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• 1. [Article] Modeling the Impact of Water Quality and Food Web Structure on Bull Trout in Two Washington Reservoirs

  Mechanistic models of the hydrodynamics and water quality were developed for Lake Kachess and Lake Keechelus in the Yakima River basin of Eastern Washington. These models were coupled to a fish bioenergetics ...

  Citation × Citation Citation Abstract Copy Title: Modeling the Impact of Water Quality and Food Web Structure on Bull Trout in Two Washington Reservoirs Author: Berger, Chris J., Wells, Scott A. Year: 2017 Mechanistic models of the hydrodynamics and water quality were developed for Lake Kachess and Lake Keechelus in the Yakima River basin of Eastern Washington. These models were coupled to a fish bioenergetics model and used to explore management strategies to improve water quality in the reservoirs affecting kokanee production. The models were also applied to evaluate the impacts of the proposed implementation of the Kachess Drought Relief Pumping Plant (KDRPP) projects. The public domain model, CEQUAL-W2 Version 4 (Cole and Wells, 2016) was adapted to model the reservoirs. CEQUAL-W2 is a 2-dimensional (longitudinal-vertical) hydrodynamic and water quality model capable of predicting water surface, velocity, temperature, nutrients, multiple algae, zooplankton, periphyton, and macrophyte species, fish bioenergetics, sediment diagenesis, dissolved oxygen, pH, alkalinity, multiple CBOD groups, multiple suspended solids groups, multiple generic constituents (such as tracer, bacteria, toxics), and multiple organic matter groups, both dissolved and particulate. The model is set up to predict these state variables at longitudinal segments and vertical layers. Comparisons of field data to model predictions were made for water level, temperature, NH4-N, NO3-N, PO4-P, total N, Total P, total organic carbon, alkalinity, zooplankton, pH, chlorophyll a, and dissolved oxygen at multiple reservoir sites at various depths. Title: Modeling the Impact of Water Quality and Food Web Structure on Bull Trout in Two Washington Reservoirs Author: Berger, Chris J., Wells, Scott A. Year: 2017 Mechanistic models of the hydrodynamics and water quality were developed for Lake Kachess and Lake Keechelus in the Yakima River basin of Eastern Washington. These models were coupled to a fish bioenergetics model and used to explore management strategies to improve water quality in the reservoirs affecting kokanee production. The models were also applied to evaluate the impacts of the proposed implementation of the Kachess Drought Relief Pumping Plant (KDRPP) projects. The public domain model, CEQUAL-W2 Version 4 (Cole and Wells, 2016) was adapted to model the reservoirs. CEQUAL-W2 is a 2-dimensional (longitudinal-vertical) hydrodynamic and water quality model capable of predicting water surface, velocity, temperature, nutrients, multiple algae, zooplankton, periphyton, and macrophyte species, fish bioenergetics, sediment diagenesis, dissolved oxygen, pH, alkalinity, multiple CBOD groups, multiple suspended solids groups, multiple generic constituents (such as tracer, bacteria, toxics), and multiple organic matter groups, both dissolved and particulate. The model is set up to predict these state variables at longitudinal segments and vertical layers. Comparisons of field data to model predictions were made for water level, temperature, NH4-N, NO3-N, PO4-P, total N, Total P, total organic carbon, alkalinity, zooplankton, pH, chlorophyll a, and dissolved oxygen at multiple reservoir sites at various depths. Close

• 2. [Article] An Analysis of Vegetation Recovery following Dam Removal at Hemlock Recreation Site, Washington

  Dam removals are becoming increasingly common as dams reach their life expectancy and face costly upgrades associated with relicensing. Though removal is often viewed as a success in terms of ecological ...

  Citation × Citation Citation Abstract Copy Title: An Analysis of Vegetation Recovery following Dam Removal at Hemlock Recreation Site, Washington Author: Ramsey, Greer Stewart Year: 2014 Dam removals are becoming increasingly common as dams reach their life expectancy and face costly upgrades associated with relicensing. Though removal is often viewed as a success in terms of ecological restoration, it also represents a major disturbance to an area. Previous research has shown that native species do not survive as well at these disturbed sites, and invasive species often dominate. This study examines the vegetation response in the drained reservoir area after the removal of Hemlock Dam on Trout Creek, a tributary to the Wind River in southern Washington. Transects were established and quadrats were sampled to determine the plant classifications and cover of vegetation and to examine possible correlations between environmental variables and the spatial distribution of plant classification groups. Sampling took place in the third and fourth years following dam removal, and the data was analyzed to determine significant changes and relationships. The results of this study showed that the site was dominated by a volunteer native forb Lotus purshianus (Spanish clover) and a planted native tree Alnus rubra (red alder). Most of the other species found were native volunteer forbs and grasses characteristic of early succession in this region. Both invasive species and planted species, with the exception of Alnus rubra, had low canopy covers. There was a significant increase in native plant canopy cover, as well as total canopy cover, from 2012 to 2013. There were also significant relationships between plant classification groups and environmental variables, including soil infiltration, elevation, and distance from stream. This study will help inform resource managers about the kinds of plants that will volunteer after dam removals and the possible success of re-vegetation projects. Title: An Analysis of Vegetation Recovery following Dam Removal at Hemlock Recreation Site, Washington Author: Ramsey, Greer Stewart Year: 2014 Dam removals are becoming increasingly common as dams reach their life expectancy and face costly upgrades associated with relicensing. Though removal is often viewed as a success in terms of ecological restoration, it also represents a major disturbance to an area. Previous research has shown that native species do not survive as well at these disturbed sites, and invasive species often dominate. This study examines the vegetation response in the drained reservoir area after the removal of Hemlock Dam on Trout Creek, a tributary to the Wind River in southern Washington. Transects were established and quadrats were sampled to determine the plant classifications and cover of vegetation and to examine possible correlations between environmental variables and the spatial distribution of plant classification groups. Sampling took place in the third and fourth years following dam removal, and the data was analyzed to determine significant changes and relationships. The results of this study showed that the site was dominated by a volunteer native forb Lotus purshianus (Spanish clover) and a planted native tree Alnus rubra (red alder). Most of the other species found were native volunteer forbs and grasses characteristic of early succession in this region. Both invasive species and planted species, with the exception of Alnus rubra, had low canopy covers. There was a significant increase in native plant canopy cover, as well as total canopy cover, from 2012 to 2013. There were also significant relationships between plant classification groups and environmental variables, including soil infiltration, elevation, and distance from stream. This study will help inform resource managers about the kinds of plants that will volunteer after dam removals and the possible success of re-vegetation projects. Close

• 3. [Article] Investigating the Effects of 17α-Ethynylestradiol on Mitochondrial Genome Stability

  Environmental toxicants are ubiquitous throughout the environment as a result of human activity. Among these toxicants, environmental estrogens are a category of particular concern due to their environmental ...

  Citation × Citation Citation Abstract Copy Title: Investigating the Effects of 17α-Ethynylestradiol on Mitochondrial Genome Stability Author: Chivers, Alicia M. Year: 2016 Environmental toxicants are ubiquitous throughout the environment as a result of human activity. Among these toxicants, environmental estrogens are a category of particular concern due to their environmental prevalence and potency in altering reproductive traits. While many studies have addressed the detrimental effects of environmental estrogens on both aquatic and terrestrial organisms, few have analyzed the potential for these compounds to alter mitochondrial function. Mitochondria are the primary energy-generating system for all eukaryotic life, supporting all aspects of development, metabolism, and growth. Each cell within the body contains many mitochondria which in turn contain multiple copies of their own DNA genome, mitochondrial DNA (mtDNA). Mutations in mtDNA are responsible for a wide range of human diseases such as metabolic syndromes, cancers, and obesity. Among these mitochondrial diseases many are characterized by increased levels of heteroplasmy, multiple mitochondrial DNA haplotypes within an individual. Increased heteroplasmy can alter normal mitochondrial function and influence disease initiation and progression. To date, no studies have investigated the effects of synthetic estrogens on mitochondrial genome stability. Synthetic estrogens have the capacity to bind to estrogen receptors and initiate estrogenic responses through translocation into the mitochondrion. Despite our knowledge about the relationship of heteroplasmy and disease, we still do not have a complete grasp of the mechanisms of heteroplasmic induction. Here we report our analysis of the effects of 17α-ethynylestradiol (EE2) exposure in three studies to investigate its effect on mitochondrial genome stability. Data analysis reveals a statistically significant relationship between EE2 exposure and increased heteroplasmic frequency. Title: Investigating the Effects of 17α-Ethynylestradiol on Mitochondrial Genome Stability Author: Chivers, Alicia M. Year: 2016 Environmental toxicants are ubiquitous throughout the environment as a result of human activity. Among these toxicants, environmental estrogens are a category of particular concern due to their environmental prevalence and potency in altering reproductive traits. While many studies have addressed the detrimental effects of environmental estrogens on both aquatic and terrestrial organisms, few have analyzed the potential for these compounds to alter mitochondrial function. Mitochondria are the primary energy-generating system for all eukaryotic life, supporting all aspects of development, metabolism, and growth. Each cell within the body contains many mitochondria which in turn contain multiple copies of their own DNA genome, mitochondrial DNA (mtDNA). Mutations in mtDNA are responsible for a wide range of human diseases such as metabolic syndromes, cancers, and obesity. Among these mitochondrial diseases many are characterized by increased levels of heteroplasmy, multiple mitochondrial DNA haplotypes within an individual. Increased heteroplasmy can alter normal mitochondrial function and influence disease initiation and progression. To date, no studies have investigated the effects of synthetic estrogens on mitochondrial genome stability. Synthetic estrogens have the capacity to bind to estrogen receptors and initiate estrogenic responses through translocation into the mitochondrion. Despite our knowledge about the relationship of heteroplasmy and disease, we still do not have a complete grasp of the mechanisms of heteroplasmic induction. Here we report our analysis of the effects of 17α-ethynylestradiol (EE2) exposure in three studies to investigate its effect on mitochondrial genome stability. Data analysis reveals a statistically significant relationship between EE2 exposure and increased heteroplasmic frequency. Close

• 4. [Article] Understanding the Importance of Intermittently Fragmented Stream Habitat for Isolated Westslope Cutthroat Trout (<i>Oncorhynchus clarki lewisi</i>) in the Colville National Forest, Washington

  Climate change and anthropogenic effects have vastly reduced Westslope Cutthroat Trout (Oncorhynchus clarki lewisi, WCT) habitat throughout their range, including the Colville National Forest in northeastern ...

  Citation × Citation Citation Abstract Copy Title: Understanding the Importance of Intermittently Fragmented Stream Habitat for Isolated Westslope Cutthroat Trout (<i>Oncorhynchus clarki lewisi</i>) in the Colville National Forest, Washington Author: Carpenter, Forrest Michael Year: 2016 Climate change and anthropogenic effects have vastly reduced Westslope Cutthroat Trout (Oncorhynchus clarki lewisi, WCT) habitat throughout their range, including the Colville National Forest in northeastern Washington where this study was conducted. Many native salmonid populations have declined in abundance since the early 1900s due to a variety of climate- and human-driven forces. Westslope Cutthroat Trout are especially sensitive to habitat loss or degradation and to climate change. Together, climate change, habitat degradation, and non-native salmonid invasions are contributing to increasingly fragmented WCT populations. Ongoing and predicted future warming trends are expected to further fragment these populations and isolate them in headwater stream reaches, with populations in the spatial margins of their distributions facing greater risk. Native salmonid populations are often separated or isolated by natural or artificial upstream migration barriers (i.e., waterfalls, culverts, etc.). Prior to continuing conservation and management actions targeting WCT, it is imperative to understand habitat requirements of this keystone species in fragmented areas. Field survey data were collected in the summer of 2015 on channel geomorphic characteristics and WCT presence/absence in 26 streams located in the Colville National Forest. A clear spatial separation was observed between Eastern Brook Trout (Salvenius fontinalis, EBT) and WCT above four culvert road crossings and the habitat in both of these areas was compared statistically to identify explicit differences. This dataset was also analyzed using logistic regression modeling to determine the best habitat predictors of the presence of isolated WCT populations existing upstream of these crossing. In general, stream habitat in the Middle and South Forks of Mill Creek had low large substrate, high fine sediments, and exhibited pool-riffle channel morphology. Pool habitat supporting isolated WCT was significantly smaller, in terms of volume and surface area, than pool habitat supporting sympatric populations of WCT and EBT, largely due to the headwater nature of channel units supporting isolated WCT populations. Additionally, due to the extreme drought conditions during 2015, stream flow was substantially diminished in the study area causing these reaches to be highly fragmented and largely disconnected from the rest of the stream channel. Fine sediments were generally higher in headwater reaches supporting isolated WCT, including in pools and riffles, which was unexpected, mainly because they exist above sediment delivery points in the longitudinal extent of the system. Logistic regression analysis indicated that the presence of isolated WCT populations was primarily positively associated with an increase in large wood and boulders, and negatively associated with increasing gravel, bedrock, habitat unit length, depth, and width (Significant x2, R2=0.174, misclassification rate = 14.9%, α=0.05). The final model correctly predicted 37.5% of isolated WCT presence observations and 96.5% of the WCT/EBT presence observations significantly better than by chance alone (k=0.81). This model, in fact, may be useful in identifying limited habitat due to the fragmented nature of the channel units supporting IWCT. Large wood and boulders were positively correlated to WCT presence, likely because both are important in the formation of pools and cascades. Channel unit length, width, depth, active channel width as well as gravel and bedrock substrates, were all negatively associated with WCT presence. This suggests that isolated WCT are primarily associated with small headwater cascades with complex shelter, which may provide greater thermal and predation refuge compared to shallow glide or large pool habitats. Future model analysis should include additional habitat variables such as water temperature, stream gradient, and species interactions to strengthen the prediction of Westslope Cutthroat Trout presence. Overall, I concluded that differences in stream habitat above and below blocking culverts are not driving Westslope Cutthroat Trout distributions in the study area due to confounding factors such as the presence of problematic barriers and small sample size. I also conclude that future conservation and management decisions specific to WCT should prioritize complex cascade habitat in headwater stream reaches because of the type and quantity of habitat they may provide, especially during severe drought or low flow conditions. Title: Understanding the Importance of Intermittently Fragmented Stream Habitat for Isolated Westslope Cutthroat Trout (<i>Oncorhynchus clarki lewisi</i>) in the Colville National Forest, Washington Author: Carpenter, Forrest Michael Year: 2016 Climate change and anthropogenic effects have vastly reduced Westslope Cutthroat Trout (Oncorhynchus clarki lewisi, WCT) habitat throughout their range, including the Colville National Forest in northeastern Washington where this study was conducted. Many native salmonid populations have declined in abundance since the early 1900s due to a variety of climate- and human-driven forces. Westslope Cutthroat Trout are especially sensitive to habitat loss or degradation and to climate change. Together, climate change, habitat degradation, and non-native salmonid invasions are contributing to increasingly fragmented WCT populations. Ongoing and predicted future warming trends are expected to further fragment these populations and isolate them in headwater stream reaches, with populations in the spatial margins of their distributions facing greater risk. Native salmonid populations are often separated or isolated by natural or artificial upstream migration barriers (i.e., waterfalls, culverts, etc.). Prior to continuing conservation and management actions targeting WCT, it is imperative to understand habitat requirements of this keystone species in fragmented areas. Field survey data were collected in the summer of 2015 on channel geomorphic characteristics and WCT presence/absence in 26 streams located in the Colville National Forest. A clear spatial separation was observed between Eastern Brook Trout (Salvenius fontinalis, EBT) and WCT above four culvert road crossings and the habitat in both of these areas was compared statistically to identify explicit differences. This dataset was also analyzed using logistic regression modeling to determine the best habitat predictors of the presence of isolated WCT populations existing upstream of these crossing. In general, stream habitat in the Middle and South Forks of Mill Creek had low large substrate, high fine sediments, and exhibited pool-riffle channel morphology. Pool habitat supporting isolated WCT was significantly smaller, in terms of volume and surface area, than pool habitat supporting sympatric populations of WCT and EBT, largely due to the headwater nature of channel units supporting isolated WCT populations. Additionally, due to the extreme drought conditions during 2015, stream flow was substantially diminished in the study area causing these reaches to be highly fragmented and largely disconnected from the rest of the stream channel. Fine sediments were generally higher in headwater reaches supporting isolated WCT, including in pools and riffles, which was unexpected, mainly because they exist above sediment delivery points in the longitudinal extent of the system. Logistic regression analysis indicated that the presence of isolated WCT populations was primarily positively associated with an increase in large wood and boulders, and negatively associated with increasing gravel, bedrock, habitat unit length, depth, and width (Significant x2, R2=0.174, misclassification rate = 14.9%, α=0.05). The final model correctly predicted 37.5% of isolated WCT presence observations and 96.5% of the WCT/EBT presence observations significantly better than by chance alone (k=0.81). This model, in fact, may be useful in identifying limited habitat due to the fragmented nature of the channel units supporting IWCT. Large wood and boulders were positively correlated to WCT presence, likely because both are important in the formation of pools and cascades. Channel unit length, width, depth, active channel width as well as gravel and bedrock substrates, were all negatively associated with WCT presence. This suggests that isolated WCT are primarily associated with small headwater cascades with complex shelter, which may provide greater thermal and predation refuge compared to shallow glide or large pool habitats. Future model analysis should include additional habitat variables such as water temperature, stream gradient, and species interactions to strengthen the prediction of Westslope Cutthroat Trout presence. Overall, I concluded that differences in stream habitat above and below blocking culverts are not driving Westslope Cutthroat Trout distributions in the study area due to confounding factors such as the presence of problematic barriers and small sample size. I also conclude that future conservation and management decisions specific to WCT should prioritize complex cascade habitat in headwater stream reaches because of the type and quantity of habitat they may provide, especially during severe drought or low flow conditions. Close

• 5. [Article] Innovative Approaches for Blue Growth in Finnish Aquaculture

  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: Innovative Approaches for Blue Growth in Finnish Aquaculture Author: Setälä, Jari, Kankainen, Markus, Virtanen, Jarno, Vielma, Jouni, Saarni, Kaija 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: Innovative Approaches for Blue Growth in Finnish Aquaculture Author: Setälä, Jari, Kankainen, Markus, Virtanen, Jarno, Vielma, Jouni, Saarni, Kaija 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

• 6. [Article] PrimeFish: WP3 Supply Chain Relations & Regulation

  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: PrimeFish: WP3 Supply Chain Relations & Regulation Author: Bostock, John, Murray, Francis, Taskov, Dimitar 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: PrimeFish: WP3 Supply Chain Relations & Regulation Author: Bostock, John, Murray, Francis, Taskov, Dimitar 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

• 7. [Article] Trout, Seabass and Seabream Value Chains. An Overview of South Europe

  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: Trout, Seabass and Seabream Value Chains. An Overview of South Europe Author: Valle, Paul S., Mora, Cristina, Santiago, José L., Sogari, Giovanni, Taskov, Dimitar 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: Trout, Seabass and Seabream Value Chains. An Overview of South Europe Author: Valle, Paul S., Mora, Cristina, Santiago, José L., Sogari, Giovanni, Taskov, Dimitar 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

• 8. [Article] A Quantitative Approach to Determine Cardiovascular and Neurodevelopment Risks and Benfits from Methylmercury and Omega 3 Fatty Acids in Fish Consumed in  the Columbia River Basin

  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: A Quantitative Approach to Determine Cardiovascular and Neurodevelopment Risks and Benfits from Methylmercury and Omega 3 Fatty Acids in Fish Consumed in  the Columbia River Basin Author: Kile, Molly, Cusack, Leanne, Harper, Barbara, Harding, Anna, Stone, Dave 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: A Quantitative Approach to Determine Cardiovascular and Neurodevelopment Risks and Benfits from Methylmercury and Omega 3 Fatty Acids in Fish Consumed in  the Columbia River Basin Author: Kile, Molly, Cusack, Leanne, Harper, Barbara, Harding, Anna, Stone, Dave 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

• 9. [Article] Economics of Trout Aquaculture - A New Benchmarking Approach

  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: Economics of Trout Aquaculture - A New Benchmarking Approach Author: Lasner, Tobias, Döring, Ralf, Behrens, Gesine 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: Economics of Trout Aquaculture - A New Benchmarking Approach Author: Lasner, Tobias, Döring, Ralf, Behrens, Gesine 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

• 10. [Article] Massively Parallel Sequencing-Based Analyses of Genome and Protein Function

  The advent of high-throughput DNA and RNA sequencing has made possible the assay of millions of nucleic acid molecules in parallel. This allows functional genomic elements to be identified from background ...

  Citation × Citation Citation Abstract Copy Title: Massively Parallel Sequencing-Based Analyses of Genome and Protein Function Author: Kamps-Hughes, Nicholas Year: 2015 The advent of high-throughput DNA and RNA sequencing has made possible the assay of millions of nucleic acid molecules in parallel. This allows functional genomic elements to be identified from background in single-tube experiments. This dissertation discusses the development of two such functional screens as well as work implementing a third that was previously developed in my thesis laboratory. Restriction-Associated DNA sequencing (RAD-Seq) is a complexity reduction sequencing method that allows the same subset of genomic sequence to be read across multiple samples. Differences in sample collection and data analysis allow manifold applications of RAD-Seq. Here we use RAD-Seq to identify mutant genes responsible for altered phenotypes in Caenorhabditis elegans and to identify hyper-invasive alleles in trout population admixtures. Apart from acquiring genomic sequence data, massively-parallel sequencing can be used for counting applications that quantify activity across a large number of test molecules. This dissertation describes the development of a technique for simultaneously quantifying the activity of a restriction enzyme across all possible DNA substrates by linking digest of a sequenced genome to Illumina-sequencing in an unbiased fashion. Finally, a powerful approach to analyze transcriptional activation is described. This method quantifies output from millions of potential DNA transcriptional enhancers via RNA amplicon sequencing of covalently-linked randomer tags and is used in conjunction with RNA-Seq to provide a mechanistic view of hypoxic gene regulation in Drosophila. This dissertation includes previously published, co-authored material Title: Massively Parallel Sequencing-Based Analyses of Genome and Protein Function Author: Kamps-Hughes, Nicholas Year: 2015 The advent of high-throughput DNA and RNA sequencing has made possible the assay of millions of nucleic acid molecules in parallel. This allows functional genomic elements to be identified from background in single-tube experiments. This dissertation discusses the development of two such functional screens as well as work implementing a third that was previously developed in my thesis laboratory. Restriction-Associated DNA sequencing (RAD-Seq) is a complexity reduction sequencing method that allows the same subset of genomic sequence to be read across multiple samples. Differences in sample collection and data analysis allow manifold applications of RAD-Seq. Here we use RAD-Seq to identify mutant genes responsible for altered phenotypes in Caenorhabditis elegans and to identify hyper-invasive alleles in trout population admixtures. Apart from acquiring genomic sequence data, massively-parallel sequencing can be used for counting applications that quantify activity across a large number of test molecules. This dissertation describes the development of a technique for simultaneously quantifying the activity of a restriction enzyme across all possible DNA substrates by linking digest of a sequenced genome to Illumina-sequencing in an unbiased fashion. Finally, a powerful approach to analyze transcriptional activation is described. This method quantifies output from millions of potential DNA transcriptional enhancers via RNA amplicon sequencing of covalently-linked randomer tags and is used in conjunction with RNA-Seq to provide a mechanistic view of hypoxic gene regulation in Drosophila. This dissertation includes previously published, co-authored material Close