Recent Submissions

  • Phylogenetic relationships within the Western United States species of Lepidium l.

    Lichvar, Robert W.; Laursen, Gary; Duffy, Lawrence; Dorn, Robert; Wolf, Paul (2019-12)
    The genus Lepidium L. is one of two global genera in the Brassicaceae. The genus has been arranged by species (geographic regions) worldwide, but no formal levels below the genus are recognized. Recent efforts to evaluate phylogenetic relationships have been performed at the global scale for about 20 percent of the species in the genus. The genus is recognized as having subtle and variable morphological characteristics to define species limits. Several nuclear and chloroplast DNA methods have been used to construct phylogenetic relationships within the genus. Incongruences between various phylogenetic trees indicate likely hybridization and/or hybrid origin of multiple species and a genus blurred with a reticulate evolutionary past. Internal Transcribed Spacer (ITS) ribosomal DNA (rDNA) sequences were developed here and combined with other ITS sequences on Genbank for other North American species of Lepidium. Two phylogenetic trees were developed, one comparing North American and another dominated by Intermountain West species. Results of a limited Intermountain Lepidium phylogenetic tree were compared to a cladistic tree developed from 123 morphological traits for select species of Lepidium from the western United States. A comprehensive ITS tree was developed to evaluate species relationships in the genus throughout this region. Ploidy levels of 22 taxa of Intermountain species of Lepidium were evaluated to assess whether ploidy levels were associated with any geographic or morphologic patterns within the group. The results show closely related species and varieties with several ploidy levels, but are lacking any relationships to morphological features. Neither ITS nor ploidy levels provided a clear understanding into the current taxonomic treatment of the many faint morphologically different taxa in the group. But Intermountain Lepidium, as a geographic group and clade, is distinct from other west coast members in the genus. The species most associated with all the radiant speciation, and the least understood, is L. montana.
  • Modeling volcanic ash and sulfur dioxide with the Weather Research Forecasting with Chemistry (WRF-Chem) model

    Egan, Sean D.; Cahill, Catherine; Stuefer, Martin; Webley, Peter; Lopez, Taryn; Simpson, William (2019-12)
    The Weather Research Forecasting with Chemistry (WRF-Chem) model is capable of modeling volcanic emissions of ash, sulfur dioxide and water vapor. Here, it is applied to eruptions from three volcanoes: the 2008 eruption of Kasatochi Volcano in Alaska, the 2010 eruption of Eyjafjallajökull in Iceland and the 2019 eruption of Raikoke in the Kurile Islands. WRF-Chem's ability to model volcanic emissions dispersion is validated through comparison of model output to remote sensing, in situ and field measurements. A sensitivity of the model to modeled plume height is discussed. This work also modifies the base WRF-Chem code in three ways and studies the effects of these modifications. First, volcanic ash aggregation parameterizations are added covering three modes of particle collisions through Brownian motion, differential settling and shear. Second, water vapor emissions from volcanic eruptions are added and coupled to the new aggregation scheme. The effects of these changes are assessed and found to produce volcanic ash concentrations in agreement with in situ measurements of plume concentrations and field measurements of tephra fallout. Third, the model is adapted to include multiple model initializations such that each is perturbed by selecting between two volcanic ash particle sizes and five initial plume heights. This modified WRF-Chem is nested in an application program interface that enables a new, automated, near real-time capability. This capability is assessed and the feasibility of its use as an augmenting tool to current operational VATD models is commented upon.
  • Mechanisms regulating the circannual rhythm of hibernation

    Frare, Carla; Drew, Kelly L.; Bult-Ito, Abel; Green, Thomas K.; Kuhn, Thomas B. (2019-08)
    Hibernation is a unique adaptation to conserve energy entering a hypometabolic (low metabolic rate) and hypothermic (low body temperature) state called torpor. Torpor is characterized by a drop in metabolism to 1-2% of basal metabolic rate and a decrease in body temperature to one to two degrees above ambient temperature. Metabolic rate is restored to basal metabolic rate and body temperature increases from 2-3⁰C to 36⁰C during the regularly timed arousal. The adenosine A1 receptor agonists promote the onset of hibernation and torpor in different species, through a yet undefined neuronal circuit. In the Arctic ground squirrel, CHA, an adenosine A1 receptor agonist, induces hibernation during the winter- hibernation season but not in summer even when the environmental conditions are kept constant (ambient temperature of 2⁰C and a light cycle of 4L:20D). Thus, the phenomenon of CHA-induced hibernation is entrained to an endogenous circannual rhythm. In this work, I aim to identify the changes in neuronal activation that reflect the circannual rhythm regulating the seasonal difference in response to CHA. Arctic ground squirrels, housed at constant ambient temperature (2°C) and light cycle (4L:20D), were implanted with body temperature transmitters. I collected tissue during Summer, Fall, Winter and Torpor conditions for seasonal analysis. For treatment analysis, I collected tissue form animals treated with CHA or vehicle in Summer and Winter. Primarily, I used immunohistochemistry to identify cell groups affected by season and treatment. I used cFos to identify neuronal activity and other immunohistochemical markers to identify neuronal phenotypes, based on specific cytoplasmic proteins. An overall seasonal decrease in thermogenesis, measured as reduced neuronal activity in the thermoregulatory pathways, and increase in vasoconstriction reflected the higher order processing necessary for CHA-induced hibernation. CHA inhibited the histaminergic neurons in the hypothalamus suppressing wakefulness and dis-inhibited the nucleus tractus solitarius, further suppressing thermogenesis. Preliminary data also suggested a seasonal change in the adenosine metabolic pathway, which may have increased adenosine receptor sensitivity during the hibernation season. Our results suggest that histaminergic neurons in the hypothalamus and the nucleus tractus solitarius are likely targets to manipulate metabolic demand in the clinical setting inducing therapeutic hypothermia or increasing metabolic rate.
  • Role of antioxidant supplementation and exercise regimen in handling oxidative stress from natural PM2.5 exposure due to boreal forest fire

    Witkop, Jacob J.; Dunlap, Kriya; Duffy, Lawrence; Reynolds, Arleigh (2019-05)
    Particulate matter 2.5 (PM2.5) exposure induces oxidative stress that causes many negative health outcomes such as cancer, cardiovascular disease and neurodegenerative disease. Research shows that dietary antioxidants and an up-regulated endogenous antioxidant response from exercise play key roles in the antioxidant defense against oxidative stress. This study is the first to use an animal model to investigate the cumulative effects of using lifestyle interventions of antioxidant supplementation (Arthrospira platensis) and exercise regimen on the antioxidant response before, during, and after ambient PM2.5 exposure. In a two-factorial, longitudinal design, sled dogs (n=48) were divided into four groups (exercise and supplemented, exercise, supplemented, and control) to (1) test the effects of exercise and antioxidant regimen on antioxidant response after one month of implemented exercise and supplementation protocol and (2) measure the antioxidant response of all groups during and after a natural forest fire event in 2015. Commercial assays for Total antioxidant Power (TAP) and the enzymatic antioxidant Superoxide Dismutase (SOD) were used as markers for the total antioxidant response and the endogenous response at all time points. During the forest fire, SOD was increased 5-10-fold over pre/post-exposure levels in all groups suggesting potential implication for using SOD as a marker for the acute response to environmental stress. TAP was increased in the exercise groups after one month of exercise protocol implementation, demonstrating the cytoprotective increase of antioxidants after repeated exercise.
  • Determining the immune status of Steller sea lions (Eumetopias jubatus): an environmental agents of disease perspective

    Kennedy, Stephanie Nichole; O'Hara, Todd; Ferrante, Andrea; Kuhn, Thomas; Trainor, Thomas; Rea, Lorrie (2019-05)
    The integrity of the immune system is paramount for preserving overall health for many organisms. Investigating environmental and physiological factors that may be associated with alterations of the immune status in non-traditional sentinel species, like the Steller sea lion (SSL), is a prominent undertaking in eco-immunology research. Changes to immune homeostasis likely impacts the health and survival of SSLs. Recent studies have reported that mercury concentrations in hair in 24 to 36% of newborn SSLs of the Western Aleutian Islands (WAI) exceed thresholds (>30 ppm) for potential adverse effects. Many of these individuals were from WAI rookeries that have historically experienced significant population declines with some slow to recover. Retrospective, and ongoing, analyses of mercury in lanugo coats (natal hair) from young pups of the WAI demonstrate in utero exposure to relatively high levels of mercury during late gestation. Therefore, this dissertation focuses on the notion that dietary acquired mercury could potentially alter immune response in SSLs, especially young pups, and may contribute to the lack of recovery from population declines. In order to gain an understanding of the potential for mercury to adversely affect the immune response of SSLs, selected aspects of immunity were measured (blood cell counts, haptoglobin, immunoglobulins, and cytokines) and investigated within the context of body condition, age, mercury exposure and regional population dynamics. In Chapter Two, the acute phase response protein, haptoglobin, was found to vary significantly with age and region. Individual SSL pups with greater concentrations of mercury had lower predicted concentrations of haptoglobin. In Chapter Three, a colorimetric protein A enzyme-linked immunosorbent assay was modified for enhancing accurate measurement of immunoglobulin concentrations in SSL serum. This improved methodology was then used in Chapter Four for comparing immunoglobulins in young developing SSL pups and dams as a measure of maternal investment of immunity among different rookeries. Lastly, Luminex multiplex technologies were employed for quantifying cell-signaling proteins (cytokines) in SSL serum to compare associations among rookery pups in Chapter Five. Although mercury concentrations in some individuals exceed adverse effects thresholds that are defined for other mammals, no statistically significant associations were found between immunoglobulins and cytokines relative to mercury concentrations in young developing pups. These thesis chapters provide a powerful baseline and improved methods for ongoing and future assessments of haptoglobin, immunoglobulins, and cytokines (combined with traditional hematologic measures) observed in young developing SSL pups in regions experiencing population decline when compared with rookeries with stable or increasing pup production. Some of these findings, especially for haptoglobin, are indicative of alterations in immune status in young SSL pups born to dams from different natal rookeries with higher mercury exposure. Understanding the cause of the differences in the immune status of young SSLs will require additional assessments of the maternal-fetal interface of immunity and other factors like nutrition, metabolic status, and infectious disease that may shape neonatal immunity leading to the regional differences observed.
  • Effects of methylmercury and theaflavin digallate on adipokines in mature 3t3-l1 adipocytes

    Chauhan, Shubhangi; Duffy, Lawrence; Drew, Kelly; Dunlap, Kriya (2019-05)
    Diabetes is a contributor to morbidity across the globe and is often associated with obesity, metabolic syndrome and other inflammatory diseases associated with aging. In addition to genetic and lifestyle factors, environmental factors such as metals and persistent organic pollutants may increase the severity or lower the threshold of these conditions. In cell culture, methylmercury is toxic to adipocytes and may impact the adipokine secretions. In this study, I determined the effects of different concentrations of theaflavin digallate on methylmercury exposed 3T3-L1 adipocytes in cell culture. Secretions of resistin, adiponectin and lipid peroxidation product, 4-HNE were monitored using ELISA assays from Day 18 to 28. Cell morphology was assessed over the period of ten days and on day 28 was observed using Lipid (Oil Red O) staining. Results showed that exposure to methylmercury increased the levels of resistin and adiponectin as well as 4-HNE when compared to the control cells. Methylmercury treated cells resulted in smaller and highly clumped lipid droplets. These results suggest that methylmercury induces reactive oxygen species leading to development of an inflammatory response. Theaflavin digallate reduced the impact of methylmercury by restoring the morphology and secretion patterns of adiponectin, resistin and 4-HNE. With this enhanced signaling model other anti-inflammatory agents could be tested at this biochemical level eventually leading to studies in animal models.
  • Metal(loid) liberation from Alaskan coal combustion products as a function of time in various aqueous media

    Milke, Kyle P.; Guerard, Jennifer J.; Hayes, Sarah M.; Trainor, Thomas P. (2018-12)
    Little is known about the fate and potential toxicity of metal(loid)s that could be leached from coal combustion products by a (sub- )Arctic environment. Several potentially toxic elements are enriched in coal combustion products relative to the average crustal abundance including As, Cu, Se, and Sb. The overarching goal of this project is to examine the release of these and other metal(loid)s from early stage coal ash and fly ash from the University of Alaska Fairbanks (UAF) power plant and identify transformations in the presence of aqueous environmental media. Bioaccessibility experiments performed indicate that early stage coal ash and fly ash contain bioaccessible Cr, As, Se, Sb, and Pb. Bioaccessible concentrations of these commonly known toxic metal(loid)s were found to exceed EPA drinking water and freshwater regulations. Early stage coal ash and fly ash was reacted with 18 MΩ H₂O (control) or simulated rainwater to quantify metal(loid) liberation as a function of time. Leachate pH increased to ca. 12.5 within the first hour. Some metal(loid)s quickly reached the maximum measured concentration and consistently decreased in concentration with time such as Ba, Pb, and Zn, while other metal(loid)s increased in concentration with increased reaction time (e.g., Al, V, and Cr). Leaching behavior of between early stage coal ash and fly ash may be controlled by total initial concentrations present in the two ashes, differences in particle size, dissolution and precipitation reactions, and heterogeneity of metal(loid) distribution within the particles. Early stage coal ash and fly ash were also reacted with reconstituted dissolved organic matter solutions to simulate possible environmental interactions. It was found that for some elements (e.g., Ca), dissolved organic matter did not affect the mobility. Other metal(loid) mobilities were affected by the presence of dissolved organic matter, such as that of Sb, As, Zn, Se, Mo, and V. Some metal(loid) concentrations decreased while others increased with increasing dissolved organic carbon concentrations. Through these experiments, we have obtained a quantitative understanding of the kinetic controls of metal(loid) release from coal ash leaching with various aqueous media. Results from these experiments can help to improve storage and remediation processes for coal combustion products in an effort to protect human and the ecosystem health.
  • Role of dietary fat and supplementation in modulating neurodegenerative pathology in two animal model systems

    Maulik, Malabika; Bult-Ito, Abel; Taylor, Barbara E.; Duffy, Lawrence; Kuhn, Thomas; Dunlap, Kriya (2018-12)
    Neurodegenerative disorders are progressive conditions that worsen over time and results in death of neurons. Parkinson's disease (PD) is a prevalent example of one such age-related disease, which is characterized by movement disorder (ataxia) and/or cognitive disability (dementia). Pathologically, PD is characterized by a toxic accumulation of α-synuclein protein in the midbrain leading to degeneration of the dopaminergic neurons. The etiology of PD is intricate, and the cause is attributed to genetic mutations and environmental factors like insecticides or heavy metals. Moreover, treatment options are limited and often aimed at treating the symptoms rather than the actual disease progression. Using the nematode model of Caenorhabditis elegans, I examined the effect of Alaskan bog blueberry (Vaccinium uliginosum) on α-synuclein overexpression and how such indigenous natural treatment can modulate key molecular targets like sirtuins, which are proteins involved in regulating cellular processes including aging, death and their resistance to stress. The impact of extrinsic factors like dietary fat on PD pathology has been sparsely explored and the molecular basis of such changes is not known. Through my thesis research, I also further investigated the influence of fat metabolism on key hallmarks of PD: α-synuclein overexpression and dopaminergic degeneration in the nematode model. Finally, I studied the interaction of dietary fat (normal, low and high fat) and Alaskan blueberry supplementation on metal induced neurotoxicity model of Mus musculus. Our results highlight the beneficial properties of Alaskan blueberries in combating proteotoxic stress and inflammation in both animal models. They also reiterate the benefit of low fat diet, on its own or in combination with supplementation in improving several PD-like molecular features and how consuming high fat can mask such health promoting outcomes. The current thesis work therefore, provides a foundation for further exploration of neurobiological changes associated with consumption of natural products and different diets and how such alterations can be extrapolated to humans.
  • The temporal and spatial distribution of dissolved and particulate iron over the Gulf of Alaska shelf

    Roberts, Megan Victoria; Aguilar-Islas, Ana M.; Trainor, Thomas P.; Simpson, William (2018-08)
    The Gulf of Alaska (GOA) is a region with contrasting ecosystems where the availability of the essential micronutrient iron (Fe) contributes to the observed productivity. However, knowledge on the temporal and spatial variability of iron species over the GOA shelf is limited. The offshore GOA displays lower annual production and residual nitrate in surface waters throughout the year due to low Fe supply, while high spring production is observed over the shelf due to ample nitrate and Fe supply, but these waters become nitrate limited by mid-summer. Processes promoting the exchange of the Fe rich shelf waters with the nitrate rich offshore GOA waters create favorable conditions for phytoplankton to bloom. Mechanisms for Fe introduction and transport are seasonal freshwater input, alongshore advection from the Alaska Coastal Current eddies, deep wintertime mixing, downwelling, downwelling relaxation, and/or upwelling conditions. Additional Fe sources from subsurface waters and sediment re-suspension can impact Fe distributions. Highly seasonal glacial and river input bring in an abundance of both particulate and dissolved Fe species, which differ in their biological availability. For example, dissolved Fe (DFe) is much more readily available than particulate Fe (PFe). The PFe pool can be separated into a labile fraction, which is potentially transferable to the dissolved phase on time scales relevant to phytoplankton blooms, and a refractory fraction, which is considered biologically unavailable. Seawater samples to determine Fe speciation were collected in spring and early fall of 2013 during three GOA scientific cruises. Trace metal clean procedures were followed during sample collection, processing and analysis. Seawater samples were collected by two methods: 1) Vertical samples were obtained using custom-made samplers (UAF vanes) and filtered offline for PFe analysis; 2) surface samples were obtained by using a towed pump system ("the Fe fish") and filtered in-line for DFe analysis. The PFe fractions of suspended particles were further processed using chemical separation: a) 25 % acetic acid leach with a reducing agent to determine leachable particulate Fe; b) complete digestion of the filter using strong acids to determine refractory particulate Fe. Quantitative determination was by inductively coupled plasma mass spectrometry. Results indicate the broader Western GOA shelf displayed higher average concentrations of total particulate Fe (~121 nM on average) compared to the narrower Southeastern GOA shelf (~18 nM on average). Areas of high glacial input, such as in the vicinity of the Copper River discharge (western side of Kayak Island) and within Prince William Sound near Columbia Glacier, exhibited highly elevated concentrations of total particulate Fe (~430 nM to ~1100 nM). When comparing geographic location, the suspended leachable particulate Fe was higher (~ 22%) over the Southeastern shelf, while the Northern and Western shelf had lower percentage of leachable Fe (11 - 12 %). Over the Southeastern shelf, DFe concentrations were higher in late spring ranging (0.22 - 3.13 nM), while in early fall concentrations were lower (0.07 - 0. 84 nM). Surface water results indicate that there is a significant input of PFe and DFe that occurs in the early fall that extends over much of the Northern shelf and at the inner Western shelf. Variability in downwelling, downwelling relaxation, and upwelling conditions were observed to impact Fe distributions over the Southeastern shelf. These results highlight the impact that the intense environmental variability characteristic of the GOA has on the distribution of Fe species seasonally and geographically.
  • New instrumentation for the detection of sulfur dioxide in the remote atmosphere

    Nicks, Dennis Keith, Jr.; Benner, Richard (1999)
    Sulfur gases are an important chemical component of the atmosphere. Gaseous sulfur compounds effect the acidity of rainwater and are important precursors to aerosol particles which affect public health, climate and visibility of scenic vistas such as the Grand Canyon. Sulfate aerosols are also known to participate in ozone catalysis in the stratosphere. A vast majority of the gaseous sulfur cycling through the atmosphere will exist as sulfur dioxide (SO2) at some time during its atmospheric lifetime. Since SO 2 is a primary component of the atmospheric sulfur cycle, quality measurements of this gas are important to understanding the cycling of sulfur through the atmosphere. The mixing ratio of SO2 in the atmosphere can be as low as a few 10's of parts-per-trillion by volume (pptv) in unpolluted areas and as high as 100's of parts-per-billion by volume (ppbv) near industrial centers. Obtaining SO2 measurements with mixing ratios that can differ by 105 in magnitude is a difficult task, especially for mixing ratios less than a few hundred pptv. The Diffusion Denuder/Sulfur Chemiluminescence Detector (DD/SCD) was developed further and tested in a rigorously blind comparison under controlled laboratory conditions. The DD/SCD exhibited excellent sensitivity and little-to-no interference from other trace gases. The DD/SCD performance was comparable to that of other state-of-the-art instruments developed for measuring SO 2 in the remote atmosphere. The Continuous SO2 Detector was developed to overcome the limitation of long sampling times (4 to 90 minutes) inherent in the DD/SCD and other state-of-the-art techniques. The Continuous SO2 Detector (CSD) was developed based on the design of the DD/SCD, but has been optimized for sensitive, high-time resolved measurements of SO2 in air. Sensitive, high-time resolved measurements would be beneficial for studying atmospheric SO2 over large geographical areas from a moving sampling platform such as an aircraft. The current prototype of the CSD is capable of measuring SO2 at mixing ratios of less than 100 pptv on the order of seconds. The DD/SCD, CSD and an automated, computer controlled dynamic dilution system described in this thesis represent a suite of instruments for the measurement of SO2 in the remote atmosphere.
  • Molecular systematics and biogeography of long-tailed shrews (Insectivora: Sorex) and northern flying squirrels (Rodentia: Glaucomys)

    Demboski, John Richard; Cook, Joseph A. (1999)
    Insight into phylogenetic and biogeographic relationships among several mammalian taxa in western North America was provided with DNA sequences of two mitochondrial genes (cytochrome b and ND4). Members of two species complexes of long-tailed shrews (genus Sorex ) and northern flying squirrels (genus Glaucomys) were examined, and a common theme of responses to past climate change and glacial cycles was evident. Diversification events indicated by the DNA sequences provide new perspectives regarding the deep and shallow history of these taxa. Analysis of seven species of the Sorex cinereus complex (and related species) revealed two major clades within the complex, Northern and Southern. These generally corroborate proposed morphological relationships and correspond to broadly defined habitat affiliations (xeric and mesic), respectively. Within the Northern clade, amphiberingian species represented a monophyletic group suggesting Beringia was a center of endemism. Next, five species of the S. vagrans complex and related species were assessed. Significant molecular variation was revealed that does not correspond to morphological differences within the complex. Two major clades within S. monticolus were observed, a widespread Continental clade (Arizona to Alaska, including S. neomexicanus) and a restricted Coastal clade (Oregon to southeast Alaska, including S. bairdi and S. pacificus). A regional examination of genetic variation in the northern flying squirrel in southeast Alaska was also performed. Results suggested that southern islands in the Alexander Archipelago were the result of recent colonization (founder event). Finally, a comparative phylogeographic analysis of a reduced data set (S. monticolus), a molecular data set for the American Pine Marten, Martes americana, and other published molecular studies were used to reexamine the role of glacial refugia in the biogeography of the north Pacific coast. Previous ideas regarding purported refugia may be overstated and may be the result of limited geographic sampling. This thesis provides new perspectives on processes (e.g., post-glacial colonization) driving mammalian phylogenetic and biogeographic structuring in western North America.
  • Investigations into model systems of neurodegeneration: Organotypic brain slice culture and in vivo microdialysis

    Clapp, Kimberly Lara; Duffy, Lawrence K. (2000)
    The mechanisms behind neurodegeneration in disease and injury have yet to be fully defined. Many in vitro and in vivo model systems, have been developed to investigate the mechanisms of neurotoxicity and its relation to human disease and injury. There are a few resounding connections between most types of neurological disorder; namely oxidative stress and inflammation. The glutamate receptor agonist, N-methyl-D-aspartate, can be used to imitate excitotoxicity during stroke as it overstimulates the glutamate receptor, leading to rises in intracellular calcium levels, which in turn lead to oxidative stress within the cell. Amyloid-beta protein (Abeta) a useful in many of its isoforms in creating in vitro model systems of Alzheimer's disease (AD). Abeta can directly cause the production of potentially harmful free radicals. This study investigates the formation of model systems of neurodegeneration: in vivo microdialysis and organotypic brain slices culture in order to assess the role of oxidative stress and inflammation morphologically and biochemically. The effect of melatonin, an endogenous antioxident, on oxidative stress associated with NMDA and Abeta neurotoxicity was determined through morphological analysis and biochemical markers of oxidative stress. This study reports that both NMDA and Abeta(25--35) cause oxidative stress in an organotypic brain slice culture model system of stroke and Alzheimer's disease as established by: (1) morphological analysis of tissue and ultrastructure, (2) redox-active assay, (3) heme-oxygenase assay, (4) 8-hydroxyguanosine assay and (5) interleukin IL-1beta and IL-6 assay (Abeta only) These investigations also demonstrate that melatonin can attenuate the oxidative stress associated with NMDA and Abeta exposure. These findings expand upon previous evidence from cell culture analysis of oxidative stress induced by NMDA and Abeta. Therefore, this evidence supports the theory that oxidative stress is involved in neurodegeneration in both excitotoxicity in stroke and in Abeta-mediated damage in Alzheimer's disease, and that endogenous antioxidant treatment may be a useful therapeutic approach in such injury and disease.
  • Oceanic emissions of sulfur: Application of new techniques

    Jodwalis, Clara Mary; Benner, Richard L. (1998)
    Sulfur gases and aerosols are important in the atmosphere because they play major roles in acid rain, arctic haze, air pollution, and climate. Globally, man-made and natural sulfur emissions are comparable in magnitude. The major natural source is dimethyl sulfide (DMS) from the oceans, where it originates from the degradation of dimethysulfonioproprionate (DMSP), a compound produced by marine phytoplankton. Global budgets of natural sulfur emissions are uncertain because of (1) the uncertainty in the traditional method used to estimate DMS sea-to-air flux, and (2) the spatial and temporal variability of DMS sea-to-air flux. We have worked to lessen the uncertainty on both fronts. The commonly used method for estimating DMS sea-to-air flux is certain to a factor of two, at best. We used a novel instrumental technique to measure, for the first time, sulfur gas concentration fluctuations in the marine boundary layer. The measured concentration fluctuations were then used with two established micrometeorological techniques to estimate sea-to-air flux of sulfur. Both methods appear to be more accurate than the commonly used one. The analytical instrument we used in our studies shows potential as a direct flux measurement device. High primary productivity in high-latitude oceans suggests a potentially large DMS source from northern oceans. To begin to investigate this hypothesis, we have measured DMS in the air over northern oceans around Alaska. For integrating and extrapolating field measurements over larger areas and longer time periods, we have developed a model of DMS ocean mixing, biological production, and sea-to-air flux of DMS. The model's main utility is in gaining intuition on which parameters are most important to DMS sea-to-air flux. This information, along with a direct flux measurement capability, are crucial steps toward the long-term goal of remotely sensing DMS flux. A remote sensing approach will mitigate the problems of spatial and temporal variability. The new developments in methodology, field sampling, and modeling put forth in this thesis are tools we have used to better understand and quantify sulfur gas emissions from northern oceans, which appear to be a significant source of sulfur to the global atmosphere.
  • Stabilization of secondary structure of synthetic Alzheimer beta-amyloid protein analogs in the presence of aluminum (III) ions

    Vyas, Sandip Bipin (1995)
    The gradual accretion of fibrillar protein deposits in a tissue or organ is a hallmark of all amyloidogenic diseases. These deposits accumulate as senile plaques and cerebrovascular deposits in the brain and are characteristics of Alzheimer's disease. A majority of the brain amyloid deposits consist of a 40 amino acid protein, the Alzheimer $\beta$-protein, A$\beta$P, which in a soluble form is ubiquitous in biological tissues. In order to provide a more detailed understanding of the structural transformations of soluble A$\beta$P, sequence analogs derived from $\beta$1-40, and having His $\to$ Arg, and scL-Asp- $\to$ scD-Asp substitutions were synthesized. The kinetic variations of $\beta$1-40 and $\beta$6-25 were studied using amide circular dichroism spectroscopy by monitoring ellipticity changes of the peptide backbone. In both peptides, the gradual loss of secondary structure was a multiphasic process which was also dependent on concentration. The circular dichroism titrations with metal ions revealed the involvement of at least two ions in the conformational transitions of $\beta$1-40 and $\beta$6-25. The association of Al(III) with scL-Asp $\to$ scD-Asp derived analogs caused surprising conformational changes in $\beta$6-25, which were distinct from $\beta$1-40. Microheterogeneous products corresponding to Al(III)-bound peptide species were resolvable on the reversed-phase surface. The association of aluminum was investigated by low field $\sp{27}$Al nuclear magnetic resonance spectroscopy. The signal corresponding to Al(III)-bound peptide species revealed that at least four Al(III) ions were bound to $\beta$1-40 and $\beta$6-25 between pH 5 and 6. Moreover, $\beta$1-40 effectively competed with EDTA to bind with Al(III). This study also describes a strategy which resolved the band broadening in reversed-phase high-performance liquid chromatography of $\beta$1-40 and derived analogs. Chromatographic parameters related to interactive contact area of $\beta$1-40 and derived analogs were determined on reversed-phase matrix. The peptides were bound to the reversed-phase surface in their monomeric form. Slow partition kinetics appear to contribute to significant band broadening, which suggests a secondary retention effect--indicating a conformational change due to unfolding on the stationary phase surface.
  • Nitrogen oxide photochemistry in high northern latitudes during spring

    Beine, Harald Jurgen; Jaffe, Daniel A.; Benner, Richard; Shaw, Glenn; Stolzberg, Richard; Wendler, Gerd (1996)
    The transport of NOy reservoir species from midlatitudes into the Arctic and the thermal and photochemical breakup of these species has been proposed to be the most important NOx source during spring, and may have an important influence on the ozone budget. This has not yet been shown to be correct. The objective of this research is to understand the sources of NOx and ozone in high latitudes during spring. To measure NOx, a high sensitivity chemiluminescence NO detector and a photolytic converter for NO$\sb2$ were constructed. The detection limits for NO and NO$\sb2$ were 1.70 and 5.67 part per trillion (pptv) in a one-hour average, respectively. Springtime NOx measurements were carried out concurrently with measurements of ozone, PAN, J(NO$\sb2$), and other species during 1994 at the Zeppelin station on Svalbard, and during 1993 and 1995 at Poker Flat, Alaska. The median mixing ratios of NOx, PAN and ozone at Svalbard were 23.7, 237.0 pptv, and 39.0 parts per billion (ppbv), respectively. During a few ozone depletion events in the Arctic marine boundary layer ozone and NOx mixing ratios were as low as 4 ppbv and 0.9 pptv, respectively. Halogen chemistry is probably responsible for both effects. The median NOx, PAN and ozone mixing ratios at Poker Flat were 79.5 pptv, 85.9 pptv, and 40.6 ppbv, respectively. During April and May diurnal cycles of PAN, ozone and temperature were observed and anticorrelated with the water mixing ratio. We interpret this to be the result of mixing with higher layers of the troposphere during the day. At both locations thermal PAN decomposition was an important NOx source. At Svalbard PAN decomposition was small, and the in-situ ozone production rates are an insignificant contribution to the ozone budget. Because of the higher temperatures, PAN decomposition rates, NOx mixing ratios, and in-situ ozone production rates are higher at Poker Flat. A contribution from this production to the overall ozone budget was visible during some periods. These results indicate that stable ozone precursors which are transported into the Arctic from anthropogenic sources can influence the ozone budget in high latitudes.
  • Nitrogen oxides in the Arctic troposphere

    Honrath, Richard Edward, Jr.; Jaffe, Daniel A.; Gosnick, Joan P.; Stolzberg, Richard J.; Stamnes, Knut; Shaw, Glenn E. (1991)
    Nitrogen oxides play a critical role in tropospheric photochemistry. In order to characterize these compounds in the arctic troposphere, ground-level concentrations of total reactive nitrogen (NO$\sb{y}$) and NO were determined over an extended period at a site near Barrow, Alaska. A high-sensitivity instrument developed for this purpose was used in three measurement campaigns: summer 1988, spring 1989, and March-December 1990. During the 1990 campaign, the detection limit for NO was 3-10 pptv (depending on averaging period), and the NO$\sb{y}$ uncertainty was $\pm$26%. A screening algorithm was applied to the data to eliminate effects from local (Barrow) sources, and the remaining data were divided into "background periods" (unaffected by local or regional NO$\sb{x}$ sources), and "events" (periods when emissions from a regional NO$\sb{x}$ source--the Prudhoe Bay oil-producing region--apparently impacted Barrow). These measurements revealed a sharp seasonal cycle of background NO$\sb{y}$ concentrations, with high values in early spring (median 560-620 pptv) and $\sim$70 pptv (median) during summer. This cycle is similar to that of other compounds in arctic haze but is partially attributed to a reduction in NO$\sb{y}$ lifetime due to organic nitrate decomposition as temperatures and insolation increased. Evidence indicates that the springtime arctic NO$\sb{y}$ reservoir was primarily composed of stable removal-resistant species, including PAN and other organic nitrates. PAN decomposition as temperatures rose in late spring likely caused an observed pulse of NO to $\sim$35 pptv (maximum hourly average); hourly-average NO concentrations were otherwise generally $<$8 pptv. NO$\sb{x}$ production from PAN decomposition due to the onset of spring or southward advection may affect springtime O$\sb3$ levels both in the Arctic and in the northern mid-latitudes. NO$\sb{y}$ and O$\sb3$ concentrations were positively correlated during summer, possibly indicating long-range transport of both and/or the presence of a mid-tropospheric NO$\sb{y}$ reservoir combined with a stratospheric O$\sb3$ source. A number of events with substantially elevated NO$\sb{y}$ concentrations (to 16 ppbv) were observed in air not impacted by emissions from the town of Barrow. Substantial evidence indicates that these events were a result of NO$\sb{x}$ emissions from the Prudhoe Bay region ($\sim$300 km to the ESE), which is also expected to affect measurements of other compounds at the Barrow site.
  • Characterization And Interpretation Of Volcanic Activity At Redoubt, Bezymianny And Karymsky Volcanoes Through Direct And Remote Measurements Of Volcanic Emissions

    Lopez, Taryn M.; Cahill, Catherine; Dehn, Jonathan; Newberry, Rainer; Simpson, William; Werner, Cynthia (2013)
    Surface measurements of volcanic emissions can provide critical insight into subsurface processes at active volcanoes such as the influx or ascent of magma, changes in conduit permeability, and relative eruption size. In this dissertation I employ direct and remote measurements of volcanic emissions to characterize activity and elucidate subsurface processes at three active volcanoes around the North Pacific. The 2009 eruption of Redoubt Volcano, Alaska, produced elevated SO2 emissions that were detected by the Ozone Monitoring Instrument (OMI) satellite sensor for over three months. This provided a rare opportunity to characterize Redoubt's daily SO2 emissions and to validate the OMI measurements. Order of magnitude variations in daily SO2 mass were observed, with over half of the cumulative SO2 emissions released during the explosive phase of the eruption. Correlations among OMI daily SO2 mass, tephra mass and acoustic energies during the explosive phase suggest that OMI data may be used to infer eruption size and explosivity. From 2007 through 2010 direct and remote measurements of volcanic gas composition and flux were measured at Bezymianny Volcano, Kamchatka, Russia. During this period Bezymianny underwent five explosive eruptions. Estimates of passive and eruptive SO2 emissions suggest that the majority of SO2 is released passively. Order of magnitude variations in total volatile flux observed throughout the study period were attributed to changes in the depth of gas exsolution and separation from the melt at the time of sample collection. These findings suggest that exsolved gas composition may be used to detect magma ascent prior to eruption at Bezymianny Volcano. Karymsky Volcano, Kamchatka, Russia, is a dynamic volcano which exhibited four end-member activity types during field campaigns in 2011 and 2012, including: discrete ash explosions, pulsatory degassing, gas jetting, and explosive eruption. These activity types were characterized quantitatively and uniquely distinguished using a multiparameter dataset based on infrasound, thermal imagery, and volcanic emissions. These observations suggest a decoupling between exsolved volatiles and magma at depth. I propose that variations in magma degassing depth influence the flux and proportions of decompression- and crystallization-induced degassing, as well as conduit permeability, can explain the variations in volcanic activity.
  • Resistance To Multi Organ Failure And Metabolic Alterations After Global Ischemia/Reperfusion In The Arctic Ground Squirrel

    Bogren, Lori Kristine; Drew, Kelly; Green, Thomas; Harris, Michael; O'Brien, Kristin (2013)
    Cardiac arrest (CA) and hemorrhagic shock (HS) are two clinically relevant situations where the body undergoes global ischemia/reperfusion (I/R). Hibernating animals such as ground squirrels have been shown to be resistant to I/R injury in various tissues. The present study compared physiological and metabolic changes occurring during global I/R in an I/R-injury prone animal, the rat, to that of I/R injury resistant animals, arctic ground squirrels (AGS). We sought to determine if AGS are protected from multi organ failure after global I/R and if any protection is dependent upon their hibernation season or the ability to maintain a stable metabolic profile during I/R. For CA, rats and euthermic AGS were asphyxiated for 8 min, inducing CA. For HS, rats, euthermic AGS, and interbout arousal AGS were subject to HS by withdrawing blood to achieve a MAP of 35 mm Hg for 20 min before reperfusion. For both I/R models, the animals' temperature was maintained at 36.5-37.5�C. After reperfusion, animals were monitored for 3 hours (HS) or 7 days (CA), then tissues and blood were collected for histopathology, clinical chemistries, cytokine level analysis (HS only), and 1H-NMR metabolomics of hydrophobic and hydrophilic metabolites (HS only). For the HS studies, a group of rats and AGS were monitored for three days after HS to access survival and physiological impairment. Regardless of season AGS showed no physiological deficit 12 hours after HS or CA. Blood chemistries and circulating cytokine levels indicated liver damage and systemic inflammation in the rats while AGS showed no signs of organ damage or inflammation. In addition, rats had a shift in their hydrophilic metabolic fingerprint and alterations in several metabolite concentrations during HS-induced I/R, indicative of metabolic adjustments and organ damage. In contrast, AGS, regardless of season, were able to maintain a 1H-NMR metabolic profile with few changes in quantified metabolites during I/R. These data demonstrate that AGS are resistant to systemic inflammation and organ damage/failure after I/R and this resistance is not dependent on their ability to become hypothermic during insult but may stem from an intrinsic resistance to disruptions in their metabolic processes during I/R.
  • Gene-By-Diet Interactions And Obesity Among Yup'ik People Living In Southwest Alaska

    Lemas, Dominick; Boyer, Bert B.; O'Brien, Diane M.; Schulte, Marvin K.; Tiwari, Hemant K. (2012)
    BACKGROUND: Molecular approaches have expedited the discovery of human obesity genes, however the heritability explained by these loci remains low (<2%). Gene-by-environment interactions may partially account for the "missing heritability" attributed to variation in obesity phenotypes. OBJECTIVE: The specific aims of this dissertation were to (i) identify genetic polymorphisms associated with obesity-related phenotypes in Yup'ik people and (ii) evaluate how n-3 polyunsaturated fatty acid (n-3 PUFA) intake modifies associations between genetic polymorphisms and obesity-related phenotypes in a population with widely varying intake of n-3 PUFAs. APPROACH: We genotyped genetic polymorphisms in (1) candidate genes with a strong physiological role in obesity pathophysiology; (2) candidate genes identified in obesity whole-genome linkage studies that were regulated by n-3 PUFAs; and (3) candidate genes reproducibly implicated in obesity genome-wide association studies (GWAS). DATA & ANALYSES: We used Center for Alaska Native Health Research (CANHR) data collected between 2001 and 2008. We estimated dietary intake of n-3 PUFA using nitrogen stable isotope ratios (delta15N) of red blood cells (RBC) and obesity-related phenotypes were obtained by trained staff. Genotype-phenotype analyses used generalized linear models that accounted for familial correlations. RESULTS: Our analyses of candidate genes based on physiology revealed a polymorphism called P479L in carnitine palmitoyltransferase 1A (CPT1A) that was associated with elevated fasting HDL-cholesterol and all obesity phenotypes. Our investigation of candidate genes that are regulated by n-3 PUFAs and implicated in obesity whole-genome linkage studies demonstrate that polymorphisms in stearoyl CoA desaturase (SCD) and steroyl regulatory element binding protein (SLC2A4) were associated with obesity-related phenotypes; however n-3 PUFA intake did not modify associations between SCD and SLC2A4 polymorphisms and obesity phenotypes. Finally, our investigation of candidate genes reproducibly implicated in obesity GWAS demonstrated that genetic predisposition to obesity is associated with adiposity and that interactions with n-3 PUFA intake accounted for more than twice the phenotypic variation in adiposity. CONCLUSION: Taken together, results from this dissertation suggest that selecting candidate genes based on large-scale genomic analyses, such as linkage analyses and GWAS, has the potential to identify gene-by-environment interactions that partially account for the "missing heritability" attributed to obesity.
  • The Effect Of Mitochondrial Ultrastructure On Function And Thermal Tolerance In Antartic Notothenioid Fishes

    Mueller, Irina Andrea; O'Brien, Kristin; Taylor, Barbara E.; Kuhn, Thomas B.; Staples, James F. (2012)
    The loss of hemoglobin in Antarctic icefishes is correlated with high mitochondrial volume densities and altered mitochondrial morphology in their oxidative muscle compared to red-blooded Antarctic notothenioid fish species. We hypothesized that differences in mitochondrial morphology between icefishes and red-blooded species might be correlated with differences in mitochondrial properties at their habitat temperature, near 0�C. We further hypothesized that differences in function might become more pronounced as temperature increases and might contribute to the lower thermal tolerance of icefishes compared to red-blooded species. Proton leak, rates of reactive oxygen species (ROS) production, membrane susceptibility to peroxidation and levels of antioxidants were measured in mitochondria isolated from hearts of the icefishes Chaenocephalus aceratus and Chionodraco rastrospinosus, and the red-blooded species Gobionotothen gibberifrons and Notothenia coriiceps. In addition, levels of oxidized proteins and lipids, and antioxidant levels were quantified in oxidative muscles of icefishes and red-blooded species exposed to their critical thermal maximum (CTmax) - an acute, short-term heat stress, and in animals exposed to 4�C for one week. Rates of ROS production increased as temperature increased in mitochondria isolated from both white- and red-blooded fishes. Yet, isolated mitochondria of icefishes are less protected against ROS. Antioxidant levels normalized to phospholipid content were lower in icefishes compared to red-blooded species, suggesting that icefishes might be more likely to experience oxidative stress as temperature increases. These findings were supported by measurements made in animals exposed to their CTmax. Levels of oxidized lipids increased in hearts of both icefishes, while levels of oxidized proteins increased only in C. aceratus in response to exposure to CTmax. In contrast, neither levels of oxidized lipids nor proteins increased in red-blooded fishes in response to exposure to CTmax. Similarly, levels of oxidized proteins did not increase in C. rastrospinosus or N. coriiceps in response to exposure to 4�C. Antioxidant levels tended to be lower in icefishes compared to red-blooded species and did not increase in any species in response to exposure to CTmax or 4�C. In summary, our findings suggest that icefishes are more vulnerable to heat-induced oxidative stress compared to red-blooded fishes.

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