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A large hypoxic zone forms every summer on the Texas-Louisiana Shelf in the northern Gulf of Mexico due to nutrient and freshwater inputs from the Mississippi/Atchafalaya River System. Efforts are underway to reduce the extent of hypoxic conditions through reductions in river nutrient inputs, but the response of hypoxia to such nutrient load reductions is difficult to predict because biological responses are confounded by variability in physical processes. The objective of this study is to identify the major physical model aspects that matter for hypoxia simulation and prediction. In order to do so, we compare three different circulation models (ROMS, FVCOM, and NCOM) implemented for the northern Gulf of Mexico, all coupled to the same simple oxygen model, with observations and against each other. By using a highly simplified oxygen model, we eliminate the potentially confounding effects of a full biogeochemical model and can isolate the effects of physical features. In a systematic assessment, we found that (1) model-to-model differences in bottom water temperatures result in differences in simulated hypoxia because temperature influences the uptake rate of oxygen by the sediments (an important oxygen sink in this system), (2) vertical stratification does not explain model-to-model differences in hypoxic conditions in a straightforward way, and (3) the thickness of the bottom boundary layer, which sets the thickness of the hypoxic layer in all three models, is key to determining the likelihood of a model to generate hypoxic conditions. These results imply that hypoxic area, the commonly used metric in the northern Gulf which ignores hypoxic layer thickness, is insufficient for assessing a model's ability to accurately simulate hypoxia, and that hypoxic volume needs to be considered as well. © 2016. American Geophysical Union. All Rights Reserved.

A large hypoxic zone forms every summer on the Texas-Louisiana Shelf in the northern Gulf of Mexico due to nutrient and freshwater inputs from the Mississippi/Atchafalaya River System. Efforts are underway to reduce the extent of hypoxic conditions through reductions in river nutrient inputs, but the response of hypoxia to such nutrient load reductions is difficult to predict because biological responses are confounded by variability in physical processes. The objective of this study is to identify the major physical model aspects that matter for hypoxia simulation and prediction. In order to do so, we compare three different circulation models (ROMS, FVCOM, and NCOM) implemented for the northern Gulf of Mexico, all coupled to the same simple oxygen model, with observations and against each other. By using a highly simplified oxygen model, we eliminate the potentially confounding effects of a full biogeochemical model and can isolate the effects of physical features. In a systematic assessment, we found that (1) model-to-model differences in bottom water temperatures result in differences in simulated hypoxia because temperature influences the uptake rate of oxygen by the sediments (an important oxygen sink in this system), (2) vertical stratification does not explain model-to-model differences in hypoxic conditions in a straightforward way, and (3) the thickness of the bottom boundary layer, which sets the thickness of the hypoxic layer in all three models, is key to determining the likelihood of a model to generate hypoxic conditions. These results imply that hypoxic area, the commonly used metric in the northern Gulf which ignores hypoxic layer thickness, is insufficient for assessing a model's ability to accurately simulate hypoxia, and that hypoxic volume needs to be considered as well. © 2016. American Geophysical Union. All Rights Reserved.

A large hypoxic zone forms every summer on the Texas-Louisiana Shelf in the northern Gulf of Mexico due to nutrient and freshwater inputs from the Mississippi/Atchafalaya River System. Efforts are underway to reduce the extent of hypoxic conditions through reductions in river nutrient inputs, but the response of hypoxia to such nutrient load reductions is difficult to predict because biological responses are confounded by variability in physical processes. The objective of this study is to identify the major physical model aspects that matter for hypoxia simulation and prediction. In order to do so, we compare three different circulation models (ROMS, FVCOM, and NCOM) implemented for the northern Gulf of Mexico, all coupled to the same simple oxygen model, with observations and against each other. By using a highly simplified oxygen model, we eliminate the potentially confounding effects of a full biogeochemical model and can isolate the effects of physical features. In a systematic assessment, we found that (1) model-to-model differences in bottom water temperatures result in differences in simulated hypoxia because temperature influences the uptake rate of oxygen by the sediments (an important oxygen sink in this system), (2) vertical stratification does not explain model-to-model differences in hypoxic conditions in a straightforward way, and (3) the thickness of the bottom boundary layer, which sets the thickness of the hypoxic layer in all three models, is key to determining the likelihood of a model to generate hypoxic conditions. These results imply that hypoxic area, the commonly used metric in the northern Gulf which ignores hypoxic layer thickness, is insufficient for assessing a model's ability to accurately simulate hypoxia, and that hypoxic volume needs to be considered as well. © 2016. American Geophysical Union. All Rights Reserved.

We examined bacterioplankton abundance and metabolic characteristics in northern San Francisco Bay, California during spring and summer 1996 at three sites: Central Bay, Suisun Bay and the Sacramento River. These sites spanned a salinity gradient from marine to freshwater, and sampling occurred during a period of seasonally declining river flow. The microbial measures included radio-labeled amino acid uptake (L-leucine, L-proline, L-serine), ectoenzyme activity (aminopeptidase and 13-D-glucosidase), and bacterial abundance using lum filters to separate free from particle-associated bacteria. We observed a seasonal decline in all bacterial metabolic measures at all stations, suggesting that a system-wide variable may be important in controlling bacterial activity. One such variable is freshwater flow into the Bay (as a proxy for organic matter flux), which positively covaried with all metabolic measures. We also observed a sharp decline in particle-associated bacteria in Suisun Bay and the Sacramento River between July and August. This may be due to combined effects of declining nutritive value of the aging particles, and increasing grazing pressure by benthic filter feeders. Aminopeptidase activity was positively related to increasing salinity and 13-D-glucosidase was negatively related to increasing salinity, indicating a gradient in the relative quality of organic matter from carbohydrate-rich riverine to protein-rich oceanic materiaL Overall, Suisun Bay had the highest proportion of particle-associated bacteria (avg. 49%), followed by Sacramento River (avg, 36%) and Central Bay (avg. 11%), Particles were the sites of enhanced ectoenzyme activity, but not amino acid incorporation. Therefore bacteria may be actively dissolving the particulate organic matter but their growth rates are not significantly enhanced on particles.

We examined bacterioplankton abundance and metabolic characteristics in northern San Francisco Bay, California during spring and summer 1996 at three sites: Central Bay, Suisun Bay and the Sacramento River. These sites spanned a salinity gradient from marine to freshwater, and sampling occurred during a period of seasonally declining river flow. The microbial measures included radio-labeled amino acid uptake (L-leucine, L-proline, L-serine), ectoenzyme activity (aminopeptidase and 13-D-glucosidase), and bacterial abundance using lum filters to separate free from particle-associated bacteria. We observed a seasonal decline in all bacterial metabolic measures at all stations, suggesting that a system-wide variable may be important in controlling bacterial activity. One such variable is freshwater flow into the Bay (as a proxy for organic matter flux), which positively covaried with all metabolic measures. We also observed a sharp decline in particle-associated bacteria in Suisun Bay and the Sacramento River between July and August. This may be due to combined effects of declining nutritive value of the aging particles, and increasing grazing pressure by benthic filter feeders. Aminopeptidase activity was positively related to increasing salinity and 13-D-glucosidase was negatively related to increasing salinity, indicating a gradient in the relative quality of organic matter from carbohydrate-rich riverine to protein-rich oceanic materiaL Overall, Suisun Bay had the highest proportion of particle-associated bacteria (avg. 49%), followed by Sacramento River (avg, 36%) and Central Bay (avg. 11%), Particles were the sites of enhanced ectoenzyme activity, but not amino acid incorporation. Therefore bacteria may be actively dissolving the particulate organic matter but their growth rates are not significantly enhanced on particles.

The Louisiana shelf, in the northern Gulf of Mexico, receives large amounts of freshwater and nutrients from the Mississippi-Atchafalaya river system. These river inputs contribute to widespread bottom-water hypoxia every summer. In this study, we use a physical-biogeochemical model that explicitly simulates oxygen sources and sinks on the Louisiana shelf to identify the key mechanisms controlling hypoxia development. First, we validate the model simulation against observed dissolved oxygen concentrations, primary production, water column respiration, and sediment oxygen consumption. In the model simulation, heterotrophy is prevalent in shelf waters throughout the year, except near the mouths of the Mississippi and Atchafalaya rivers, where primary production exceeds respiratory oxygen consumption during June and July. During this time, efflux of oxygen to the atmosphere, driven by photosynthesis and surface warming, becomes a significant oxygen sink. A substantial fraction of primary production occurs below the pycnocline in summer. We investigate whether this primary production below the pycnocline is mitigating the development of hypoxic conditions with the help of a sensitivity experiment where we disable biological processes in the water column (i.e., primary production and water column respiration). With this experiment we show that below-pycnocline primary production reduces the spatial extent of hypoxic bottom waters only slightly. Our results suggest that the combination of physical processes (advection and vertical diffusion) and sediment oxygen consumption largely determine the spatial extent and dynamics of hypoxia on the Louisiana shelf. © Author(s) 2015.

The Louisiana shelf, in the northern Gulf of Mexico, receives large amounts of freshwater and nutrients from the Mississippi-Atchafalaya river system. These river inputs contribute to widespread bottom-water hypoxia every summer. In this study, we use a physical-biogeochemical model that explicitly simulates oxygen sources and sinks on the Louisiana shelf to identify the key mechanisms controlling hypoxia development. First, we validate the model simulation against observed dissolved oxygen concentrations, primary production, water column respiration, and sediment oxygen consumption. In the model simulation, heterotrophy is prevalent in shelf waters throughout the year, except near the mouths of the Mississippi and Atchafalaya rivers, where primary production exceeds respiratory oxygen consumption during June and July. During this time, efflux of oxygen to the atmosphere, driven by photosynthesis and surface warming, becomes a significant oxygen sink. A substantial fraction of primary production occurs below the pycnocline in summer. We investigate whether this primary production below the pycnocline is mitigating the development of hypoxic conditions with the help of a sensitivity experiment where we disable biological processes in the water column (i.e., primary production and water column respiration). With this experiment we show that below-pycnocline primary production reduces the spatial extent of hypoxic bottom waters only slightly. Our results suggest that the combination of physical processes (advection and vertical diffusion) and sediment oxygen consumption largely determine the spatial extent and dynamics of hypoxia on the Louisiana shelf. © Author(s) 2015.

The Louisiana shelf, in the northern Gulf of Mexico, receives large amounts of freshwater and nutrients from the Mississippi-Atchafalaya river system. These river inputs contribute to widespread bottom-water hypoxia every summer. In this study, we use a physical-biogeochemical model that explicitly simulates oxygen sources and sinks on the Louisiana shelf to identify the key mechanisms controlling hypoxia development. First, we validate the model simulation against observed dissolved oxygen concentrations, primary production, water column respiration, and sediment oxygen consumption. In the model simulation, heterotrophy is prevalent in shelf waters throughout the year, except near the mouths of the Mississippi and Atchafalaya rivers, where primary production exceeds respiratory oxygen consumption during June and July. During this time, efflux of oxygen to the atmosphere, driven by photosynthesis and surface warming, becomes a significant oxygen sink. A substantial fraction of primary production occurs below the pycnocline in summer. We investigate whether this primary production below the pycnocline is mitigating the development of hypoxic conditions with the help of a sensitivity experiment where we disable biological processes in the water column (i.e., primary production and water column respiration). With this experiment we show that below-pycnocline primary production reduces the spatial extent of hypoxic bottom waters only slightly. Our results suggest that the combination of physical processes (advection and vertical diffusion) and sediment oxygen consumption largely determine the spatial extent and dynamics of hypoxia on the Louisiana shelf. © Author(s) 2015.

Physical and biogeochemical processes determining the distribution, transport, and fate of nutrients delivered by the Mississippi and Atchafalaya river basin (MARB) to the inner Louisiana continental shelf (LCS) were examined using a three-dimensional hydrodynamic model and observations of hydrography, nutrients, and organic carbon collected during 12 cruises. Two aspects of nutrient transport and fate on the inner LCS (50 m depth) were evaluated: (1) along-shelf and cross-shelf transports were calculated and (2) nutrient sinks and sources were inferred. On average, 47% of the lower Mississippi River freshwater traveled westward on the LCS, but this percentage was reduced during summer when currents reversed to a predominately upcoast direction. Changes from mainly inorganic to organic nutrients were observed at salinity between 20 and 30, and above 30, organic nutrients were the dominant forms. Westward transport of dissolved inorganic nitrogen (DIN) was about 25% of the combined DIN load from the MARB, whereas westward transport of dissolved organic nitrogen (DON) was 2.8-fold larger than the MARB DON load. Different from dissolved inorganic nutrients, for which the rivers were the primary source, the dominant source of organic nutrients was advection from offshore. Overall, the inner LCS was estimated to be a net sink for total nitrogen in the amount of -3.14 mmol N m-2 d-1 and a net sink for total phosphorus in the amount of -0.28 mmol P m-2 d-1. These sinks were approximately 33% and 59% of the total N and P sources, respectively, to the inner LCS., Pub in Journal of Geophysical Research: Oceans, v118 p4822-4838, 2013.

We use a novel, microfluidics-based technique to deconstruct the classical wound healing scratch assay, decoupling the contribution of free space and cell damage on the migratory dynamics of an epithelial sheet. This method utilizes multiple laminar flows to selectively cleave cells enzymatically, and allows us to present a 'damage free' denudation. We therefore isolate the influence of free space on the onset of sheet migration. First, we observe denudation directly to measure the retraction in the cell sheet that occurs after cell-cell contact is broken, providing direct and quantitative evidence of strong tension within the sheet. We further probe the mechanical integrity of the sheet without denudation, instead using laminar flows to selectively inactivate actomyosin contractility. In both cases, retraction is observed over many cell diameters. We then extend this method and complement the enzymatic denudation with analogies to wounding, including gradients in signals associated with cell damage, such as reactive oxygen species, suspected to play a role in the induction of movement after wounding. These chemical factors are evaluated in combination with the enzymatic cleavage of cells, and are assessed for their influence on the collective migration of a non-abrasively denuded epithelial sheet. We conclude that free space alone is sufficient to induce movement, but this movement is predominantly limited to the leading edge, leaving cells further from the edge less able to move towards the wound. Surprisingly, when coupled with a gradient in ROS to simulate the chemical effects of abrasion however, motility was not restored, but further inhibited., Massachusetts Institute of Technology. Presidential Fellowship, National Institutes of Health (U.S.). Biotechnology Training Fellowship, Singapore-MIT Alliance for Research and Technology, Massachusetts Institute of Biotechnology Training Grant, Massachusetts Institute of Technology (Open-source Funding)

The Sea-viewing Wide Field-of-View Sensor (SeaWiFS) derived diffuse light attenuation along the Louisiana continental shelf (LCS) was examined at monthly scales from 1998 to 2007 to characterize temporal and spatial patterns, and responsible physical forcing conditions. The SeaWiFS diffuse light attenuation ranged from 0.10 to 2.64 m(-1). Stepwise multiple linear regression analysis suggested that spatial and temporal patterns in diffuse light attenuation were influenced by wind speed, nutrient loading, and river discharge from the Mississippi and Atchafalaya River Basin. SeaWiFS daily integrated surface photosynthetically active radiation (PAR, 400-700 nm) and diffuse light attenuation were used to calculate the absolute PAR and percentage of surface PAR that reached the sediment water interface (SWI) on the LCS. Large portions of the LCS were euphotic to the SWI especially during April and May. This finding implied that significant primary production was possible beneath the pycnocline during spring and early summer. In addition, this study was the first to demonstrate that the euphotic depth was correlated to the depth at which the water column turned hypoxic on the LCS. The development of hypoxic waters may be influenced by decreased light availability below the pycnocline in addition to aforementioned physical forcing., Published in Remote Sensing of Environment v115 p3748-3757, 2011.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2009., Cataloged from PDF version of thesis., Includes bibliographical references (p. 223-234)., The varied movements of the epithelium play vital roles in the development and renewal of complex tissues, from the separation of tissues in the early embryo, to homeostasis in the adult. Their movement is intricately connected to their proper functioning as selective barriers of the intestinal mucosae, as well re-epithelialization in the healing of wounds. Yet, considering their ubiquity and relevance, the basic origin of the collective motion of sheets has eluded a clear and quantitative interpretation in physical terms, prohibited by the lack of understanding of the relationship between motility, cell-cell contact, and their mediation by the mechanical properties of the substratum to which they adhere. Therefore, within this context, this thesis defines the prerequisites for both equilibrium and non-equilibrium coordinated cell motion. The timescales and lengthscales of the in vitro migration of an epithelial monolayer were calculated and compared under imposed constraints designed to mimic various states of in vivo epithelia. These constraints include assays that recreate the wound response of the epithelium such as what is seen in the cornea and epidermis, by unequivocally separating the influence of free space from cell damage in the induction of coordinated motion. The motion of the epithelium was further explored by the generation of gradients that reproduce asymmetry in the capacity for cells to migrate, divide, or undergo apoptosis, such as what is found along the crypt-villus axis of the intestine. Finally, as the epithelium adheres and migrates against the basal lamina, a substrate of uncertain in vivo mechanical properties, we explored the contribution of substrate viscoelasticity to the dynamics of coordinated migration. Parameterized this way, multiple modes of motility emerge, each distinct dynamically, phenotypically, and in their dependence on cell-cell contact., by Michael Peter Murrell., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2009., Cataloged from PDF version of thesis., Includes bibliographical references (p. 223-234)., The varied movements of the epithelium play vital roles in the development and renewal of complex tissues, from the separation of tissues in the early embryo, to homeostasis in the adult. Their movement is intricately connected to their proper functioning as selective barriers of the intestinal mucosae, as well re-epithelialization in the healing of wounds. Yet, considering their ubiquity and relevance, the basic origin of the collective motion of sheets has eluded a clear and quantitative interpretation in physical terms, prohibited by the lack of understanding of the relationship between motility, cell-cell contact, and their mediation by the mechanical properties of the substratum to which they adhere. Therefore, within this context, this thesis defines the prerequisites for both equilibrium and non-equilibrium coordinated cell motion. The timescales and lengthscales of the in vitro migration of an epithelial monolayer were calculated and compared under imposed constraints designed to mimic various states of in vivo epithelia. These constraints include assays that recreate the wound response of the epithelium such as what is seen in the cornea and epidermis, by unequivocally separating the influence of free space from cell damage in the induction of coordinated motion. The motion of the epithelium was further explored by the generation of gradients that reproduce asymmetry in the capacity for cells to migrate, divide, or undergo apoptosis, such as what is found along the crypt-villus axis of the intestine. Finally, as the epithelium adheres and migrates against the basal lamina, a substrate of uncertain in vivo mechanical properties, we explored the contribution of substrate viscoelasticity to the dynamics of coordinated migration. Parameterized this way, multiple modes of motility emerge, each distinct dynamically, phenotypically, and in their dependence on cell-cell contact., by Michael Peter Murrell., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2009., Cataloged from PDF version of thesis., Includes bibliographical references (p. 223-234)., The varied movements of the epithelium play vital roles in the development and renewal of complex tissues, from the separation of tissues in the early embryo, to homeostasis in the adult. Their movement is intricately connected to their proper functioning as selective barriers of the intestinal mucosae, as well re-epithelialization in the healing of wounds. Yet, considering their ubiquity and relevance, the basic origin of the collective motion of sheets has eluded a clear and quantitative interpretation in physical terms, prohibited by the lack of understanding of the relationship between motility, cell-cell contact, and their mediation by the mechanical properties of the substratum to which they adhere. Therefore, within this context, this thesis defines the prerequisites for both equilibrium and non-equilibrium coordinated cell motion. The timescales and lengthscales of the in vitro migration of an epithelial monolayer were calculated and compared under imposed constraints designed to mimic various states of in vivo epithelia. These constraints include assays that recreate the wound response of the epithelium such as what is seen in the cornea and epidermis, by unequivocally separating the influence of free space from cell damage in the induction of coordinated motion. The motion of the epithelium was further explored by the generation of gradients that reproduce asymmetry in the capacity for cells to migrate, divide, or undergo apoptosis, such as what is found along the crypt-villus axis of the intestine. Finally, as the epithelium adheres and migrates against the basal lamina, a substrate of uncertain in vivo mechanical properties, we explored the contribution of substrate viscoelasticity to the dynamics of coordinated migration. Parameterized this way, multiple modes of motility emerge, each distinct dynamically, phenotypically, and in their dependence on cell-cell contact., by Michael Peter Murrell., Ph.D.

In the 1970s, the Pena Blanca region (~50 km north of Chihuahua City, Mexico) was a target of uranium exploration and mining by the Mexican government. Since that time the Nopal I uranium deposit, located in unsaturated volcanic tuff, has been studied extensively because it is a good analogue for evaluating the fate of spent fuel, associated actinides, and fission products at a Yucca Mountainrepository. Water samples were collected from various locations (aditseepage, perched water, water supply well) near the Nopal I uranium deposit. 234U/238U ratios were higher in samples collected previously during relatively wet (summer) conditions (Pickett and Murphy 1999) than those of our data collected over the last two years from the same locations during dry (winter) conditions. Wet season samples have uranium concentrations <6 ppb and 234U/238U ratios of 76'10-6 to 278'10-6 (Pickett and Murphy 1999). Dry season samples show uranium concentrations of <68 ppb and 234U/238U ratios of 50'10-6 to 156'10-6. Two processes could be responsible for the seasonal variations in uranium isotopic composition at the site: 1) increased uranium dissolution and/or lower a-recoil-associated 234U enrichment rates in the vadose zone near the deposit during the dry season; and 2) increased evaporation under low-humidity conditions. Large variations in the 238U concentration and 234U/238U ratio were also found in samples collected from the saturated zone during the dry season. Observations such as these are important to performance assessments for evaluating the effects of climate on the long-term behavior of uranium in an oxidizing geologic environment. To correct analytical model results for the possible effect of evaporative concentration, chloride and stable isotope measurements made on water samples from the vadose zone are compared to those of rainwater. The U-series model results contribute toward understanding of the 3-D transport of uranium and radiogenic daughter products at Pen

In the 1970s, the Pena Blanca region (~50 km north of Chihuahua City, Mexico) was a target of uranium exploration and mining by the Mexican government. Since that time the Nopal I uranium deposit, located in unsaturated volcanic tuff, has been studied extensively because it is a good analogue for evaluating the fate of spent fuel, associated actinides, and fission products at a Yucca Mountainrepository. Water samples were collected from various locations (aditseepage, perched water, water supply well) near the Nopal I uranium deposit. 234U/238U ratios were higher in samples collected previously during relatively wet (summer) conditions (Pickett and Murphy 1999) than those of our data collected over the last two years from the same locations during dry (winter) conditions. Wet season samples have uranium concentrations <6 ppb and 234U/238U ratios of 76'10-6 to 278'10-6 (Pickett and Murphy 1999). Dry season samples show uranium concentrations of <68 ppb and 234U/238U ratios of 50'10-6 to 156'10-6. Two processes could be responsible for the seasonal variations in uranium isotopic composition at the site: 1) increased uranium dissolution and/or lower a-recoil-associated 234U enrichment rates in the vadose zone near the deposit during the dry season; and 2) increased evaporation under low-humidity conditions. Large variations in the 238U concentration and 234U/238U ratio were also found in samples collected from the saturated zone during the dry season. Observations such as these are important to performance assessments for evaluating the effects of climate on the long-term behavior of uranium in an oxidizing geologic environment. To correct analytical model results for the possible effect of evaporative concentration, chloride and stable isotope measurements made on water samples from the vadose zone are compared to those of rainwater. The U-series model results contribute toward understanding of the 3-D transport of uranium and radiogenic daughter products at Pen