• Linkages between protein ubiquitination, proteasome activity and the expression of oxygen-binding proteins in Antarctic notothenioid fishes

      Oldham, Corey A.; O'Brien, Kristin; Dunlap, Kriya; Taylor, Barbara (2015-12)
      Antarctic icefishes lack hemoglobin (Hb), and some species lack cardiac myoglobin (Mb). As iron-centered proteins, Hb and Mb can promote the formation of reactive oxygen species that may damage biological macromolecules. Consistent with this, we find higher levels of oxidized proteins in some tissues of red-blooded notothenioids than in icefishes. Oxidized proteins are marked for degradation by the conjugation of the protein ubiquitin. I hypothesized that levels of ubiquitinated proteins and 20S proteasome activity (which degrades oxidized proteins) would be higher in +Hb and +Mb notothenioids than icefishes lacking the proteins. Levels of ubiquitinated proteins and rates of proteasome activity were measured in the heart ventricle, pectoral adductor, and liver of six species of notothenioids differing in Hb and Mb expression. Previous studies in notothenioids suggest that oxidative stress declines following acclimation to 4°C. I also hypothesized that levels of ubiquitinated proteins and 20S proteasome activity would decline in response to acclimation to 4°C. Levels of ubiquitinated proteins and rates of proteasome activity were measured in the heart ventricle, pectoral adductor, and liver of the red-blooded Notothenia coriiceps held at ambient temperature and acclimated to 4°C for 3 weeks. Levels of ubiquitinated proteins were higher in tissues of the red-blooded N. coriiceps compared to icefishes, but the activity of the 20S proteasome did not follow a similar trend, suggesting that icefishes do not incur an energetic benefit resulting from reduced rates of protein degradation. Levels of ubiquitinated proteins were equivalent in heart ventricle and oxidative skeletal muscle, and proteasome activities were equivalent in all tissues between acclimated N. coriiceps and those held at ambient temperature, suggesting that protein damage and rates of protein degradation are not altered in notothenioids by long-term exposure to 4°C.
    • Linking climate history and ice crystalline fabric evolution in polar ice sheets

      Kennedy, Joseph Huston; Pettit, Erin; Truffer, Martin; Bueler, Ed; Newman, David; Szuberla, Curt (2015-08)
      An ice sheet consists of an unfathomable number of ice crystallites (grains) that typically have a preferred orientation of the crystalline lattices, termed fabric. At the surface of ice sheets, the microstructural processes that control the grain structure and fabric evolution are influenced by climate variables. Layers of firn, in different climate regimes, may have an observable variation in fabric which can persist deep into the ice sheet; fabric may have 'memory' of these past climate regimes. To model the evolution of a subtle variation in fabric below the firn-ice transition, we have developed and released an open-source Fabric Evolution with Recrystallization (FEvoR) model. FEvoR is an anisotropic stress model that distributes stresses through explicit nearest-neighbor interaction. The model includes parameterizations of grain growth, rotation recrystallization and migration recrystallization which account for the major recrystallization processes that affect the macroscopic grain structure and fabric evolution. Using this model, we explore the evolution of a subtle variation in near-surface fabric using both constant applied stress and a stress-temperature history based on data from Taylor Dome, East Antarctica. Our results show that a subtle fabric variation will be preserved for ~200ka in compressive stress regimes with temperatures typical of polar ice-sheets. The addition of shear to compressive stress regimes preserves fabric variations longer than in compression-only regimes because shear drives a positive feedback between crystal rotation and deformation. We find that temperature affects how long the fabric variation is preserved, but does not affect the strain-integrated fabric evolution profile except when crossing the thermal-activation-energy threshold (~-10°C). Even at high temperatures, migration recrystallization does not rid the fabric of its memory under most conditions. High levels of nearest-neighbor interactions between grains will rid the fabric of its memory more quickly than low levels of nearest-neighbor interactions. Because FEvoR does not compute flow, an integrated fabric-flow model is needed to investigate the flow-fabric feedbacks that arise in ice sheets. Using the open-source Parallel Ice Sheet Model (PISM) and FEvoR, we develop a combined flow-fabric model (PISM-FEvoR). We provide the first integrated flow-fabric model that explicitly computes the fabric evolution and includes all three major recrystallization processes. We show that PISM-FEvoR is able to capture the flow enhancement due to fabric by modeling a slab-on-slope glacier, initialized with a variety of fabric profiles. We also show that the entire integrated fabric-flow history affects the final simulated flow. This provides a further, independent validation of using an integrated fabric-flow model over a constant enhancement factor in ice-sheet models.
    • Linking local knowledge and fisheries science: the case with humpback whitefish (Coregonus pidschian) in Interior Alaska

      Robinson, Melissa Anne (2005-05)
      Humpback whitefish (Coregonus pidschian) are the main subsistence fish for the residents of the Athabascan village of Northway. Local residents' concerns over whitefish and gaps in knowledge in the scientific community about whitefish basic ecology provided a basis for collaboration between fisheries scientists, social scientists, and Northway Village. Through semi-directed interviews and participant observation, I documented and linked local and scientific knowledge about whitefish. Trust, formed in part by my engagement with the community, was essential to meaningful collaboration between local and scientific experts. Through collaboration, insights emerged about the long-distance migrations of whitefish (up to 230 km), their small-scale use of creek channels, annual site fidelity, and repeated long-term use of seasonal habitats. Partially due to gendered fishing roles, women and men differed in their knowledge about whitefish. Women observed seasonal and annual variation in the prevalence of parasite-infected whitefish, while both men and women observed increased sedimentation in area lakes. Questions surfaced about the behavioral response of whitefish to increasing water temperatures and the effects of siltation on their health. I argue that the fusion of local and scientific knowledge, gained through collaboration, enhanced the information required to make management decisions regarding whitefish in the Upper Tanana drainage and the resilience of this social-ecological system.
    • Linking proteomics to microbial kinetics

      Cherian, Suraj (2008-08)
      Oligobacterial physiology is mostly unstudied due to cultivation difficulty. New isolation techniques such as extinction culture have produced cultivable representatives of the aquatic environment namely Sphingopyxis alaskensis. Attempts were made to grow the bacterium in batch cultures using glucose and tyrosine as ideal substrates as determined from growth studies. Differential protein expression from cytoplasmic and membrane fractions of the putative culture were compared so as to identify key proteins involved in substrate uptake and metabolism followed by incorporation of protein quantities into mathematical models of oligotroph growth. However artifactual results from two dimensional gel electrophoresis led to the question of culture purity, which was eventually confirmed by light microscopy, flow cytometry and 16S rRNA gene sequencing. This research gives better insight into the possible problems that can crop up while working with hard to culture marine oligobacteria. I demonstrate the rationale used to identify the contaminant, which was difficult to detect because its slow growth was similar to the target organism. A major achievement was successful cell fractionation as it has never been attempted in oligobacteria due to culturing difficulties and the procedure is different from the routine methods adopted in bacteria and fungi. Also the research demonstrates a complete protocol for eliminating uncertainties in culture purity.
    • Lithium Storage and Release from Lacustrine Sediments: Implications for Lithium Enrichment and Sustainability in Continental Brines

      Coffey, Daniel; Munk, Lee Ann; Ibarra, Daniel; Butler, Kristina; Boutt, David; Jenckes, Jordan (2021)
      Despite current and projected future reliance on lithium as a resource, deficiencies remain in genesis models of closed-basin Li brines. Subsurface geochemical interactions between water and bulk solid phases from lacustrine sediments, are shown here to be the most important process for brine genesis and sustainability of the Clayton Valley, NV brine deposit. A new subsurface basin model was developed and used to select Li-bearing solids to test the release mechanisms for Li. Ash (20-350 ppm Li) and bulk sediments (1000-1700 ppm Li) samples across depths in the basin represent the majority of the subsurface Li-bearing materials. Temperature dependent (25-95 oC) batch reaction experiments using low-salinity groundwater from the basin indicate a positive relationship between the amount of Li released and temperature. Four-step sequential extractions on a subset of bulk sediments indicate most Li is released from water and weak acid-soluble portions with approximately 30% of the total Li contained in the sediments released overall. We conceptualize that lithium is released from these samples via three mechanisms: 1) release of adsorbed Li; 2) cation exchange of Li and Mg and; 3) possible minor release from silicate structure at elevated temperatures. Based on these results and the abundance of Li-bearing sediments in the subsurface we estimate the mean Li mass in the basin materials to be between 24.4 to 58.0 Mt. This Li provides a continuous supply from water-rock interactions. This is now the largest known accumulation of Li in a basin-fill continental setting on a global scale.
    • Loading Deformation On Various Timescales Using Gps And Grace Measurements

      Fu, Yuning; Freymueller, Jeff (2012)
      Tidal, seasonal and long-term surface mass movements cause the earth to deform and the gravity field to change. Current geodetic satellites, GPS and GRACE, accurately measure these geophysical signals. I examine the effect on GPS solutions of using inconsistent reference frames to model ocean tidal loading (OTL). For seasonal loading, I choose two study areas, Nepal Himalaya and southern Alaska, and compare GPS-measured and GRACE-modeled seasonal hydrological ground loading deformation. Globally distributed stations are employed to compare GPS coordinate solutions with OTL corrections computed in different reference frames: center of mass of the solid Earth (CE), and center of mass of the Earth system (CM). A strong spectral peak at a period of ~14 days appears when inconsistent OTL models are applied along with smaller peaks at ~annual and ~semi-annual periods. Users of orbit/clock products must ensure to use OTL coefficients computed in the same frame as the OTL coefficients used by the analysis centers; otherwise, systematic errors will be introduced into position solutions. Continuous GPS measurements of seasonal deformation in Nepal Himalaya are compared with load model predictions derived from GRACE observations. The GPS seasonal height variation and GRACE-modeled seasonal vertical displacement due to the changing hydrologic load exhibit consistent results, for both amplitude and phase. GRACE indicates a long-term mass loss in the Himalaya region, which leads to crustal uplift since the earth behaves as an elastic body. We model this effect and remove it from GPS observed vertical rates. Then most GPS vertical rates can be explained by interseismic strain from the Main Himalayan Thrust. In southern Alaska, vertical seasonal loading deformation observed by GPS stations and modeled displacements due to seasonal hydrological loading inferred from GRACE are highly correlated. The effects of atmosphere and non-tidal ocean loading are important. Adding the AOD1B de-aliasing model to the GRACE solutions improves the correlation between these two geodetic measurements, because the displacements due to these loads are present in the GPS data. Weak correlations are found for some stations located in areas where the magnitude of the load changes over a short distance, due to GRACE's limited spatial resolution.
    • Local scale structures in earth's thermospheric winds and their consequences for wind driven transport

      Dhadly, Manbharat Singh; Conde, Mark; Collins, Richard; Olson, John; Hampton, Donald; Smith, Roger (2015-12)
      In the traditional picture of Earth's upper thermosphere (~190-300 km), it is widely presumed that its convective stability and enormous kinematic viscosity attenuate wind gradients, and hence smooth out any structure present in the wind over scale size of several hundreds of kilometers. However, several independent experimental studies have shown that observed upper thermospheric wind fields at high latitudes contain stronger than expected local-scale spatial structures. The motivation of this dissertation is to investigate how the resulting local-scale gradients would distort neutral air masses and complicate thermospheric wind transport. To achieve this goal, we examined the behavior of a simple parameter that we refer to as the "distortion gradient". It incorporates all of the wind field's departures from uniformity, and is thus capable of representing all resulting contributions to the distortion or mixing of air masses. Climatological analysis of the distortion gradient using 2010, 2011, and 2012 wind data from the All-sky Scanning Doppler Imager (SDI) located at Poker Flat (65.12N, 147.47W) revealed the diurnal and seasonal trends in distortion of thermospheric masses. Distortion was observed to be dependent on geomagnetic activity and orientation of the interplanetary magnetic field. To understand the time-cumulative influence of these local-scale non-uniformities on thermospheric wind driven transport, time-resolved two-dimensional maps of the thermospheric vector wind fields were used to infer forward and backward air parcel trajectories. Tracing air parcel trajectories through a given geographic location indicates where they came from previously, and where they will go in the future. Results show that wind driven transport is very sensitive to small-scale details of the wind field. Any local-scale spatial wind gradients can significantly complicate air parcel trajectories. Transport of thermospheric neutral species in the presence of the local-scale wind gradients that we observed was found to be far more complicated than what current models typically predict. To validate these findings, we cross-compared the upper thermospheric neutral winds inferred from a narrow field of view Fabry-Perot interferometer with winds measured by our all-sky SDI. A high degree of correlation was present between their measurements. This cross-validation study suggests the presence of small-scale short-lived, and previously unobserved wind features in the upper thermosphere, with typical length scales less than ~40 km. The spatially and temporally localized wind features implied by this study represent a new and unexplored regime of dynamics in the thermosphere.
    • Localization of Francisella pathogenicity island-encoded secreted proteins and their secretion system

      Hare, Rebekah Frances; Hueffer, Karsten; Taylor, Barbara; Duffy, Larry (2014-05)
      Intracellular pathogens have evolved virulence genes that allow them to exploit host cells for their life cycles, and virulence genes are commonly located in pathogenicity islands, such as the Francisella pathogenicity island of Francisella tularensis. The Francisella pathogenicity island is linked to virulence, intracellular growth, and a type VI secretion system. Since the Francisella pathogenicity island encodes a secretion system, I hypothesize that Francisella pathogenicity island encoded proteins are secreted during infection of host cells. The molecular mechanisms involved in the pathogenesis of this bacterium are not well understood and there are no readily available tools for studying these mechanisms. Therefore, I developed expression plasmids of all Francisella pathogenicity island encoded proteins as C-terminal and N-terminal epitope FLAG-tagged proteins. The Francisella pathogenicity island encoded proteins expressed from these plasmids successfully restored the intramacrophage growth phenotype in mutants of their respective genes that were deficient for intramacrophage growth. Immuno-fluorescence microscopy experiments of cells infected with bacteria containing the expression plasmids showed some of the Francisella pathogenicity island encoded proteins were secreted. To test if protein localization is dependent on the type VI secretion system, localization observed in wild type was compared to the localization of Francisella pathogenicity island encoded proteins in a pdpB mutant, a gene that is homologous to a type VI secretion system structural inner membrane protein. The localization of FLAG-tagged proteins was significantly reduced when expressed in the pdpB mutant compared to expression in wild type. Two of the secreted proteins, pdpC and pdpE, were tested for their roles in pathogenicity. pdpC was required for virulence in vivo but not for growth within macrophages. Plasmid expression of PdpC-FLAG and FLAG-PdpC in the pdpC mutant restored the virulent phenotype to that of the wild type. PdpE was not required for intramacrophage growth or virulence in mice. These data further support the hypothesis that the Francisella pathogenicity island encodes a secretome that contributes to the virulence of Francisella.
    • Long-Period Seismicity At Shishaldin Volcano, Alaska

      Petersen, Tanja; McNutt, Stephen R. (2006)
      Since it last erupted in 1999, Shishaldin Volcano, Aleutian Islands, Alaska, has been characterized by a continuous and extremely high level of seismicity. The activity consists of many hundreds to thousands long-period (LP; 1-2 Hz) earthquakes per day. The rate of one LP event every 0.5-5 minutes has remained more or less constant for the last 7 years. A high rate of LP seismicity has been associated with pre-eruptive activity at many other volcanoes presented in the volcano seismology literature. Shishaldin, however, shows no other signs of volcanic unrest except for a ~200 m high steam plume that nearly always emanates from the volcano's summit and occasional weak thermal anomalies observed in satellite imagery. This thesis investigates the nature of Shishaldin's unusual volcanic behavior, and provides a case-study that mainly focuses on seismic data recorded by the short-period monitoring network surrounding the volcano, but also integrates local infrasound data, visual observations and SO2 measurements. The observations suggest a steady-state volcanic process within an open conduit system that is capable of releasing a large amount of energy, approximately equivalent to at least one magnitude 1.8-2.6 earthquake per clay. Shishaldin infrasound signals recorded by a pressure sensor co-located with a seismic instrument are used to confine the source locations of the LP events to a depth of 240 +/- 200 m below the crater rim. The seismo-acoustic data suggest that the LP earthquakes are associated with degassing explosions, created by complex gas volume ruptures from a fluid-air interface. Measurements of the SO2 flux within the puffing summit plume have revealed low values (58 tons/day), suggestive of a hydrothermal system. Four time periods of increased earthquake amplitudes, which each lasted about 1-2 months; have been analyzed. The periods of elevated seismicity are characterized by an abundance of LP events with highly similar waveforms that represent a spatially confined, repetitive, and non-destructive source process. A mechanism, known as choked flow, fulfills all the requirements implied by the observed repeating events and provides a plausible trigger mechanism for Shishaldin's LP events. The observations suggest that the hydrothermal system at Shishaldin is multi-fractured, regulating a pressure gradient within the gas flow through the uppermost conduit.
    • Long-term monitoring of geodynamic surface deformation using SAR interferometry

      Gong, Wenyu; 龚文瑜; Meyer, Franz; Atwood, Donald; Freymueller, Jeff; Lu, Zhong; Webley, Peter (2014-05)
      Synthetic Aperture Radar Interferometry (InSAR) is a powerful tool to measure surface deformation and is well suited for surveying active volcanoes using historical and existing satellites. However, the value and applicability of InSAR for geodynamic monitoring problems is limited by the influence of temporal decorrelation and electromagnetic path delay variations in the atmosphere, both of which reduce the sensitivity and accuracy of the technique. The aim of this PhD thesis research is: how to optimize the quantity and quality of deformation signals extracted from InSAR stacks that contain only a low number of images in order to facilitate volcano monitoring and the study of their geophysical signatures. In particular, the focus is on methods of mitigating atmospheric artifacts in interferograms by combining time-series InSAR techniques and external atmospheric delay maps derived by Numerical Weather Prediction (NWP) models. In the first chapter of the thesis, the potential of the NWP Weather Research & Forecasting (WRF) model for InSAR data correction has been studied extensively. Forecasted atmospheric delays derived from operational High Resolution Rapid Refresh for the Alaska region (HRRRAK) products have been compared to radiosonding measurements in the first chapter. The result suggests that the HRRR-AK operational products are a good data source for correcting atmospheric delays in spaceborne geodetic radar observations, if the geophysical signal to be observed is larger than 20 mm. In the second chapter, an advanced method for integrating NWP products into the time series InSAR workflow is developed. The efficiency of the algorithm is tested via simulated data experiments, which demonstrate the method outperforms other more conventional methods. In Chapter 3, a geophysical case study is performed by applying the developed algorithm to the active volcanoes of Unimak Island Alaska (Westdahl, Fisher and Shishaldin) for long term volcano deformation monitoring. The volcano source location at Westdahl is determined to be approx. 7 km below sea level and approx. 3.5 km north of the Westdahl peak. This study demonstrates that Fisher caldera has had continuous subsidence over more than 10 years and there is no evident deformation signal around Shishaldin peak.
    • Longwave Radiative Transfer In The Atmosphere: Model Development And Applications

      Delamere, Jennifer Simmons; Stamnes, Knut H. (2003)
      A FLexible Radiative Transfer Tool (FLRTT) has been developed to facilitate the construction of longwave, correlated k-distribution, radiative transfer models. The correlated k-distribution method is a technique which accelerates calculations of radiances, fluxes, and cooling rates in inhomogeneous atmospheres; therefore, correlated k-distribution models are appropriate for simulations of satellite radiances and inclusion into general circulation models. FLRTT was used to build two new rapid radiative transfer models, RRTM_HIRS and RRTM_v3.0, which maintain accuracy comparable to the line-by-line radiative transfer model LBLRTM. Iacono et al. [2003] evaluated upper tropospheric water vapor (UTWV) simulated by the National Center for Atmospheric Research Community Climate Model, CCM3, by comparing modeled, clear-sky brightness-temperatures to those observed from space by the High-resolution Radiation Sounder (HIRS). CCM3 was modified to utilize the rapid radiative transfer model RRTM and the separate satellite-radiance module, RRTM_HIRS, which calculates brightness temperatures in two HIRS channels. By incorporating these accurate radiative transfer models into CCM3, the longwave radiative transfer calculations have been removed as a significant source of error in the simulations. An important result of this study is that CCM3 exhibits moist and dry discrepancies in UTWV of 50% in particular climatic regions, which may be attributed to errors in the CCM3 dynamical schemes. RRTM_v3.0, an update of RRTM, is a rapid longwave radiative transfer appropriate for use in general circulation models. Fluxes calculated by RRTM_v3.0 agree with those computed by the LBLRTM to within 1.0 W/m2 at all levels, and the computed cooling rates agree to within 0.1 K/day and 0.3 K/day in the troposphere and stratosphere, respectively. This thesis also assessed and improved the modeling of clear-sky, longwave radiative fluxes at the Atmospheric Radiation Measurement Program North Slope of Alaska site by simultaneously addressing the specification of the atmosphere, radiometric measurements, and radiative transfer modeling. Consistent with findings from other field sites, the specification of the atmospheric water vapor is found to be a large source of uncertainty in modeled radiances and fluxes. Improvements in the specification of carbon dioxide optical depths within LBLRTM resulted, in part, from this analysis.
    • Lung breathing in the bullfrog: generating respiratory rhythm and pattern

      Davies, Brittany L. (2008-08)
      This research investigated location of the lung respiratory rhythm generator (RRG) in the bullfrog brainstem using neurokinin-1 (NK1R) and [mu]opioid ([mu]OR) receptor colocalization and characterized the role of these receptors in breathing pattern formation. colocalization was distinct near the facial nucleus in juvenile bullfrogs but not in tadpoles. NK1R intensity exhibited no developmental change, while [mu]OR intensity increased from late-stage tadpoles to juvenile frogs. Substance P (NK1R agonist; bath applied) increased lung burst frequency, lung burst cycle frequency (BCF), episode frequency, lung burst amplitude and area, but decreased number of lung bursts per episode and lung burst duration. Antagonist D decreased lung burst frequency and BCF, episode frequency, and the number of lung bursts per episode, and increased lung burst duration and area. DAMGO ([mu]OR agonist; bath applied) decreased lung burst frequency and BCF, episode frequency, and number of lung bursts per episode, but increased all lung burst parameters. Naloxone ([mu]OR antagonist) increased lung burst frequency and BCF, episode frequency, lung bursts per episode but decreased all lung burst parameters. Together these results indicate that NK1R and [mu]OR colocalization represents the lung RRG, and that episode formation is intrinsic to the respiratory control network but may or may not originate in the RRG.
    • Macro description of public beach attributes that may effect turtle nesting in Playa de Coco, La Flor (Pacific, southwest Nicaragua) and Pacuare and Tortuguero, (Caribbean, Costa Rica), July 2013

      Huettmann, Falk (Maderas Rainforest Conservancy, 2013-07-29)
      We observed several macro beach features of four public sea turtle nesting beaches for Playa Coco (latitude11.15382, longitude 85.80051; geographic datum WGS84) and La Flor (latitude 11.14282, longitude 85.79418) in southwest Nicaragua (Pacific), and Pacuare Reserve (latitude10.20123, longitude, 83.25925) and Tortugero (latitude 10.59583, longitude 83.52520) in Costa Rica (Caribbean). Recorded features included the intensity of tourism, number of different predator species of sea turtle hatchlings, number of tourists, and line transects for density of plastic, wood, metal, and crab burrows. Light and sound disturbances at night were also recorded as well as man-made objects left overnight on the shore of the beaches. This data set is part of a sea turtle class with Maderas Rainforest Conservancy and provides a basic and non-invasive description and a snap shot in time and space for public nesting beaches of relevance for Olive Ridley (Lepidochelys olivacea, TSN 173840), Green (Chelonia mydas TSN 173833), Hawksbill (Eretmochelys imbricata TSN ) and Leatherback (Dermochelys coriacea TSN 173843 ) sea turtles. Some photos were taken for vizualisation purposes.
    • Mafic -Silicic Magma Interactions From Volcanic To Plutonic: Implications For The Evolution And Eruption Of Silicic Magma Chambers

      Chertkoff, Darren Grant; Eichelberger, John C. (2002)
      In order to investigate the role that mafic-silicic magma interactions play in the origin, evolution, and eruption of shallow crustal magma chambers, a three-part study was undertaken of both effusive (Mt. Dutton volcano, Alaska) and explosive (Volcan Ceboruco, Mexico) eruptions, as well as associated volcanic (Unalaska Formation) and plutonic (Captain's Bay pluton) suites. Major- and trace-element variations suggest that the eruptive products (both andesite and dacite) of Mt. Dutton are not simply a result of fractional crystallization, but instead are affected to varying degrees by two-component mixing of distinct and separate magmas. In this case, petrologic and geochemical evidence, as well as eruptive stratigraphy, suggests the evolution of shallow, silicic magmatic systems inferred to exist beneath small stratovolcanoes can be modeled as resulting from repeated intrusion of mantle-derived mafic magmas into shallow, silicic, crystal-rich, crustal magma chambers. Volcan Ceboruco, Mexico, erupted ~1000 years ago, producing the Jala Pumice and forming a ~4 km wide caldera. During that eruption, 2.8 to 3.5 km3 of rhyodacite magma and 0.2 to 0.5 km 3 of mixed dacite magma were tapped and deposited as the Jala Pumice. Subsequently, the caldera was partially filled by extrusion of the Dos Equis Dome, a low-silica dacite dome with a volume of ~1.3 km3. In this case, petrographic evidence indicates that the Jala and Dos Equis dacites originated largely through the mixing of three end-member magmas: (1) rhyodacite magma, (2) dacite magma, and (3) mafic magma. Study of the Captain's Bay pluton and Unalaska Formation volcanics from Unalaska Island, Alaska, indicates that whole-rock compositions between the two suites span a similar range and particular plutonic units correspond chemically to specific volcanic products. Plagioclase phenocrysts from these chemically similar units also display comparable textures and compositional zoning patterns. Most strikingly, magmatic enclaves found within the pluton show a chemical affinity to andesite lavas from the volcanic suite. In this case, mixing of melts and extrusion of hybrid lava may be a prompt response to recharge, whereas the enclaves may represent "leftovers" that thermally equilibrated with the reservoir as a whole.
    • Magmas In Motion: Degassing In Volcanic Conduits And Fabrics Of Pyroclastic Density Current

      Burgisser, Alain; Eichelberger, John (2003)
      Volcanoes are caused by the transport of magma batches from the Earth's crust to the surface. These magmas in motion undergo drastic changes of rheologic properties during their journey to the surface and this work explores how these changes affect volcanic eruptions. The first part of this study is devoted to the dynamic aspects of degassing and permeability in magmas with high pressure, high temperature experiments on natural volcanic rocks. Degassing is measured by the influence of decompression rate on the growth of the bubbles present in the magma while permeability is deduced from the temporal evolution of these bubbles. The parameterization of our results in a numerical model of volcanic conduit flow show that previous models based on equilibrium degassing overestimate the acceleration and the decompression rate of the magma. Assessing permeability effects derived form our results show that the transition between explosive and effusive eruptions is a strong function of the magma initial ascent rate. The second part of this work is a unification of two end-members of pyroclastic currents (highly concentrated pyroclastic flows and dilute, turbulent pyroclastic surges) using theoretical scaling arguments based on multiphase physics. Starting from the dynamics of the particle interactions with a fundamental eddy, we consider the full spectrum of eddies generated within a turbulent current. We demonstrate that the presence of particles with various sizes induces a density stratification of the current, leading to its segregation into a basal concentrated part overlain by a dilute cloud. To verify our predictions on the interactions of such a segregated pyroclastic current with its surroundings (hills and sea), we studied the products of the 2050 BP caldera-forming eruption of Okmok Volcano (Alaska). This field study allowed us to reconstruct the eruptive sequence and to validate the main aspects of our theoretical model, such as the superposition of a dense and dilute part, their decoupling at sea entrance and the characteristics of the particles they transport.
    • Magnetic Reconnection As A Chondrule Heating Mechanism

      Lazerson, Samuel A.; Wiechen, Heinz (2010)
      The origin of chondrules (sub-millimeter inclusions found in stony meteorites) remains today an open question despite over century of examination. The age of these proto-solar relics shows a well defined cutoff of around 4.5 billion years ago. This places them as the oldest solids in the solar system. Chemical examination indicates that they experienced heating events on the order of 5000 K/hr for periods of around 30 minutes, followed by extending periods of cooling. Additional examination indicates the presence of large magnetic fields during their formation. Most attempts to explain chondrule formation in the proto-solar nebula neglect the existence of a plasma environment, with even less mention of dust being a charge carrier (dusty plasma). Simulations of magnetic reconnection in a dusty plasma are forwarded as a mechanism for chondrule formation in the proto-solar nebula. Here large dust-neutral relative velocities are found in the reconnection region. These flows are associated with the dynamics of reconnection. The high Knudsen number of the dust particles allows for a direct calculation of frictional heating due to collisions with neutrals (allowing for the neglect of boundary layer formation around the particle). Test particle simulations produce heating equivalent to that recorded in the chondrule mineral record. It is shown that magnetic reconnection in a dusty plasma is of fundamental importance to the formation of the most primitive solids in the solar system.
    • Magnetic reconnection in the presence of sheared plasma flow

      La Belle-Hamer, Annette Louise; Lee, L. C. (1994)
      Classical models of magnetic reconnection consist of a small diffusion region bounded by two slow shocks, across which the plasma is accelerated. Most space plasma current sheets separate two different plasmas, violating symmetry conditions across the current sheet. One form of asymmetry is a sheared plasma flow. In this thesis, I investigate the magnetic reconnection process in the presence of a shear flow across the current sheet using two-dimensional magnetohydrodynamic (MHD) simulations. The results show that only for sheared flow below the average Alfven velocity of the inflow regions can steady state magnetic reconnection occur. A detailed examination of the Rankine-Hugoniot jump conditions reveals that the two slow shocks of earlier models are replaced by a strong intermediate shock and a weaker slow shock in the presence of shear flow. Both symmetric and asymmetric density profiles are examined. Depending upon the direction of the flow in the adjacent inflow region, the effects from the sheared flow and the effects from the density asymmetry will compete with or enhance each other. The results are applied to the dayside and flank regions of the magnetosphere. For tailward flow in the flanks, the two asymmetries compete making the magnetic field transition layer broad with the high speed flow contained within the transition region. For the dayside region, the magnetic field transition region is thin and the accelerated flow is earthward of the sharp current layer (magnetopause). These results are consistent with the data. A velocity shear in the invariant direction was examined under otherwise symmetric conditions. With the magnetic field initially only in the $x-y$ plane, $B\sb{z},$ and consequently field-aligned current, is generated by the initial $v\sb{z}.$ The field-aligned current depends on the velocity profiles in all directions. For a velocity sheared in both the z and the y direction, the results show a very localized region of large field-aligned currents.
    • Magnetohydrodynamic Simulations Of Plasma Dynamics In The Magnetospheric Cusp Region

      Adamson, Eric T.; Otto, Antonius (2012)
      The Earth's magnetospheric cusp regions are rich in interesting plasma physics. The geomagnetic cusps offer solar wind plasma a relatively easy entry point into the magnetosphere through magnetic reconnection with the interplanetary magnetic field. The cusp regions are characterized by various interesting and important observations such as low energy particle precipitation, significant outflow of ionospheric material, and the frequent presence of energetic particles in regions of depressed magnetic field strength. The physical mechanisms that lead to these observations is often unresolved, for instance the acceleration mechanism for energetic cusp populations is not understood, nor is it known what implications they may have on magnetospheric dynamics. It is however, well accepted that magnetic reconnection plays a critical role in the vicinity of the cusps and is likely responsible for much of the dynamics in the region. Modeling of the geomagnetic cusps is notoriously challenging. Global magnetospheric models have proven indispensable in the study of the interaction of the solar wind plasma with the Earth's magnetosphere, however, the exterior cusp region poses a significant challenge for these models due to their relatively small scale. I have developed a mesoscale cusp-like magnetic field model in order to provide a better resolution (up to 300 km) of the entire cusp region than is possible in these global models. Typical observational features of the high-altitude cusps are well reproduced by the simulation. Results for both strongly northward and strongly southward interplanetary magnetic field indicate extended regions of depressed magnetic field and strongly enhanced plasma beta (cusp diamagnetic cavities). The Alfvenic nature of the outer boundary between the cusp and magnetosheath, in addition to the flow characteristics in the region, indicate that magnetic reconnection plays an important role in structuring the high-altitude cusp region. The inner boundaries with magnetosphere are gradual transitions forming a clear funnel. These cavities further present a unique configuration in which reconnecting magnetic flux tubes may gain a significant amount of flux tube entropy (H = p1/gammaV) through topological changes due to magnetic reconnection.
    • Magnetospheric imaging of EUV emissions at 83.4 and 30.4 nm wavelengths

      Garrido, Dante Espino; Smith, R. W. (1994)
      Magnetospheric images are constructed from resonant scattering of emissions by He$\sp+$ 30.4-nm and O$\sp+$ 83.4-nm ions from different spatial locations to study the structure of the intensities and its relation to the distribution of He$\sp+$ and O$\sp+$ ions around the Earth. The image intensities at these EUV wavelengths were obtained from a knowledge of ion scattering rates and available data on ion densities. This particular approach is called forward modelling and consists of the calculation of simulated EUV images of the magnetosphere. Different regions in the magnetosphere have been considered in this study to determine the dependence of the image intensities on ion energies and ion drift speeds with respect to the Sun-Earth line. Hot O$\sp+$ ions in the energy range from 1 keV to 50 keV are present in the plasma sheet with typical densities of the order of 0.1 ions cm$\sp{-3}$ arising during disturbed times. Image intensities of the order of a few millirayleighs were obtained in our simulations for these densities. During quiet times the densities are of the order of 0.05 ions cm$\sp{-3}.$ The reduction of the image intensities as a result of Doppler shifts caused by ion motion relative to the Sun-Earth line is discussed in detail and the effects of ion dynamics (particle acceleration) in the polar cap on the image intensities have also been analyzed for both He$\sp+$ and O$\sp+$ ions. The possibility of detecting polar outflows may also depend on the location of the imager. Simulated images of the plasmasphere and trough regions in both 30.4-nm and 83.4-nm wavelengths have been obtained to reflect the relative abundance of the ions in these regions. Photometric intensities of He$\sp+$ at 30.4 nm were obtained from a spinning rocket at an altitude of 435 km. The different viewing angles covered a wide range of regions in the magnetosphere, and this particular rocket geometry offered the possibility of obtaining the He$\sp+$ ion distribution from the measured intensities. This method (forward inversion) can be applied to 2-D images and it is shown that it is possible to extract 3-D ion distributions from the images.
    • Managing The National Wildlife Refuge System With Climate Change: The Interaction Of Policy, Perceptions, And Ecological Knowledge

      Magness, Dawn Robin (2009)
      The National Wildlife Refuge System (NWRS) is committed to conserving fish, wildlife, and plants for current and future generations of Americans. Given a rapidly changing climate, managers may employ various adaptation strategies to meet legislated mandates. I explore how ecological context, policy, perceptions and available ecological knowledge inform adaptation strategies. In Chapter 2, I develop an ecosystem vulnerability framework to better understand how climate change risk and ecosystem resilience interact to impact the NWRS. With GIS, I rank refuges based on historic temperature change, historic precipitation change, and sea-level rise risk. To index resilience, I rank refuges based on refuge size, landscape road density, and elevation range. Using this GIS analysis and the ecosystem vulnerability framework, I categorize the 527 refuges into four groups (refugia, ecosystem maintenance, facilitate transitions, and experiments in natural adaptation) that provide a necessary context for national, strategic adaptation planning. In Chapter 3, I survey 32% of NWRS biologists and managers to understand how policy and their perceptions of climate change influence adaptation choice. Currently, managers and biologists independently decide if climate change is natural or anthropogenic for wildlife management, and this conceptualization becomes important for deciding whether reactionary or anticipatory adaptation approaches are more appropriate. Although respondents considered practicability, they prefer historic condition. Respondents also prefer ecosystems and species adapt naturally. In a rapidly changing climate, natural adaptation may not be feasible without large-scale extinction. Nonetheless, many biologists and managers are uncomfortable with the alternative of manipulating ecosystems and species assemblages toward future conditions. Finally, understanding climate change impacts requires the analysis of complex ecological relationships over time and this complexity creates another barrier for implementing a national adaptation strategy. In Chapter 4, using a data-mining approach on data from scaled-down GCMs and an atypical monitoring approach, I build bioclimatic envelope models to show how the distributions of two passerines will potentially shift in response to climate change over the next 100 years on Kenai National Wildlife Refuge. In order to effectively manage species within the context of strategic adaptation planning, the NWRS must design future biological monitoring approaches with spatial modeling in mind.