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• 1. [Article] Engineering a Healthier Watershed: Middle School Students Use Engineering Design to Lessen the Impact of Their Campus' Impervious Surfaces on Their Local Watershed

  It is important that students understand not only how their local watershed functions, but also how it is being impacted by impervious surfaces. Additionally, students need experience exploring the scientific ...

  Citation × Citation Citation Abstract Copy Title: Engineering a Healthier Watershed: Middle School Students Use Engineering Design to Lessen the Impact of Their Campus' Impervious Surfaces on Their Local Watershed Author: Gardner, Elizabeth Claire Year: 2015 It is important that students understand not only how their local watershed functions, but also how it is being impacted by impervious surfaces. Additionally, students need experience exploring the scientific and engineering practices that are necessary for a strong STEM background. With this knowledge students can be empowered to tackle this real and local problem using engineering design, a powerful practice gaining momentum and clarity through its prominence in the recent Framework for K-12 Science Education. Twenty classes of suburban sixth-graders participated in a new five-week Watershed Engineering Design Unit taught by their regular science teachers. Students engaged in scientific inquiry to learn about the structure, function, and health of their local watersheds, focusing on the effects of impervious surfaces. In small groups, students used the engineering design process to propose solutions to lessen the impact of runoff from their school campuses. The goal of this evaluation was to determine the effectiveness of the curriculum in terms of student gains in understanding of (1) watershed function, (2) the impact of impervious surfaces, and (3) the engineering design process. To determine the impact of this curriculum on their learning, students took multiple-choice pre- and post-assessments made up of items covering the three categories above. This data was analyzed for statistical significance using a lower-tailed paired sample t-test. All three objectives showed statistically significant learning gains and the results were used to recommend improvements to the curriculum and the assessment instrument for future iterations. Title: Engineering a Healthier Watershed: Middle School Students Use Engineering Design to Lessen the Impact of Their Campus' Impervious Surfaces on Their Local Watershed Author: Gardner, Elizabeth Claire Year: 2015 It is important that students understand not only how their local watershed functions, but also how it is being impacted by impervious surfaces. Additionally, students need experience exploring the scientific and engineering practices that are necessary for a strong STEM background. With this knowledge students can be empowered to tackle this real and local problem using engineering design, a powerful practice gaining momentum and clarity through its prominence in the recent Framework for K-12 Science Education. Twenty classes of suburban sixth-graders participated in a new five-week Watershed Engineering Design Unit taught by their regular science teachers. Students engaged in scientific inquiry to learn about the structure, function, and health of their local watersheds, focusing on the effects of impervious surfaces. In small groups, students used the engineering design process to propose solutions to lessen the impact of runoff from their school campuses. The goal of this evaluation was to determine the effectiveness of the curriculum in terms of student gains in understanding of (1) watershed function, (2) the impact of impervious surfaces, and (3) the engineering design process. To determine the impact of this curriculum on their learning, students took multiple-choice pre- and post-assessments made up of items covering the three categories above. This data was analyzed for statistical significance using a lower-tailed paired sample t-test. All three objectives showed statistically significant learning gains and the results were used to recommend improvements to the curriculum and the assessment instrument for future iterations. Close

• 2. [Article] Assessing Hydrologic and Water Quality Sensitivities to Precipitation Changes, Urban Growth and Land Management Using SWAT

  Precipitation changes and urban growth are two factors altering the state of water quality. Changes in precipitation will alter the amount and timing of flows, and the corresponding sediment and nutrient ...

  Citation × Citation Citation Abstract Copy Title: Assessing Hydrologic and Water Quality Sensitivities to Precipitation Changes, Urban Growth and Land Management Using SWAT Author: Psaris, Alexander Michael Year: 2014 Precipitation changes and urban growth are two factors altering the state of water quality. Changes in precipitation will alter the amount and timing of flows, and the corresponding sediment and nutrient dynamics. Meanwhile, densification associated with urban growth will create more impervious surfaces which will alter sediment and nutrient loadings. Land and water managers often rely on models to develop possible future scenarios and devise management responses to these projected changes. We use the Soil and Water Assessment Tool (SWAT) to assess the sensitivities of stream flow, sediment, and nutrient loads in two urbanizing watersheds in Northwest Oregon, USA to various climate and urbanization scenarios. We evaluate the spatial patterns climate change and urban growth will have on water, sediment and nutrient yields. We also identify critical source areas (CSAs) and investigate how implementation of vegetative filter strips (VFS) could ameliorate the effects of these changes. Our findings suggest that: 1) Water yield is tightly coupled to precipitation. 2) Large increases in winter and spring precipitation provide enough sub-surface storage to increase summertime water yields despite a moderate decrease in summer precipitation. 3) Expansion of urban areas increases surface runoff and has mixed effects on sediment and nutrients. 4) Implementation of VFS reduces pollutant loads helping overall watershed health. This research demonstrates the usefulness of SWAT in facilitating informed land and water management decisions. Title: Assessing Hydrologic and Water Quality Sensitivities to Precipitation Changes, Urban Growth and Land Management Using SWAT Author: Psaris, Alexander Michael Year: 2014 Precipitation changes and urban growth are two factors altering the state of water quality. Changes in precipitation will alter the amount and timing of flows, and the corresponding sediment and nutrient dynamics. Meanwhile, densification associated with urban growth will create more impervious surfaces which will alter sediment and nutrient loadings. Land and water managers often rely on models to develop possible future scenarios and devise management responses to these projected changes. We use the Soil and Water Assessment Tool (SWAT) to assess the sensitivities of stream flow, sediment, and nutrient loads in two urbanizing watersheds in Northwest Oregon, USA to various climate and urbanization scenarios. We evaluate the spatial patterns climate change and urban growth will have on water, sediment and nutrient yields. We also identify critical source areas (CSAs) and investigate how implementation of vegetative filter strips (VFS) could ameliorate the effects of these changes. Our findings suggest that: 1) Water yield is tightly coupled to precipitation. 2) Large increases in winter and spring precipitation provide enough sub-surface storage to increase summertime water yields despite a moderate decrease in summer precipitation. 3) Expansion of urban areas increases surface runoff and has mixed effects on sediment and nutrients. 4) Implementation of VFS reduces pollutant loads helping overall watershed health. This research demonstrates the usefulness of SWAT in facilitating informed land and water management decisions. Close

• 3. [Article] Advances in Aquatic Target Localization with Passive Sonar

  New underwater passive sonar techniques are developed for enhancing target localization capabilities in shallow ocean environments. The ocean surface and the seabed act as acoustic mirrors that reflect ...

  Citation × Citation Citation Abstract Copy Title: Advances in Aquatic Target Localization with Passive Sonar Author: Gebbie, John Thomas Year: 2014 New underwater passive sonar techniques are developed for enhancing target localization capabilities in shallow ocean environments. The ocean surface and the seabed act as acoustic mirrors that reflect sound created by boats or subsurface vehicles, which gives rise to echoes that can be heard by hydrophone receivers (underwater microphones). The goal of this work is to leverage this "multipath" phenomenon in new ways to determine the origin of the sound, and thus the location of the target. However, this is difficult for propeller driven vehicles because the noise they produce is both random and continuous in time, which complicates its measurement and analysis. Further, autonomous underwater vehicles (AUVs) pose additional challenges because very little is known about the sound they generate, and its similarity to that of boats. Existing methods for localizing propeller noise using multiple hydrophones have approached the problem either purely theoretically, or empirically such as by analyzing the interference patterns between multipath arrivals at different frequencies, however little has been published on building localization techniques that directly measure and utilize the time delays between multipath arrivals while simultaneously accounting for relevant environmental parameters. This research develops such techniques through a combination of array beamforming and advanced ray-based modeling that account for variations in bathymetry (seabed topography) as well as variations of the sound speed of the water. The basis for these advances come from several at-sea experiments in which different configurations of passive sonar systems recorded sounds emitted by different types of targets, including small boats and an autonomous underwater vehicle. Ultimately, these contributions may reduce the complexity and cost of passive systems that need to be deployed close to shore, such as for harbor security applications. Further, they also create new possibilities for applying passive sonar in remote ocean regions for tasks such as detecting illegal fishing activity. This dissertation makes three key contributions: 1. Analysis of the aspect-dependent acoustic radiation patterns of an underway autonomous underwater vehicle (AUV) through full-field wave modeling. 2. A two-hydrophone cross-correlation technique that leverages multipath as well as bathymetric variations to estimate the range and bearing of a small boat, supported by a mathematically rigorous performance analysis. 3. A multi-target localization technique based on directly measuring multipath from multiple small surface vessels using a small hydrophone array mounted to the nose of an AUV, which operates by cross-correlating two elevation beams on a single bearing. Title: Advances in Aquatic Target Localization with Passive Sonar Author: Gebbie, John Thomas Year: 2014 New underwater passive sonar techniques are developed for enhancing target localization capabilities in shallow ocean environments. The ocean surface and the seabed act as acoustic mirrors that reflect sound created by boats or subsurface vehicles, which gives rise to echoes that can be heard by hydrophone receivers (underwater microphones). The goal of this work is to leverage this "multipath" phenomenon in new ways to determine the origin of the sound, and thus the location of the target. However, this is difficult for propeller driven vehicles because the noise they produce is both random and continuous in time, which complicates its measurement and analysis. Further, autonomous underwater vehicles (AUVs) pose additional challenges because very little is known about the sound they generate, and its similarity to that of boats. Existing methods for localizing propeller noise using multiple hydrophones have approached the problem either purely theoretically, or empirically such as by analyzing the interference patterns between multipath arrivals at different frequencies, however little has been published on building localization techniques that directly measure and utilize the time delays between multipath arrivals while simultaneously accounting for relevant environmental parameters. This research develops such techniques through a combination of array beamforming and advanced ray-based modeling that account for variations in bathymetry (seabed topography) as well as variations of the sound speed of the water. The basis for these advances come from several at-sea experiments in which different configurations of passive sonar systems recorded sounds emitted by different types of targets, including small boats and an autonomous underwater vehicle. Ultimately, these contributions may reduce the complexity and cost of passive systems that need to be deployed close to shore, such as for harbor security applications. Further, they also create new possibilities for applying passive sonar in remote ocean regions for tasks such as detecting illegal fishing activity. This dissertation makes three key contributions: 1. Analysis of the aspect-dependent acoustic radiation patterns of an underway autonomous underwater vehicle (AUV) through full-field wave modeling. 2. A two-hydrophone cross-correlation technique that leverages multipath as well as bathymetric variations to estimate the range and bearing of a small boat, supported by a mathematically rigorous performance analysis. 3. A multi-target localization technique based on directly measuring multipath from multiple small surface vessels using a small hydrophone array mounted to the nose of an AUV, which operates by cross-correlating two elevation beams on a single bearing. Close

• 4. [Article] The West Tidewater Earthflow, Northern Oregon Coast Range

  The West Tidewater earthflow, one of the largest in Oregon's history, occurred in December of 1994. The earthflow is located approximately 15 km north of Jewel, Oregon near the summit ofthe Northern Oregon ...

  Citation × Citation Citation Abstract Copy Title: The West Tidewater Earthflow, Northern Oregon Coast Range Author: Sanford, Barry A. Year: 2014 The West Tidewater earthflow, one of the largest in Oregon's history, occurred in December of 1994. The earthflow is located approximately 15 km north of Jewel, Oregon near the summit ofthe Northern Oregon Coast Range Mountains. The earthflow is 900 m long and 250 m wide, giving it a surface area of 9 ha, or 22 acres. Volume is 3.5 million m3. The earthflow occurred in low strength, well-bedded, tuffaceous, carbonaceous, micaceous, clay-rich mudstone, and very fine-grained, feldspathic, clay-rich siltstone of the lower Miocene age Northrup Creek Formation. The soil clay fractions contain up to 90% smectite with indications ofhalloysite. This earthflow is a reactivation ofa 650-year-old landslide (C-14 dating of uncovered buried trees). The failure mode is examined using a Janbu slope analysis and includes double wedge failure near the headscarp. High soil pore water pressure is one of the major causes of this slope failure. Rainfall levels for October, November, and December of 1994 were twice the previous five-year average. Present day groundwater level within the basin is less than one meter below ground surface. The earthflow is partially controlled by two faults of regional extent that dissect the basin near the headscarp in NW-SE and NE-SW directions. The Inceptisol soils in the basin remain moist below 20 cm year around. Soil in the basin may have been further weakened due to loss of root strength following timber harvest on the site in 1991. Soil liquid limits range from 42% to 95%, with PI values ranging from 2% to 77%. Soil clay content ranges between 18% and 30%. Direct shear tests on the mudstone and siltstone bedrock in both drained and undrained conditions produced internal friction angles of 14-18°, with cohesion values of 4 - 8 kPa. Back calculation of study area soil strength using the modified Bishop method results in a residual friction angle of 20.7°. The failure mode ofthe earthflow is from the headscarp downward and is modeled using Janbu methods. The study includes a detailed topographic map and a failure analysis of the earthflow basin. Title: The West Tidewater Earthflow, Northern Oregon Coast Range Author: Sanford, Barry A. Year: 2014 The West Tidewater earthflow, one of the largest in Oregon's history, occurred in December of 1994. The earthflow is located approximately 15 km north of Jewel, Oregon near the summit ofthe Northern Oregon Coast Range Mountains. The earthflow is 900 m long and 250 m wide, giving it a surface area of 9 ha, or 22 acres. Volume is 3.5 million m3. The earthflow occurred in low strength, well-bedded, tuffaceous, carbonaceous, micaceous, clay-rich mudstone, and very fine-grained, feldspathic, clay-rich siltstone of the lower Miocene age Northrup Creek Formation. The soil clay fractions contain up to 90% smectite with indications ofhalloysite. This earthflow is a reactivation ofa 650-year-old landslide (C-14 dating of uncovered buried trees). The failure mode is examined using a Janbu slope analysis and includes double wedge failure near the headscarp. High soil pore water pressure is one of the major causes of this slope failure. Rainfall levels for October, November, and December of 1994 were twice the previous five-year average. Present day groundwater level within the basin is less than one meter below ground surface. The earthflow is partially controlled by two faults of regional extent that dissect the basin near the headscarp in NW-SE and NE-SW directions. The Inceptisol soils in the basin remain moist below 20 cm year around. Soil in the basin may have been further weakened due to loss of root strength following timber harvest on the site in 1991. Soil liquid limits range from 42% to 95%, with PI values ranging from 2% to 77%. Soil clay content ranges between 18% and 30%. Direct shear tests on the mudstone and siltstone bedrock in both drained and undrained conditions produced internal friction angles of 14-18°, with cohesion values of 4 - 8 kPa. Back calculation of study area soil strength using the modified Bishop method results in a residual friction angle of 20.7°. The failure mode ofthe earthflow is from the headscarp downward and is modeled using Janbu methods. The study includes a detailed topographic map and a failure analysis of the earthflow basin. Close

• 5. [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

• 6. [Article] 3D Numerical Temperature Model Development and Calibration for Lakes and Reservoirs: A Case Study

  A 3D hydrodynamic and temperature numerical model was developed and calibrated for Lake Chaplain, Washington, USA. The governing equations are the continuity equation, free surface equation, momentum equation, ...

  Citation × Citation Citation Abstract Copy Title: 3D Numerical Temperature Model Development and Calibration for Lakes and Reservoirs: A Case Study Author: Al-Zubaidi, Hussein A. M., Wells, Scott A. Year: 2017 A 3D hydrodynamic and temperature numerical model was developed and calibrated for Lake Chaplain, Washington, USA. The governing equations are the continuity equation, free surface equation, momentum equation, and conservation equation of transport. The model employs the semi-implicit finite difference scheme to solve the governing equations and higher order schemes (QUICK and Quickest) for mass and heat transport in contrast to simpler but more diffusive first order UPWIND scheme. A unique feature of the 3D numerical solution of the model free surface equation is that the solution uses a tri-diagonal matrix form rather than a more common pentadiagonal matrix. The surface heat exchange and turbulence structure were based on the CE-QUAL-W2 model. Comparisons in water surface levels and temperature vertical profiles between model predictions and data were performed using different advective transport schemes. The model matched data with good error statistics. Title: 3D Numerical Temperature Model Development and Calibration for Lakes and Reservoirs: A Case Study Author: Al-Zubaidi, Hussein A. M., Wells, Scott A. Year: 2017 A 3D hydrodynamic and temperature numerical model was developed and calibrated for Lake Chaplain, Washington, USA. The governing equations are the continuity equation, free surface equation, momentum equation, and conservation equation of transport. The model employs the semi-implicit finite difference scheme to solve the governing equations and higher order schemes (QUICK and Quickest) for mass and heat transport in contrast to simpler but more diffusive first order UPWIND scheme. A unique feature of the 3D numerical solution of the model free surface equation is that the solution uses a tri-diagonal matrix form rather than a more common pentadiagonal matrix. The surface heat exchange and turbulence structure were based on the CE-QUAL-W2 model. Comparisons in water surface levels and temperature vertical profiles between model predictions and data were performed using different advective transport schemes. The model matched data with good error statistics. Close

• 7. [Article] Estimation of Surface Water Temperature of the Tigris River System in Iraq

  Monitoring surface water temperatures (Tw) in lakes, rivers, and reservoirs is a key component of environmental management and influences water quality by affecting bio-geo chemical reaction rates, altering ...

  Citation × Citation Citation Abstract Copy Title: Estimation of Surface Water Temperature of the Tigris River System in Iraq Author: Al-Murib, M., Wells, Scott A., Talke, Stefan A. Year: 2017 Monitoring surface water temperatures (Tw) in lakes, rivers, and reservoirs is a key component of environmental management and influences water quality by affecting bio-geo chemical reaction rates, altering the saturation concentration of dissolved oxygen (DO), and influencing the susceptibility of fish to disease. Temperatures in the Tigris River, one of the largest rivers in the Middle East, are influenced by factors such as heat fluxes at the air-water and human activities such as direct discharge of water to the river. However, modeling and management of water temperature is limited by a paucity of in-situ data, which prevents calibration of models. In this study, we infill data gaps by estimating Tw using the thermal bands of both the Landsat 5 TM and Landsat 7 ETM+ sensors. These satellite-based estimates, typically measured once or twice a month with 60-120m resolution, are then used to develop a regression model that relates daily water temperature to daily air temperature and river flow. These estimates are used to define the Tw boundary conditions for a hydrodynamic and water quality model of the Tigris River based on a 2D implementation of the CE-QUAL-W2 (W2) numerical model. Initial results suggest that there is a significant agreement between modeled and remotely estimated data of Tw. Results suggest that short-wave solar radiation is the most important factor that controls seasonal Tw variations. However, anthropogenic influence is observed as a result of return irrigation flows and flows from Tharthar Lake. Title: Estimation of Surface Water Temperature of the Tigris River System in Iraq Author: Al-Murib, M., Wells, Scott A., Talke, Stefan A. Year: 2017 Monitoring surface water temperatures (Tw) in lakes, rivers, and reservoirs is a key component of environmental management and influences water quality by affecting bio-geo chemical reaction rates, altering the saturation concentration of dissolved oxygen (DO), and influencing the susceptibility of fish to disease. Temperatures in the Tigris River, one of the largest rivers in the Middle East, are influenced by factors such as heat fluxes at the air-water and human activities such as direct discharge of water to the river. However, modeling and management of water temperature is limited by a paucity of in-situ data, which prevents calibration of models. In this study, we infill data gaps by estimating Tw using the thermal bands of both the Landsat 5 TM and Landsat 7 ETM+ sensors. These satellite-based estimates, typically measured once or twice a month with 60-120m resolution, are then used to develop a regression model that relates daily water temperature to daily air temperature and river flow. These estimates are used to define the Tw boundary conditions for a hydrodynamic and water quality model of the Tigris River based on a 2D implementation of the CE-QUAL-W2 (W2) numerical model. Initial results suggest that there is a significant agreement between modeled and remotely estimated data of Tw. Results suggest that short-wave solar radiation is the most important factor that controls seasonal Tw variations. However, anthropogenic influence is observed as a result of return irrigation flows and flows from Tharthar Lake. Close

• 8. [Article] Invertebrate Community Composition Across Inundation Regimes and Its Potential to Reduce Plant Stress

  Appreciation of the ecological and economic values associated with healthy salt marshes has led to a recent rise in the number of marshes that are being targeted for restoration by dike removal. The success ...

  Citation × Citation Citation Abstract Copy Title: Invertebrate Community Composition Across Inundation Regimes and Its Potential to Reduce Plant Stress Author: Lawson, Inez Ilicia Year: 2017 Appreciation of the ecological and economic values associated with healthy salt marshes has led to a recent rise in the number of marshes that are being targeted for restoration by dike removal. The success of restoration is often measured by the return of marsh plants, though this overlooks a key component of salt marshes, that of the invertebrate community within marsh sediments. To evaluate the short-term recovery of these invertebrates, sediment cores were collected across an elevational gradient in a recent dike removal marsh, one and two years post removal, and a nearby reference marsh. Abundance, richness and diversity as well as morphospecies community composition were compared across treatment groups (Reference, Removal) and elevation zone (High Marsh, Low Marsh). Morphospecies richness, abundance and diversity were significantly higher in Low Marsh samples than in High Marsh samples, though no statistically significant differences were found across treatments of the same elevation (e.g., Reference Low Marsh versus Removal Low Marsh). Pair-wise ANOSIM results found significant differences between community compositions across treatments, specifically Reference Low Marsh and Removal Low Marsh. The marsh edge, the lowest point of vascular plant growth before transitioning to tide flats, is considered a high stress environment for emergent vegetation. Plant establishment and survival in this low elevation zone is limited by the tolerance to inundation duration and frequency and anoxic sediments. Bioturbation and burrowing by macroinvertebrates increases the surface area exposed to surface water for gas exchange, increasing the depth of the redox potential discontinuity layer. Crabs that make stable, maintained burrows have been shown to increase oxygen penetration into sediment, improving plant productivity. Such crabs are not found in salt marshes of the Pacific Northwest of North America. However, other burrowing invertebrates may have a positive impact on plant health in these areas by reducing abiotic stress due to anoxic sediments, thereby allowing plants to establish and survive lower in the intertidal zone. To assess this potential relationship, study plots of Distichlis spicata were selected at equivalent elevations at the lowest point of plant establishment at the marsh edge. Focal plant rhizomes were severed from upland ramets and assigned an invertebrate abundance treatment based on a visual burrow count surrounding each plant (9 cm diameter). Focal plants were visited monthly from July to September 2016, plant health variables of chlorophyll content and chlorophyll fluorescence (photosynthetic efficiency), and sediment ORP readings were collected. Plant survivorship was significantly higher in plots with invertebrates, 96% of plants in "With Invertebrate" plots and 50% of plants in "No Invertebrates" plots survived the duration of the study. Plant health (chlorophyll content and chlorophyll fluorescence) generally increased with increased invertebrate presence though, not statistically significant. There may be potential for improved plant productivity and resilience to plants at the marsh edge due to invertebrate burrowing activity. This benefit could help mitigate projected losses in plant productivity due to sea level rise, though more research is needed to investigate the mechanism by which these invertebrates confer a health benefit to plants at the marsh edge. Title: Invertebrate Community Composition Across Inundation Regimes and Its Potential to Reduce Plant Stress Author: Lawson, Inez Ilicia Year: 2017 Appreciation of the ecological and economic values associated with healthy salt marshes has led to a recent rise in the number of marshes that are being targeted for restoration by dike removal. The success of restoration is often measured by the return of marsh plants, though this overlooks a key component of salt marshes, that of the invertebrate community within marsh sediments. To evaluate the short-term recovery of these invertebrates, sediment cores were collected across an elevational gradient in a recent dike removal marsh, one and two years post removal, and a nearby reference marsh. Abundance, richness and diversity as well as morphospecies community composition were compared across treatment groups (Reference, Removal) and elevation zone (High Marsh, Low Marsh). Morphospecies richness, abundance and diversity were significantly higher in Low Marsh samples than in High Marsh samples, though no statistically significant differences were found across treatments of the same elevation (e.g., Reference Low Marsh versus Removal Low Marsh). Pair-wise ANOSIM results found significant differences between community compositions across treatments, specifically Reference Low Marsh and Removal Low Marsh. The marsh edge, the lowest point of vascular plant growth before transitioning to tide flats, is considered a high stress environment for emergent vegetation. Plant establishment and survival in this low elevation zone is limited by the tolerance to inundation duration and frequency and anoxic sediments. Bioturbation and burrowing by macroinvertebrates increases the surface area exposed to surface water for gas exchange, increasing the depth of the redox potential discontinuity layer. Crabs that make stable, maintained burrows have been shown to increase oxygen penetration into sediment, improving plant productivity. Such crabs are not found in salt marshes of the Pacific Northwest of North America. However, other burrowing invertebrates may have a positive impact on plant health in these areas by reducing abiotic stress due to anoxic sediments, thereby allowing plants to establish and survive lower in the intertidal zone. To assess this potential relationship, study plots of Distichlis spicata were selected at equivalent elevations at the lowest point of plant establishment at the marsh edge. Focal plant rhizomes were severed from upland ramets and assigned an invertebrate abundance treatment based on a visual burrow count surrounding each plant (9 cm diameter). Focal plants were visited monthly from July to September 2016, plant health variables of chlorophyll content and chlorophyll fluorescence (photosynthetic efficiency), and sediment ORP readings were collected. Plant survivorship was significantly higher in plots with invertebrates, 96% of plants in "With Invertebrate" plots and 50% of plants in "No Invertebrates" plots survived the duration of the study. Plant health (chlorophyll content and chlorophyll fluorescence) generally increased with increased invertebrate presence though, not statistically significant. There may be potential for improved plant productivity and resilience to plants at the marsh edge due to invertebrate burrowing activity. This benefit could help mitigate projected losses in plant productivity due to sea level rise, though more research is needed to investigate the mechanism by which these invertebrates confer a health benefit to plants at the marsh edge. Close

• 9. [Article] A Facile Route to Tailoring Peptide-Stabilized Gold Nanoparticles Using Glutathione as a Synthon

  The preparation of gold nanoparticles (AuNPs) of high purity and stability remains a major challenge for biological applications. This paper reports a simple synthetic strategy to prepare water-soluble ...

  Citation × Citation Citation Abstract Copy Title: A Facile Route to Tailoring Peptide-Stabilized Gold Nanoparticles Using Glutathione as a Synthon Author: Ho Wu, Rosina, Nguyen, Tan P., Marquart, Grant W., Miesen, Thomas J., Mau, Theresa, Mackiewicz, Marilyn R. Year: 2014 The preparation of gold nanoparticles (AuNPs) of high purity and stability remains a major challenge for biological applications. This paper reports a simple synthetic strategy to prepare water-soluble peptide-stabilized AuNPs. Reduced glutathione, a natural tripeptide, was used as a synthon for the growth of two peptide chains directly on the AuNP surface. Both nonpolar (tryptophan and methionine) and polar basic (histidine and dansylated arginine) amino acids were conjugated to the GSH-capped AuNPs. Ultracentrifugation concentrators with polyethersulfone (PES) membranes were used to purify precursor materials in each stage of the multi-step synthesis to minimize side reactions. Thin layer chromatography, transmission electron microscopy, UV-Visible, 1H-NMR, and fluorescence spectroscopies demonstrated that ultracentrifugation produces high purity AuNPs, with narrow polydispersity, and minimal aggregation. More importantly, it allows for more control over the composition of the final ligand structure. Studies under conditions of varying pH and ionic strength revealed that peptide length, charge, and hydrophobicity influence the stability as well as solubility of the peptide-capped AuNPs. The synthetic and purification strategies used provide a facile route for developing a library of tailored biocompatible peptide-stabilized AuNPs for biomedical applications. Title: A Facile Route to Tailoring Peptide-Stabilized Gold Nanoparticles Using Glutathione as a Synthon Author: Ho Wu, Rosina, Nguyen, Tan P., Marquart, Grant W., Miesen, Thomas J., Mau, Theresa, Mackiewicz, Marilyn R. Year: 2014 The preparation of gold nanoparticles (AuNPs) of high purity and stability remains a major challenge for biological applications. This paper reports a simple synthetic strategy to prepare water-soluble peptide-stabilized AuNPs. Reduced glutathione, a natural tripeptide, was used as a synthon for the growth of two peptide chains directly on the AuNP surface. Both nonpolar (tryptophan and methionine) and polar basic (histidine and dansylated arginine) amino acids were conjugated to the GSH-capped AuNPs. Ultracentrifugation concentrators with polyethersulfone (PES) membranes were used to purify precursor materials in each stage of the multi-step synthesis to minimize side reactions. Thin layer chromatography, transmission electron microscopy, UV-Visible, 1H-NMR, and fluorescence spectroscopies demonstrated that ultracentrifugation produces high purity AuNPs, with narrow polydispersity, and minimal aggregation. More importantly, it allows for more control over the composition of the final ligand structure. Studies under conditions of varying pH and ionic strength revealed that peptide length, charge, and hydrophobicity influence the stability as well as solubility of the peptide-capped AuNPs. The synthetic and purification strategies used provide a facile route for developing a library of tailored biocompatible peptide-stabilized AuNPs for biomedical applications. Close

• 10. [Article] Assessing a Fluorescence Spectroscopy Method for In-Situ Microbial Drinking Water Quality

  Waterborne disease is a significant contributor to the global burden of disease, in particular among high-risk populations in developing nations. State-of-the-art methods for the enumeration of microbial ...

  Citation × Citation Citation Abstract Copy Title: Assessing a Fluorescence Spectroscopy Method for In-Situ Microbial Drinking Water Quality Author: Sharpe, Taylor Jeffery Year: 2017 Waterborne disease is a significant contributor to the global burden of disease, in particular among high-risk populations in developing nations. State-of-the-art methods for the enumeration of microbial pathogens in drinking water sources have important limitations, including high initial cost, 24-48 hour delays in results, high staffing and facility requirements, and training requirements which all become especially problematic in the developing nation context. A number of alternative approaches to microbial water quality testing have been proposed, with the goal of decreasing the required testing time, decreasing overall costs, leveraging appropriate technology approaches, or improving sensitivity or specificity of the water quality testing method. One approach that may offer solutions to some of these limitations involves the deployment of sensor networks using fluorescent spectroscopy to detect intrinsic protein fluorescence in water samples as a proxy for microbial activity. In recent years, a number of researchers have found significant and meaningful correlations between indicator bacteria species and the protein fluorescence of drinking water samples. Additionally, advances in the semiconductor industry could be used to drive down the cost of such sensors. This technology may also be extensible to other water quality parameters, including dissolved organic matter or the presence of fluorescent pollutants. In this thesis, a literature review describes the fundamentals of fluorescence spectroscopy, historical and recent work regarding the fluorescence of the amino acid tryptophan and associated bacterial fluorescence, possible mechanisms for this association, and potential applications of this technology for drinking water quality monitoring and waste water process control. Extensibility of the technology is also discussed. Next, experimental methodology in reproduction of similar results is described. Samples were taken from seven (7) surface water sources and tested using membrane filtration and an off-the-shelf fluorescence spectrometer to help examine the association between the presence of indicator bacteria and the tryptophan fluorescence of the water sample. The results, showing an association of R2 = 0.560, are compared to the results of recent similar experiments. Finally, two prototypes are described, including their design requirements and data from prototype testing. The results of the testing are briefly discussed, and next steps are outlined with the goal of developing a low-cost, in-situ microbial water quality sensor using fluorescence spectroscopy principles. Title: Assessing a Fluorescence Spectroscopy Method for In-Situ Microbial Drinking Water Quality Author: Sharpe, Taylor Jeffery Year: 2017 Waterborne disease is a significant contributor to the global burden of disease, in particular among high-risk populations in developing nations. State-of-the-art methods for the enumeration of microbial pathogens in drinking water sources have important limitations, including high initial cost, 24-48 hour delays in results, high staffing and facility requirements, and training requirements which all become especially problematic in the developing nation context. A number of alternative approaches to microbial water quality testing have been proposed, with the goal of decreasing the required testing time, decreasing overall costs, leveraging appropriate technology approaches, or improving sensitivity or specificity of the water quality testing method. One approach that may offer solutions to some of these limitations involves the deployment of sensor networks using fluorescent spectroscopy to detect intrinsic protein fluorescence in water samples as a proxy for microbial activity. In recent years, a number of researchers have found significant and meaningful correlations between indicator bacteria species and the protein fluorescence of drinking water samples. Additionally, advances in the semiconductor industry could be used to drive down the cost of such sensors. This technology may also be extensible to other water quality parameters, including dissolved organic matter or the presence of fluorescent pollutants. In this thesis, a literature review describes the fundamentals of fluorescence spectroscopy, historical and recent work regarding the fluorescence of the amino acid tryptophan and associated bacterial fluorescence, possible mechanisms for this association, and potential applications of this technology for drinking water quality monitoring and waste water process control. Extensibility of the technology is also discussed. Next, experimental methodology in reproduction of similar results is described. Samples were taken from seven (7) surface water sources and tested using membrane filtration and an off-the-shelf fluorescence spectrometer to help examine the association between the presence of indicator bacteria and the tryptophan fluorescence of the water sample. The results, showing an association of R2 = 0.560, are compared to the results of recent similar experiments. Finally, two prototypes are described, including their design requirements and data from prototype testing. The results of the testing are briefly discussed, and next steps are outlined with the goal of developing a low-cost, in-situ microbial water quality sensor using fluorescence spectroscopy principles. Close