• Investigation of North Pacific sea ice anomalies in the context of atmospheric and oceanic variability

      Tivy, Adrienne (2001-08)
      This study investigates the main mode of variability in North Pacific sea ice and examines the relationship between sea ice concentration and northern hemispheric climate variability for the period 1968-1997. Through empirical orthogonal function (EOF) analysis, correlations, and composite analysis, it was found that the seesaw pattern (first EOF of wintertime sea ice concentrations) between ice concentrations in the Bering Sea and the Sea of Okhotsk, generally used to characterize North Pacific sea ice, does not adequately address variability in the Sea of Okhotsk. Relationships between the sea ice dipole and the large-scale circulation were investigated and were found to change with the 1977 and 1989 regime shifts in the North Pacific climate. Before 1977 the sea ice dipole is strongly related to tropical variability while after 1977 the dipole is more strongly related to mid-latitude variability.
    • Investigation of novel secondary metabolites of colophospermum mopane

      Englund, Brian Michael (2005-05)
      Labdanes are a large and important class of diterpenes. Colophospermum mopane seems to be a source of 'primitive' 9, 13-epoxylabdanes. The structures of these compounds are 'missing links' in the biogenesis of 9, 13-epoxylabdanes. This research reports a new compound extracted from the seeds of C. mopane. The structures of this compound has been completely elucidated by NMR spectroscopy, and the stereochemistry of the compound supports predictions based on biosynthetic arguments. Furthermore, this thesis also corrects NMR assignments previously reported by another group.
    • Investigation of strongly ducted infrasonic dispersion using a vertical eigenfunction expansion of the Helmholtz equation in a modal broad band acoustic propagation code

      Edon, Robert Alexander; Olson, John V.; Fee, David E.; Szuberla, Curt A. (2015-12)
      This study investigates an infrasound propagation model created by the National Center for Physical Acoustics (NCPA) which is applied to atmospheric data with a strong temperature inversion in the lower atmosphere. This temperature inversion is believed to be the primary cause of a dispersed infrasonic signal recorded by an infrasound sensor array located on the Southern California coast in August, 2012. The received signal is characterized by initial low frequency content followed by a high frequency content tail. It is shown the NCPA model is hindered by limited atmospheric data and no ground truth for the source function which generated the received signal. The results of the NCPA model are shown to not reproduce the recorded signal and provide inconclusive evidence for infrasonic dispersion.
    • Investigation Of The Allosteric Modulators Desformylflustrabromine And 4-(2-Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) Interactions On Nicotinic Acetylcholine Receptors

      Daniello-Weltzen, Maegan M.; Schulte, Marvin K. (2011)
      Neuronal nicotinic acetylcholine receptors (nAChRs) are members of the Cys-loop super family of ligand gated ion channels. Dysregulation of nAChRs can lead to pathologies such as Alzheimer's disease, Parkinson's disease, Autism and nicotine addiction. Possible new therapeutic avenues are positive allosteric modulators (PAMs). The natural product desformylflustrabromine (dFBr), a tryptophan metabolite of the marine bryozoan Flustra foliacea, was found to be PAM of alpha4beta2 nAChR. Evaluation of our synthetic water soluble dFBr salt by two-electrode voltage clamp of Xenopus laevis oocytes expressing human nAChR confirmed that synthetic dFBr displayed similar properties as the natural product. Low concentrations of the synthetic dFBr enhanced ACh's efficacy on alpha4beta2 receptors. At higher dFBr concentrations, dFBr inhibited ACh potentiated responses. On alpha7 receptors, dFBr inhibited ACh induced currents. Further pharmacological characterization of dFBr revealed that dFBr was able to enhance partial agonist potencies and efficacies. Evaluation of dFBr on antagonists showed no effect on antagonist inhibition. The mechanisms of biphasic modulation (potentiation and inhibition) of dFBr on alpha4beta2 nAChR were also investigated. Enhanced efficacy of ACh induced currents by dFBr appeared to be accomplished by dFBr stabilization of the open receptor conformation by destabilization of the desensitized state. The inhibition of ACh potentiated currents by dFBr appeared to involve open-channel block. To better understand dFBr mechanisms, its putative binding site was examined. Alanine mutations were made in non-orthosteric clefts on the beta2+ and alpha4- faces. Results revealed residues located on these faces are involved in ACh induced conformational change of the receptor. In addition our data supports our hypothesis that allosteric modulation by dFBr interacts with residues located on the beta2+ and alpha4- faces. The new novel actions of (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) (HEPES) as a alpha4beta2 stoichiometric PAM was discovered and characterized. We showed that HEPES, a common buffering agent, potentiated the high ACh sensitivity alpha4beta2 receptor while only inhibiting the low ACh sensitivity alpha4beta2 receptor. Mutagenesis results suggested that residue beta2D217 is a critical residue in the HEPES binding site. Results from these studies will aid in the development of therapeutic ligands that will assist in the treatment of diseases where nAChRs are dysregulated.
    • Investigation of thin midlevel ice clouds in the Arctic using calipso data and radiative transfer modeling

      Kayetha, Vinay Kumar; Collins, Richard; Meyer, Franz; Prakash, Anupma; Bhatt, Uma (2015-08)
      In this research we investigate the global occurrence and properties of optically thin midlevel ice clouds. These clouds are difficult to detect with passive radiometric techniques and are under-represented in current studies. We use the Cloud Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) data set to identify thin midlevel ice clouds and determine their global occurrence and distribution. For the first time, we find that the global mean occurrence of these clouds is at least 4.5%, being at least 7.3% of all the tropospheric clouds detected at a horizontal scale of 10 km. Seasonally, these clouds are found most commonly in the polar regions. These clouds occur most commonly in the Arctic in winter and least commonly in the summer. In winter these clouds can occur up to 19% of the time. The occurrence of these clouds decreases with increasing spatial scale and are most commonly found at spatial scales of 25 km or less. We found five large distinct clouds over the Arctic and investigated them for their meteorological conditions and radiative effects. These thin midlevel ice clouds are formed along the frontal zones in weakly ascending air masses. Our model simulations show that thin midlevel ice clouds have a net warming effect on the surface of 23-48 W/m². We conclude that these clouds have a significant impact on the radiation budget in Arctic winters. Our study highlights the importance of active satellite-based remote sensing in globally detecting and characterizing optically thin clouds. Our estimates of occurrence and fraction of clouds represents a lower bound, as these clouds can be obscured by optically thicker clouds. The volume of measurements provided by the satellite allowed us to identify a small but consistent set of large clouds with which we could conduct a contemporary radiative analysis. These findings can be used to improve the representation of clouds and their impacts in regional and global climate models.
    • Investigation On Cirrus Clouds By The Cloud-Aerosol Lidar And Infrared Pathfinder Satellite Observation Data

      Zhu, Jiang; Sassen, Kenneth (2011)
      Understanding and describing the role of clouds in the climate system need intensive and extensive research on cloud properties. The albedo and greenhouse effects of clouds and their relations with the physical properties of clouds are analyzed. Cloud-top height and ice water content are key factors in impacting the longwave and shortwave radiation, respectively. Lidar and infrared radiometer measurement technologies are introduced. Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) level 1 Lidar profile, level 2 cloud layer, and level 2 Lidar/IIR track products are briefly reviewed. The algorithms for identification of cirrus clouds, Linear Depolarization Ratio (LDR), and effective diameter are presented. An average LDR profile is calculated by using the sum of total attenuated backscattering profiles and the sum of perpendicular attenuated backscattering profiles. A weight-average method is applied to calculate the average LDR. A split-window method is applied to estimate the effective diameters of clouds. A set of bulk ice crystal models and a radiative transfer model are applied to produce a look-up table that includes the radiative transfer simulation results. The macro-physical properties of cirrus clouds are analyzed. The frequency of occurrence of cirrus clouds varies with latitude, and strongly relates to the atmospheric circulation. Cirrus clouds are few in high-pressure zones and abundant where seasonal monsoonal circulation occurs. Cloud-top height decreases with increasing latitude. Cloud-top temperature is lower in the tropical regions than in the midlatutude and the polar regions. The measured cloud thickness shows a great diurnal variation.
    • Investigation on the impacts of low-sulfur fuel used in residential heating and oil-fired power plants on PM₂.₅₋ concentrations and its composition in Fairbanks, Alaska

      Leelasakultum, Ketsiri; Mölders, Nicole; Bhatt, Uma; Collins, Richard (2013-08)
      The effects of using low-sulfur fuel for oil-heating and oil-burning facilities on the PM₂.₅-concentrations at breathing level in an Alaska city surrounded by vast forested areas were examined with the Weather Research and Forecasting model coupled with chemistry packages that were modified for the subarctic. Simulations were performed in forecast mode for a cold season using the National Emission Inventory 2008 and alternatively emissions that represent the use of low-sulfur fuel for oil-heating and oil-burning facilities while keeping the emissions of other sources the same as in the reference simulation. The simulations suggest that introducing low-sulfur fuel would decrease the monthly mean 24h-averaged PM₂.₅-concentrations over the city's PM₂.₅-nonattainment area by 4%, 9%, 8%, 6%, 5% and 7% in October, November, December, January, February and March, respectively. The quarterly mean relative response factors for PM₂.₅ of 0.96 indicate that with a design value of 44.7 µg/m³ introducing low-sulfur fuel would lead to a new design value of 42 .9µg/m³ that still exceeds the US National Ambient Air Quality Standard of 35µg/m³ . The magnitude of the relation between the relative response of sulfate and nitrate changes differs with temperature. The simulations suggest that in the city, PM₂.₅-concentrations would decrease more on days with low atmospheric boundary layer heights, low hydrometeor mixing ratio, low downward shortwave radiation and low temperatures. Furthermore, a literature review of other emission control measure studies is given, and recommendations for future studies are made based on the findings.
    • Investigations in phylogenetics: tree inference and model identifiability

      Yourdkhani, Samaneh; Rhodes, John A.; Allman, Elizabeth S.; McIntyre, Julie; Williams, Gordon (2020-05)
      This thesis presents two projects in mathematical phylogenetics. The first presents a new, statistically consistent, fast method for inferring species trees from topological gene trees under the multispecies coalescent model. The algorithm of this method takes a collection of unrooted topological gene trees, computes a novel intertaxon distance from them, and outputs a metric species tree. The second establishes that numerical and non-numerical parameters of a specic Prole Mixture Model of protein sequence evolution are generically identifiable. Algebraic techniques are used, especially a theorem of Kruskal on tensor decomposition.
    • 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.
    • Investigations of patterns of vegetation, distribution and abundance of small mammals and nesting birds, and behavioral ecology of arctic foxes at Demarcation Bay, Alaska

      Burgess, Robert M. (1984-05)
      Analyses of habitat use, activity budget and activity patterns of arctic foxes (Alopex lagopus) at known distribution and abundance of prey are presented. Behavioral data on foxes were collected by direct observation of 2 radio-collared females and their mates in summer 1979. Prey availability was determined through monitoring bird nest success and phenology, mark-recapture studies of small mammals, and analysis of vegetation patterns and distribution of prey in 1978 and 1979. Prey availability fluctuated dramatically within each season and between years. Foxes relied almost exclusively on avian prey in 1979. Small mammal densities were extremely low in 1979 and foxes failed to rear pups in that year. Fluctuating prey availability did not affect fox activity patterns, activity budget or habitat use. The significance of caching in regulating food availability and the relationship between scent-marking and foraging efficiency are discussed.
    • Investigations On The Impacts Of Land-Cover Changes And/Or Increased Carbon Dioxide Concentrations On Four Regional Water Cycles And Their Interactions With The Global Water Cycle

      Li, Zhao; Molders, Nicole (2007)
      A suite of simulations that combine reference (355ppmv), doubled and tripled CO2 concentrations alternatively without and with land-cover changes in four similar-sized study regions, the Yukon, Ob, St. Lawrence and Colorado basin and adjacent land, are performed with the fully coupled Community Climate System Model to investigate the impact on global and regional water cycles and the interaction of these regional water cycles with the global water cycle. The relative changes in water-cycle quantities caused by increased CO 2 enhance with latitude and CO2 concentrations. Regional and global water cycles interactions are more pronounced in a warmer climate, but regional precipitation and evapotranspiration is affected differently in high-latitudes (Yukon, Ob) than mid-latitudes (Colorado, St. Lawrence). Land-cover changes can have comparable impacts on regional water cycles than increased CO2 concentrations do. Land-cover changes substantially alter the high-latitude water cycles through enhanced snow-albedo feedback and mid-latitude water cycles through vegetation activity in the warm season. The land-cover changes in different regions interact with each other through heat and moisture advections and secondary effects. This interaction enhances with increasing CO2 concentrations. Interactions between land-cover changes and increasing CO2 concentrations enhance with increasing CO2 due to the high sensitivity of regional water cycles to temperature changes.
    • Ion dynamics in auroral potential structures and formation of ion conic distribution

      Yang, Wei-hong (1981-12)
      This thesis is concerned with the problem of how the positive ions are energized by the two-dimensional potential structures along auroral field lines; these auroral potential structures are known to be responsible for accelerating electrons into the ionosphere to produce discrete auroras. A systematic numerical study of the test ion dynamics in auroral potential structures, either V-shaped or S-shaped, has been carried out. Transverse ion accelerations occur if the width of the auroral potential structure (Lx ≤ ρi). This result shows that the conic distribution of upstreaming ions observed on auroral field lines can be generated by the same potential structures which produce the thin auroral arcs (Lx ≤ ρi). This transverse acceleration mechanism operates more effectively on heavier ions, resulting in O+ ions more energetic than H+ ions as indicated by observations.
    • Ionospheric correction of interferometric SAR data with application to the cryospheric sciences

      Liao, Heming; Meyer, Franz J.; Freymueller, Jeffrey T.; Tape, Carl; Watkins, Brenton (2018-08)
      The ionosphere has been identified as an important error source for spaceborne Synthetic Aperture Radar (SAR) data and SAR Interferometry (InSAR), especially for low frequency SAR missions, operating, e.g., at L-band or P-band. Developing effective algorithms for the correction of ionospheric effects is still a developing and active topic of remote sensing research. The focus of this thesis is to develop robust and accurate techniques for ionospheric correction of SAR and InSAR data and evaluate the benefit of these techniques for cryospheric research fields such as glacier ice velocity tracking and permafrost deformation monitoring. As both topics are mostly concerned with high latitude areas where the ionosphere is often active and characterized by turbulence, ionospheric correction is particularly relevant for these applications. After an introduction to the research topic in Chapter 1, Chapter 2 will discuss open issues in ionospheric correction including processing issues related to baseline-induced spectrum shifts. The effect of large baseline on split spectrum InSAR technique has been thoroughly evaluated and effective solutions for compensating this effect are proposed. In addition, a multiple sub-band approach is proposed for increasing the algorithm robustness and accuracy. Selected case studies are shown with the purpose of demonstrating the performance of the developed algorithm. In Chapter 3, the developed ionospheric correction technology is applied to optimize InSAR-based ice velocity measurements over the big ice sheets in Greenland and the Antarctic. Selected case studies are presented to demonstrate and validate the effectiveness of the proposed correction algorithms for ice velocity applications. It is shown that the ionosphere signal can be larger than the actual glacier motion signal in the interior of Greenland and Antarctic, emphasizing the necessity for operational ionospheric correction. The case studies also show that the accuracy of ice velocity estimates was significantly improved once the developed ionospheric correction techniques were integrated into the data processing flow. We demonstrate that the proposed ionosphere correction outperforms the traditionally-used approaches such as the averaging of multi-temporal data and the removal of obviously affected data sets. For instance, it is shown that about one hundred multi-temporal ice velocity estimates would need to be averaged to achieve the estimation accuracy of a single ionosphere-corrected measurement. In Chapter 4, we evaluate the necessity and benefit of ionospheric-correction for L-band InSAR-based permafrost research. In permafrost zones, InSAR-based surface deformation measurements are used together with geophysical models to estimate permafrost parameters such as active layer thickness, soil ice content, and permafrost degradation. Accurate error correction is needed to avoid biases in the estimated parameters and their co-variance properties. Through statistical analyses of a large number of L-band InSAR data sets over Alaska, we show that ionospheric signal distortions, at different levels of magnitude, are present in almost every InSAR dataset acquired in permafrost-affected regions. We analyze the ionospheric correction performance that can be achieved in permafrost zones by statistically analyzing correction results for large number of InSAR data. We also investigate the impact of ionospheric correction on the performance of the two main InSAR approaches that are used in permafrost zones: (1) we show the importance of ionospheric correction for permafrost deformation estimation from discrete InSAR observations; (2) we demonstrate that ionospheric correction leads to significant improvements in the accuracy of time-series InSAR-based permafrost products. Chapter 5 summarizes the work conducted in this dissertation and proposes next steps in this field of research.
    • Isolation and characterization of Photobacterium phosphoreum from migrating Alaskan salmon

      Budsberg, Kevin Jon (2004-05)
      We isolated luminous bacteria from drying chum salmon, Oncorhynchus keta, reported by Alaska native fishermen to be 'glowing in the dark.' The salmon were harvested for subsistence use from the Yukon River, Alaska. We identified our luminous bacterial isolates as Photobacterium phosphoreum based on nutritional versatility, and 16S rDNA and luxA gene sequences. P. phosphoreum has previously only been isolated from the marine environment. We tested whether our strains, isolated from fish harvested in freshwater, represent cold-adapted, freshwater-tolerant strains of P. phosphoreum. We also analyzed lux operon composition and organization, and examined the 5' promoter region of the lux operon for shared genes and regulatory elements from strains of P. phosphoreum from Alaska, the Black Sea, Oregon, and from near the Canary Islands. Our results indicate our P. phosphoreum strains have a lower optimal growth temperature than other strains but rapidly lose viability after inoculation into river water. Analyses of the P. phosphoreum lux operon reveal a striking pattern of conservation of composition and organization, and suggest there is conservation in the location of the transcriptional start among geographically separated strains of the same species.
    • Isostasy and origin of the Alpha-Mendeleev Ridge, Arctic Ocean

      Williams, Christina C. (2006-12)
      The Alpha-Mendeleev Ridge is an aseismic ridge bisecting the Amerasian Basin, Arctic Ocean. There is no widely accepted theory of formation. Gravity and bathymetry data from the poorly understood ridge are used to constrain the isostatic compensation of the feature in the frequency domain. Spectral analysis of the cross correlation between gravity and bathymetry along nine data transects collected from submarines and ice breakers over the ridge yield an average crustal thickness estimate of 30 km and density estimate of 2.75 g-cm⁻³. It also suggests compensation by local isostasy, as a near-ridge oceanic plateau or an extended fragment of continental shelf. These parameters are used to constrain gravity models of crustal structure. The analysis suggests no difference between the compensation of the Alpha and Mendeleev Ridges. These results are discussed in the broader tectonic context of the Amerasian Basin, in light of the current controversy over the formation of the ridge.
    • Jakobshavn Isbr�_: velocity variations from hourly to decadal time scales at Greenland's fastest tidewater glacier

      Podrasky, David Bryan; Truffer, Martin; Bueler, Edward; Hock, Regine; Larsen, Christopher; Motyka, Roman (2013-12)
      Outlet glaciers in Greenland, and elsewhere, have recently shown large variations in terminus position and ice flux. One example is the tidewater retreat of Jakobshavn Isbr�_, which began in the late 1990s with high thinning rates, acceleration and collapse of the floating glacier tongue. The retreat has continued to the present, with glacier speeds more than doubling in two decades' time. A campaign of in-situ measurements was initiated in 2006 with the aim of determining the importance of short-term forcing as a control on the continuing evolution of the glacier. Three years of continuous GPS measurements along the centerline of Jakobshavn Isbr�_ reveal seasonal velocity variations due to seasonally varying terminus position. The relationship between glacier speed and surface melt is complex, with both speed-up and slowdown events in response to variations in the rate of surface melt. During a particularly long and intense melt season in 2007, a series of melt-driven slowdowns effectively reduced the mean ice flow over the whole year. On shorter timescales, the response to surface meltwater input is more predictable with diurnal velocity variations of 1-2 % that closely match changes in meltwater input. The influence of iceberg calving and tidal forcing is restricted to the lower 10 km of the glacier, imposing an upper limit on longitudinal stress coupling length of a few ice thicknesses. The response to these forcings does not exceed 5 % of mean flow. This is consistent with a glacier operating under high driving stresses. Ice sheet velocities as far as 120 km inland of the margin have responded to the continuing retreat with increases in speed. The flow has also rotated toward the centerline of the main channel. This speedup and channelization of flow are the result of evolving ice surface gradients as the glacier continues to respond to changes initiated at the periphery. This shows that ocean driven changes have led to increased ice flux far inland on the Greenland Ice Sheet, implying a continuing large-scale evolution of the Jakobshavn Isbr�_ drainage basin.
    • Kaposi’s sarcoma-associated herpesvirus replication and transcription activator regulates extracellular matrix signal pathway

      Pfalmer, Daniel; Chen, Jiguo "Jack"; Ferrante, Andrea; Hueffer, Karsten (2016-08)
      Kaposi’s Sarcoma (KS) is a malignancy caused by infection with Kaposi’s Sarcoma-associated Herpesvirus [KSHV; also known as Human Herpesvirus 8 (HHV8)] in which tumor cells show a characteristic ‘spindle-like’ morphology. The transcription factor RTA (Replication and Transcription Activator) is the viral protein responsible for reactivating KSHV from its latent state. Production of RTA in latently infected cells causes a number of viral proteins to be produced and leads to a cascade of gene expression changes in both viral and host genes. Previous work in our lab showed that RTA was capable of reprogramming cells in vitro to display a spindle-like morphology. In this study we aimed to identify the host gene expression changes caused directly by RTA which could be responsible for that reprogramming. To that end, Madin-Darby Canine Kidney cells (MDCK cells) were chosen as a model for KSHV-naïve mammalian cells. Differences in host gene expression levels in a culture of MDCK cells transfected with a plasmid coding for expression of RTA compared to MDCK cells transfected with a similar plasmid lacking the RTA gene were measured by whole transcriptome sequencing (RNA-Seq). Cells containing the RTA-coding plasmid adopted a spindle-like morphology and showed at least a two-fold change in expression level in approximately 180 genes. Those 180 genes were then screened for known associations to signaling pathways in order to determine which might be involved with the morphological changes observed and/or biological significance. The expression levels of the 10 genes identified by that screening were then verified by quantitative real time PCR (qPCR). Of those 10 genes, eight were identified as potentially associated with the morphological changes, including three genes associated with extra cellular matrix (ECM) destruction (MMP9, CTSD, and CTSS) that were down-regulated; two genes associated with blocking ECM destruction (TIMP1 and TIMP2) that were pregulated; two ECM component genes (LAMC2 and COL1A2) that were upregulated; and one gene associated with blocking cell-cell and cell-ECM adhesion (MUC1) that was downregulated. The remaining two genes (MAP2K1 and podoplanin) were identified as potentially biologically significant, but not directly involved in regulating morphology. MAP2K1 is associated with epithelial dedifferentiation and was down-regulated; and the lymphatic endothelial specific marker podoplanin (PDPN) was up-regulated. Taken together, the differences in morphology and gene expression between RTA-producing cells and controls suggest a possible role for RTA in the formation of the spindle cells that characterize Kaposi’s sarcoma.
    • Kelvin-Helmholtz Instability And Magnetic Reconnection At The Earth's Magnetospheric Boundary

      Ma, Xuanye; Otto, Antonius; Lummerzheim, Dirk; Newman, David; Ng, Chung-Sang; Zhang, Hui (2012)
      Magnetic reconnection and Kelvin-Helmholtz (KH) instability are the two most important mechanisms for plasma transport across the Earth's magnetospheric boundary layer. Magnetic reconnection is considered as the dominant process for southward interplanetary magnetic field (IMF), and the KH instability is suggested to play an important role for northward IMF. It is interesting to note that this plasma entry is associated with a dramatic entropy increase, which indicates the existence of strong nonadiabatic heating during the entry process. Observations indicate a plasma entropy increase by two orders of magnitude during the transport from solar wind into the Earth's magnetosphere. Therefore, it is important to examine whether magnetic reconnection can provide sufficient nonadiabatic heating to explain the observed plasma properties and to identify plasma conditions that allow strong nonadiabatic heating. This thesis demonstrates that the entropy can indeed strongly increase during magnetic reconnection provided that the plasma beta, i.e., the ratio of thermal to magnetic energy density is small. A realistic three-dimensional configuration of the Earth's magnetopause for southward IMF conditions includes large anti-parallels magnetic components with a fast perpendicular shear flow. Thus, it is expected that KH modes and magnetic reconnection operate simultaneously and interact with each other. This thesis provides a systematic study on this interaction between reconnection and KH modes by means of three-dimensional MHD and Hall MHD numerical simulations. It is demonstrated that both reconnection and nonlinear KH waves change the other modes onset condition by changing the width of the transition layer. It is shown that dynamics of the system can be strongly modified by a guide field or Hall physics. In the presence of plasma flow, magnetic reconnection is also associated with the generation of field-aligned currents (FACs), which play a critical role in the coupling between the magnetosphere and ionosphere. This thesis also examines systematically the generation of FACs. It is demonstrated that such currents are generated either by a guide magnetic field, by shear flow, or by the inclusion of Hall physics already in two-dimensional magnetic reconnection.
    • King eider migration and seasonal interactions at the individual level

      Oppel, Steffen; Powell, Abby; Murphy, Edward; Verbyla, Dave; O'Brien, Diane (2008-12)
      Seasonal interactions describe how events during one season of the annual cycle of a migratory bird affect its fitness in subsequent seasons. Understanding the strength and mechanism of seasonal interactions is important to predict how migratory birds will respond to future challenges caused by habitat loss and climate change. This dissertation explores seasonal interactions between different stages of the annual cycle in an arctic-breeding sea duck, the King Eider (Somateria spectabilis). Concerns over recent population declines and potential effects of climate change on marine habitats used by the species highlight the need for a better understanding of its life history. I used satellite telemetry to describe migration routes, timing of migration events, and geographic regions used by King Eiders throughout the year. I found highly variable movement patterns, and wide dispersion of King Eiders to three regions in the Bering Sea during winter. I then developed stable isotope techniques to examine seasonal interactions at the individual level. First, I examined the relative contribution of body reserves to egg production using stable isotope analysis of egg components and blood. I found that most birds use only small proportions of body reserves to produce eggs, but rather rely on nutrients obtained on breeding grounds to form a clutch. Thus, contrary to general expectation, King Eiders use an income strategy to produce eggs, and I hypothesize that they may retain body reserves for incubation. Body reserves may reflect the residual body condition from the previous winter. I further examined whether females wintering in different regions in the Bering Sea had different rates of nest survival. The northern Bering Sea has a higher benthic biomass and is closer to breeding grounds than winter regions farther south. However, nest survival rates of female King Eiders in northern Alaska did not differ between females that had wintered in the northern or southern Bering Sea. Overall, I found large individual variation in movement and breeding strategies, and little evidence for strong seasonal interactions between winter, spring, and summer. This indicates that King Eiders are a very adaptable species that depend on resources acquired on breeding grounds to a larger extent than previously assumed.
    • King eider wing molt: inferences from stable isotope analyses

      Knoche, Michael J. (2004-12)
      The western North American population of the king eider is thought to have declined by over 50% between 1974 and 1996 without an apparent cause. The non-breeding period of king eiders consists of 80-100% of their annual cycle if not impossible by observation. I used stable carbon and nitrogen isotope values of feathers and muscle to examine the wing molt and migration ecology of king eiders in 2003. Eider primary feathers were isotopically homogenous along the length of the feather, implying invariable diets during wing molt. Captive eiders in their hatch-year did not fractionate nitrogen isotopes, potentially indicating preferential protein allocation associated with growth. Six percent of female eiders sampled molted primary feathers on their breeding grounds, which had not been previously substantiated. Tissue samples from both genders corroborated dietary shifts inherent in switching from a marine to terrestrial diet. Carbon isotopes of feathers from satellite-transmittered males were correlated with longitude of their known wing molt locations indicating that the gradient of carbon isotopes can be used to draw inferences about molt location of eiders.