use efficiency (WUE), biomass allocation, and water use characteristics of common plant species in Owens Valley, California, USA. The species studied were ...

  Citation × Citation Citation Abstract Copy Title: Biomass production and water use of common plant species in Owens Valley, California, USA Author: Evans, Tracie L. This study evaluated biomass production, water-use efficiency (WUE), biomass allocation, and water use characteristics of common plant species in Owens Valley, California, USA. The species studied were the grasses Distichlis spicata, Leymus triticoides, and Sporobolus airoides, the forbs Glycyrrhiza lepidota, Juncus arcticus, and Salsola tragus (annual), the desert shrubs Artemisia tridentata, Atriplex confertifolia, and Ericameria nauseosa, and the riparian shrub Salix exigua. Plants of each species were established and grown in 2.4 m X 2.4 m plots in a common garden since 2005. Our first experiment was conducted in 2009 and 2010 and included four monthly summer water treatments: control (no additional water), low (1.3 cm), medium (2.6 cm) and high (3.9 cm). Biomass production and WUE (the amount of water that a plant uses to produce a unit of biomass) were lower in 2009 than in 2010. Water-use efficiency of grasses increased with increasing water application in 2009 but decreased with increasing water application in 2010. The difference between years was attributed to the difference in timing of natural precipitation with higher spring precipitation in 2010. Biomass production and WUE of desert shrubs were not significantly affected by water treatments. Water-use efficiency varied by species; some desert shrubs and the annual S. tragus were 13 times more efficient than the riparian S. exigua. Total standing crop and root-to-shoot ratio (RSR) varied by species, but not by watering treatments. Although in general desert shrubs had higher standing crop than herbaceous species, the grass S. airoides had the highest standing crop overall. Graminoids had much higher RSR (3 to 6) than the shrubs did (< 1). Our second experiment was conducted in 2010 using the experimental setting of the first experiment with the objective of determining soil water use and depth of soil water extraction by species. Three monthly watering treatments were applied during the summer months: low (1.3 cm), medium (2.6 cm), and high (3.9 cm). Plant water use was determined by calculating soil water depletion during irrigation cycles using time domain reflectometry (TDR) at two depths (0 - 25 cm and 0 - 50 cm) in vegetated plots. Evaporation was also obtained by water depletion on bare ground plots and subtracted from evapotranspiration to calculate water use. Water use varied by species; those with shallow, fibrous, and rhizomatous root systems such as J. arcticus and L. triticoides had higher water use than shrubs, including the riparian S. exigua. The ratio of deep water (25 - 50 cm) to shallow water (0 - 25 cm) use was 19 to 21 in desert shrubs and 1 to 2 in herbaceous species, indicating that shrubs may be more dependent on groundwater that shallow-rooted species such as grasses. In general, we observed large variability in biomass production, water-use efficiency, biomass allocation, and water-use characteristics among the typical plants of the Owens Valley, which should be considered in land and water management decisions. A potential increase in summer precipitation in the area might favor higher water utilization and higher production of shallow-rooted, high RSR plants such as grasses in detriment of desert shrubs. Title: Biomass production and water use of common plant species in Owens Valley, California, USA Author: Evans, Tracie L. This study evaluated biomass production, water-use efficiency (WUE), biomass allocation, and water use characteristics of common plant species in Owens Valley, California, USA. The species studied were the grasses Distichlis spicata, Leymus triticoides, and Sporobolus airoides, the forbs Glycyrrhiza lepidota, Juncus arcticus, and Salsola tragus (annual), the desert shrubs Artemisia tridentata, Atriplex confertifolia, and Ericameria nauseosa, and the riparian shrub Salix exigua. Plants of each species were established and grown in 2.4 m X 2.4 m plots in a common garden since 2005. Our first experiment was conducted in 2009 and 2010 and included four monthly summer water treatments: control (no additional water), low (1.3 cm), medium (2.6 cm) and high (3.9 cm). Biomass production and WUE (the amount of water that a plant uses to produce a unit of biomass) were lower in 2009 than in 2010. Water-use efficiency of grasses increased with increasing water application in 2009 but decreased with increasing water application in 2010. The difference between years was attributed to the difference in timing of natural precipitation with higher spring precipitation in 2010. Biomass production and WUE of desert shrubs were not significantly affected by water treatments. Water-use efficiency varied by species; some desert shrubs and the annual S. tragus were 13 times more efficient than the riparian S. exigua. Total standing crop and root-to-shoot ratio (RSR) varied by species, but not by watering treatments. Although in general desert shrubs had higher standing crop than herbaceous species, the grass S. airoides had the highest standing crop overall. Graminoids had much higher RSR (3 to 6) than the shrubs did (< 1). Our second experiment was conducted in 2010 using the experimental setting of the first experiment with the objective of determining soil water use and depth of soil water extraction by species. Three monthly watering treatments were applied during the summer months: low (1.3 cm), medium (2.6 cm), and high (3.9 cm). Plant water use was determined by calculating soil water depletion during irrigation cycles using time domain reflectometry (TDR) at two depths (0 - 25 cm and 0 - 50 cm) in vegetated plots. Evaporation was also obtained by water depletion on bare ground plots and subtracted from evapotranspiration to calculate water use. Water use varied by species; those with shallow, fibrous, and rhizomatous root systems such as J. arcticus and L. triticoides had higher water use than shrubs, including the riparian S. exigua. The ratio of deep water (25 - 50 cm) to shallow water (0 - 25 cm) use was 19 to 21 in desert shrubs and 1 to 2 in herbaceous species, indicating that shrubs may be more dependent on groundwater that shallow-rooted species such as grasses. In general, we observed large variability in biomass production, water-use efficiency, biomass allocation, and water-use characteristics among the typical plants of the Owens Valley, which should be considered in land and water management decisions. A potential increase in summer precipitation in the area might favor higher water utilization and higher production of shallow-rooted, high RSR plants such as grasses in detriment of desert shrubs. Close

• 117. [Article] Coarse woody debris in forest regions of Russia

  To assess regional stores of coarse woody debris (CWD) in seven major forest regions of Russia, we combined data collected as part of the routine forest inventory with measurements in 1044 sample plots ...

  Citation × Citation Citation Abstract Copy Title: Coarse woody debris in forest regions of Russia Author: Harmon, Mark E., Protasov, Nikolai A., Kukuev, Yuri A., Povarov, Ewgeni D., Treyfeld, Rudolf F., Spycher, Gody, Kresnov, Vladimir G., Kashpor, Nikolai N., Yatskov, Mikhail, Krankina, Olga N., Skudin, Viktor M. To assess regional stores of coarse woody debris (CWD) in seven major forest regions of Russia, we combined data collected as part of the routine forest inventory with measurements in 1044 sample plots and the results of density sampling of 922 dead trees. The stores of CWD in the western part of Russia (St. Petersburg, Central, Khanty- Mansi, and Novosibirsk regions) were on average lower (14–20 m3/ha or 4.0–5.8 Mg/ha) than in the East Siberian and Far Eastern regions (40–51 m3/ha or 11.0–14.4 Mg/ha). The difference in CWD stores was particularly large between young forests in two western regions (2.4 Mg/ha in St. Petersburg and 3.4 Mg/ha in the Central region) and in the east (20.4–24.4 Mg/ha). This difference is associated with the prevailing disturbance type: clear-cut harvest in western Russia and natural disturbances in the east. Analysis of variance in CWD stores indicates that region, dominant species, forest age group, productivity class, and interactions of these factors explain 87–88% of the total variance and the strongest effects are for age group and region. Lower stores of CWD within the intensively managed forest regions suggest that further expansion of forest use in many regions of Russia may reduce regional stores of CWD and carbon. Title: Coarse woody debris in forest regions of Russia Author: Harmon, Mark E., Protasov, Nikolai A., Kukuev, Yuri A., Povarov, Ewgeni D., Treyfeld, Rudolf F., Spycher, Gody, Kresnov, Vladimir G., Kashpor, Nikolai N., Yatskov, Mikhail, Krankina, Olga N., Skudin, Viktor M. To assess regional stores of coarse woody debris (CWD) in seven major forest regions of Russia, we combined data collected as part of the routine forest inventory with measurements in 1044 sample plots and the results of density sampling of 922 dead trees. The stores of CWD in the western part of Russia (St. Petersburg, Central, Khanty- Mansi, and Novosibirsk regions) were on average lower (14–20 m3/ha or 4.0–5.8 Mg/ha) than in the East Siberian and Far Eastern regions (40–51 m3/ha or 11.0–14.4 Mg/ha). The difference in CWD stores was particularly large between young forests in two western regions (2.4 Mg/ha in St. Petersburg and 3.4 Mg/ha in the Central region) and in the east (20.4–24.4 Mg/ha). This difference is associated with the prevailing disturbance type: clear-cut harvest in western Russia and natural disturbances in the east. Analysis of variance in CWD stores indicates that region, dominant species, forest age group, productivity class, and interactions of these factors explain 87–88% of the total variance and the strongest effects are for age group and region. Lower stores of CWD within the intensively managed forest regions suggest that further expansion of forest use in many regions of Russia may reduce regional stores of CWD and carbon. Close

• 118. [Article] Lactic streptococci and the fruity flavor defect of cheddar cheese

  The tendency for certain single- and mixed-strain lactic starter cultures to develop a fruity and/or fermented off-flavor in ripening Cheddar cheese was traced to certain strains of Streptococcus lactis ...

  Citation × Citation Citation Abstract Copy Title: Lactic streptococci and the fruity flavor defect of cheddar cheese Author: Bodyfelt, F. W. (Floyd W.), 1937- The tendency for certain single- and mixed-strain lactic starter cultures to develop a fruity and/or fermented off-flavor in ripening Cheddar cheese was traced to certain strains of Streptococcus lactis in the starter. A very intense fruity and/or fermented flavor developed in experimental cheeses when one particular S. lactis strain was used as a component microorganism in the starter culture. Contrary to previous implications, strains of Streptococcus diacetilactis did not produce a fruity and/or fermented flavor in experimental cheeses made with starter cultures containing these organisms. Mixed-strain cultures of Streptococcus cremoris were used to produce control cheeses, which did not develop the fruity and/or fermented flavor defect. The starter culture and treatment of the cheese milk were the only variables used in the cheesemaking trials. Results obtained indicate that the specific species and/or strain of lactic streptococci contained in the starter culture affect the flavor score and type of flavor in the resultant cheese, independent of the temperature of the heat treatment or hydrogen peroxide-catalase treatment of cheese milk. There were no apparent correlations between "normal" and "defective" starter cultures for the level of proteolytic activity or production of acetaldehyde or diacetyl to the development of fruity and/or fermented off-flavor in cheeses. Existing procedures for the quantification of acetaldehyde, diacetyl and volatile esters were adapted and modified for determining the concentration of these compounds in cheese curd and ripened cheese. The method of slurry preparation, type of diluent and the pH were factors found to affect the recovery rate for acetaldehyde from cheese. The relative flavor preference for typical experimental cheeses was determined with the aid of a flavor panel. A sample of fermented- unclean cheese received the lowest hedonic flavor score, whereas the flavor score of a slight fruity and/or fermented sample compared favorably with that of the reference sample. Title: Lactic streptococci and the fruity flavor defect of cheddar cheese Author: Bodyfelt, F. W. (Floyd W.), 1937- The tendency for certain single- and mixed-strain lactic starter cultures to develop a fruity and/or fermented off-flavor in ripening Cheddar cheese was traced to certain strains of Streptococcus lactis in the starter. A very intense fruity and/or fermented flavor developed in experimental cheeses when one particular S. lactis strain was used as a component microorganism in the starter culture. Contrary to previous implications, strains of Streptococcus diacetilactis did not produce a fruity and/or fermented flavor in experimental cheeses made with starter cultures containing these organisms. Mixed-strain cultures of Streptococcus cremoris were used to produce control cheeses, which did not develop the fruity and/or fermented flavor defect. The starter culture and treatment of the cheese milk were the only variables used in the cheesemaking trials. Results obtained indicate that the specific species and/or strain of lactic streptococci contained in the starter culture affect the flavor score and type of flavor in the resultant cheese, independent of the temperature of the heat treatment or hydrogen peroxide-catalase treatment of cheese milk. There were no apparent correlations between "normal" and "defective" starter cultures for the level of proteolytic activity or production of acetaldehyde or diacetyl to the development of fruity and/or fermented off-flavor in cheeses. Existing procedures for the quantification of acetaldehyde, diacetyl and volatile esters were adapted and modified for determining the concentration of these compounds in cheese curd and ripened cheese. The method of slurry preparation, type of diluent and the pH were factors found to affect the recovery rate for acetaldehyde from cheese. The relative flavor preference for typical experimental cheeses was determined with the aid of a flavor panel. A sample of fermented- unclean cheese received the lowest hedonic flavor score, whereas the flavor score of a slight fruity and/or fermented sample compared favorably with that of the reference sample. Close

• 119. [Article] Immunohistochemistry Studies of Tumor Necrosis Factor Αlpha and Interferon Gamma Expression in Pseudocapillaria tomentosa Infected and Uninfected Zebrafish

  Tumor necrosis factor alpha (TNF α) and interferon gamma (IFN γ) were initially recognized as inflammatory mediators produced by immune cells in response to infectious agents or foreign material. (1,5) ...

  Citation × Citation Citation Abstract Copy Title: Immunohistochemistry Studies of Tumor Necrosis Factor Αlpha and Interferon Gamma Expression in Pseudocapillaria tomentosa Infected and Uninfected Zebrafish Author: Lo, Lalee C. Tumor necrosis factor alpha (TNF α) and interferon gamma (IFN γ) were initially recognized as inflammatory mediators produced by immune cells in response to infectious agents or foreign material. (1,5) However, over the past decade much research in mammalian species has indicated that these proteins also play key roles in development and homeostasis of many tissues such as adipose tissue and endocrine islets of pancreas (2,3,12). Our goal was to determine whether the levels of these mediators were elevated in tissues of zebrafish following infection with intestinal nematodes. We examined protein expression for these mediators in whole histologic sections of zebrafish using immunohistochemistry applied to uninfected fish and fish infected with the intestinal nematode Pseudocapillaria tomentosa. Fish were sampled for histologic study at selected time points following infection with the nematodes. We utilized commercially available antibodies to mammalian TNF α and IFN γ and the DAKO Envision Plus Immunohistochemistry polymer system for detection of these proteins in fish tissues. Contrary to our initial hypothesis that parasite infected fish would have increased levels of these inflammatory mediators in tissues, we found no overall increase in these mediators in parasite infected fish using immunohistochemistry at the 12 week post-infection sample point. However, the early 5 week post-infection sample point showed that there was an increase in the levels of these mediators in parasite infected fish. Similar with observations in mammals that these mediators play important roles in tissue development and homeostasis, we found consistent, specific, moderate to strong baseline expression of these mediators in several tissues of zebrafish. In assays conducted at 5 weeks following parasite infection we saw increased levels of TNF α and IFN γ in inflamed skeletal muscle and saw increased TNF α in segments of bowel in which recent inflammation occurred. Title: Immunohistochemistry Studies of Tumor Necrosis Factor Αlpha and Interferon Gamma Expression in Pseudocapillaria tomentosa Infected and Uninfected Zebrafish Author: Lo, Lalee C. Tumor necrosis factor alpha (TNF α) and interferon gamma (IFN γ) were initially recognized as inflammatory mediators produced by immune cells in response to infectious agents or foreign material. (1,5) However, over the past decade much research in mammalian species has indicated that these proteins also play key roles in development and homeostasis of many tissues such as adipose tissue and endocrine islets of pancreas (2,3,12). Our goal was to determine whether the levels of these mediators were elevated in tissues of zebrafish following infection with intestinal nematodes. We examined protein expression for these mediators in whole histologic sections of zebrafish using immunohistochemistry applied to uninfected fish and fish infected with the intestinal nematode Pseudocapillaria tomentosa. Fish were sampled for histologic study at selected time points following infection with the nematodes. We utilized commercially available antibodies to mammalian TNF α and IFN γ and the DAKO Envision Plus Immunohistochemistry polymer system for detection of these proteins in fish tissues. Contrary to our initial hypothesis that parasite infected fish would have increased levels of these inflammatory mediators in tissues, we found no overall increase in these mediators in parasite infected fish using immunohistochemistry at the 12 week post-infection sample point. However, the early 5 week post-infection sample point showed that there was an increase in the levels of these mediators in parasite infected fish. Similar with observations in mammals that these mediators play important roles in tissue development and homeostasis, we found consistent, specific, moderate to strong baseline expression of these mediators in several tissues of zebrafish. In assays conducted at 5 weeks following parasite infection we saw increased levels of TNF α and IFN γ in inflamed skeletal muscle and saw increased TNF α in segments of bowel in which recent inflammation occurred. Close

• 120. [Article] Wet Meadow Plant Associations, Double O Unit, Malheur National Wildlife Refuge, Harney County, Oregon

  Jess Wenick and Chad Karges of Malheur National Wildlife Refuge (MNWR) provided guidance, logistical support, and funding to The Wetlands Conservancy (TWC) for this project. Esther Lev of TWC coordinated ...

  Citation × Citation Citation Abstract Copy Title: Wet Meadow Plant Associations, Double O Unit, Malheur National Wildlife Refuge, Harney County, Oregon Author: Christy, John A. Jess Wenick and Chad Karges of Malheur National Wildlife Refuge (MNWR) provided guidance, logistical support, and funding to The Wetlands Conservancy (TWC) for this project. Esther Lev of TWC coordinated the project and provided guidance as a member of the Ecology Woring Group (EWG). Vegetation sampling was done by Bruce Newhouse, Richard Brainerd, Jess Wenick, and Barry Smith. Title: Wet Meadow Plant Associations, Double O Unit, Malheur National Wildlife Refuge, Harney County, Oregon Author: Christy, John A. Jess Wenick and Chad Karges of Malheur National Wildlife Refuge (MNWR) provided guidance, logistical support, and funding to The Wetlands Conservancy (TWC) for this project. Esther Lev of TWC coordinated the project and provided guidance as a member of the Ecology Woring Group (EWG). Vegetation sampling was done by Bruce Newhouse, Richard Brainerd, Jess Wenick, and Barry Smith. Close