• Basal shear strength inversions for ice sheets with an application to Jakobshavn Isbræ, Greenland

      Habermann, Marijke; Truffer, Martin; Maxwell, David; Freymueller, Jeff; Pettit, Erin; Tape, Carl (2013-12)
      Satellite and in situ observations of ice sheet outlet glaciers around the turn of the 21st century showed that rapid changes in ice dynamics are possible and important for the evolution of ice sheets. When attempting to model these dynamic changes the conditions at the ice-bed interface are crucial. Inverse methods can be used to infer basal properties, such as the basal yield stress, from abundant surface velocity observations by using a physical model of ice flow. Inverse methods are very powerful, but they need to be applied with care, otherwise errors can dominate the solution. In this study we investigate the potentials and caveats of inverse methods. Synthetic experiments can be designed where basal conditions are assumed and an ice flow model is used to produce a set of 'synthetic' surface velocities. These can then be used to examine and evaluate inverse methods. We find that in iterative inverse methods it is essential to use a stopping criterion that will prevent overfitting the data. We introduce a new and rapidly-converging iterative inverse method called Incomplete Gauss Newton method, where the linearized problem is partly minimized in each step.In a practical application of inverse methods to the terminus region of Jakobshavn Isbræ, Greenland we investigate changes in basal conditions over time by performing inversions for different years of available surface velocity data. We find a decrease in basal yield stress in the lower areas of the glacier that agrees with effective pressure changes due to the changes in ice geometry. This supports an ocean and terminus driven system. The difference between the modeled and observed velocity fields, called residual, contains information about the ability to reproduce the velocities when only adjustment of the basal condition is allowed. With a properly regularized inversion the residual patterns can be used to investigate sources of error in the system. We find that the ice geometry and the model simplifications influence the ability to reproduce observed velocity fields more than the error in observed velocity does. This indicates that further progress must come from model improvements and improved capabilities to measure bedrock geometry.
    • Bayesian methods in glaciology

      Brinkerhoff, Douglas; Truffer, Martin; Aschwanden, Andy; Tape, Carl; Bueler, Ed (2017-12)
      The problem of inferring the value of unobservable model parameters given a set of observations is ubiquitous in glaciology, as are large measurement errors. Bayes' theorem provides a unified framework for addressing such problems in a rigorous and robust way through Monte Carlo sampling of posterior distributions, which provides not only the optimal solution for a given inverse problem, but also the uncertainty. We apply these methods to three glaciological problems. First, we use Markov Chain Monte Carlo sampling to infer the importance of different glacier hydrological processes from observations of terminus water flux and surface speed. We find that the opening of sub-glacial cavities due to sliding over asperities at the glacier bed is of a similar magnitude to the opening of channels due to turbulent melt during periods of large input flux, but also that the processes of turbulent melting is the greatest source of uncertainty in hydrological modelling. Storage of water in both englacial void spaces and exchange of water between the englacial and subglacial systems are both necessary to explain observations. We next use Markov Chain Monte Carlo sampling to determine distributed glacier thickness from dense observations of surface velocity and mass balance coupled with sparse direct observations of thickness. These three variables are related through the principle of mass conservation. We develop a new framework for modelling observational uncertainty, then apply the method to three test cases. We find a strong relationship between measurement uncertainty, measurement spacing, and the resulting uncertainty in thickness estimates. We also find that in order to minimize uncertainty, measurement spacing should be 1-2 times the characteristic length scale of variations in subglacial topography. Finally, we apply the method of particle filtering to compute robust estimates of ice surface velocity and uncertainty from oblique time-lapse photos for the rapidly retreating Columbia Glacier. The resulting velocity fields, when averaged over suitable time scales, agree well with velocity measurements derived from satellites. At higher temporal resolution, our results suggest that seasonal evolution of the subglacial drainage system is responsible for observed changes in ice velocity at seasonal scales, and that this changing configuration produces varying degrees of glacier flow sensitivity to changes in external water input.
    • A Bayesian mixed multistate open-robust design mark-recapture model to estimate heterogeneity in transition rates in an imperfectly detected system

      Badger, Janelle J.; McIntyre, Julie; Barry, Ron; Goddard, Scott; Breed, Greg (2020-12)
      Multistate mark-recapture models have long been used to assess ecological and demographic parameters such as survival, phenology, and breeding rates by estimating transition rates among a series of latent or observable states. Here, we introduce a Bayesian mixed multistate open robust design mark recapture model (MSORD), with random intercepts and slopes to explore individual heterogeneity in transition rates and individual responses to covariates. We fit this model to simulated data sets to test whether the model could accurately and precisely estimate five parameters, set to known values a priori, under varying sampling schemes. To assess the behavior of the model integrated across replicate fits, we employed a two-stage hierarchical model fitting algorithm for each of the simulations. The majority of model fits showed no sign of inadequate convergence according to our metrics, with 81.25% of replicate posteriors for parameters of interest having general agreement among chains (r < 1.1). Estimates of posterior distributions for mean transition rates and standard deviation in random intercepts were generally well-defined. However, we found that models estimated the standard deviation in random slopes and the correlation among random effects relatively poorly, especially in simulations with low power to detect individuals (e.g. low detection rates, study duration, or secondary samples). We also apply this model to a dataset of 200 female grey seals breeding on Sable Island from 1985-2018 to estimate individual heterogeneity in reproductive rate and response to near-exponential population growth. The Bayesian MSORD estimated substantial variation among individuals in both mean transition rates and responses to population size. The correlation among effects trended positively, indicating that females with high reproductive performance (more positive intercept) were also more likely to respond better to population growth (more positive slope) and vice versa. Though our simulation results lend confidence to analyses using this method on well developed datasets on highly observable systems, we caution the use of this framework in sparse data situations.
    • Bayesian predictive process models for historical precipitation data of Alaska and southwestern Canada

      Vanney, Peter; Short, Margaret; Goddard, Scott; Barry, Ronald (2016-05)
      In this paper we apply hierarchical Bayesian predictive process models to historical precipitation data using the spBayes R package. Classical and hierarchical Bayesian techniques for spatial analysis and modeling require large matrix inversions and decompositions, which can take prohibitive amounts of time to run (n observations take time on the order of n3). Bayesian predictive process models have the same spatial framework as hierarchical Bayesian models but fit a subset of points (called knots) to the sample which allows for large scale dimension reduction and results in much smaller matrix inversions and faster computing times. These computationally less expensive models allow average desktop computers to analyze spatially related datasets in excess of 20,000 observations in an acceptable amount of time.
    • Beetles and spiders as indicators of forest recovery on Prince of Wales Island, Alaska

      Stockbridge, Jill M.; Sikes, Derek S.; Wagner, Diane; Kruse, James J. (2014-08)
      Commercial logging is among the most important disturbance factors affecting forest biota. An indirect effect of commercial logging is minimal understory within young even-aged forests, which can decrease forest biodiversity. To improve management of young even-aged forest stands within the Tongass National Forest (TNF), foresters are testing alternative forestry practices under the Tongass-Wide Young-Growth Studies (TWYGS). However, little is known about how the new thinning treatments included in the TWYGS will affect forest biota and the recovery of young even-aged forest stands as they transition back into old growth forests. To investigate the effects of thinned secondary growth on forest biota in the TNF on Prince of Wales Island, Alaska, I compared spider and beetle biodiversity in thinned secondary growth to old growth forest stands, clearcuts, and un-thinned secondary growth. Pitfall traps, Berlese funnels, and Lindgren© funnel traps were used to collect spiders and beetles in each forest type to compare species richness, diversity, and assemblages, as well as to identify possible ecological indicators within each habitat. I hypothesized that thinned secondary growth would have a mix of old growth and clearcut species and be further in the process of recovery than un-thinned secondary growth. I found that (1) spider and beetle species richness and diversity from thinned secondary growth were not significantly different from other forest treatments; (2) spider assemblages in thinned secondary growth were significantly different from other forest treatments, whereas beetle assemblages were not different; (3) spider and beetle assemblage structure was mainly influenced by Leaf Area Index (LAI) and; (4) spider and beetle ecological indicators of clearcuts and old growth stands were found within thinned and un-thinned secondary growth stands. These findings support my hypothesis that thinned secondary growth would have both old growth and clearcut species; however, thinned secondary growth was not found to be further in the process of recovery than unthinned secondary growth at the time of this study. Although thinned secondary growth was not further in the process of recovery, it did not adversely affect the biodiversity of spiders and beetles. My results suggest that logging on Prince of Wales Island can change spider and beetle assemblages, but it doesn't negatively impact species richness or diversity. Thinned secondary growth spider and beetle biodiversity may be in the process of recovery to the biodiversity seen in old growth forests. Therefore, spider and beetle biodiversity may resemble old growth forest biodiversity as LAI values increase with closing canopy in thinned secondary growth forest stands. In addition, a checklist of arthropods collected on Prince of Wales Island, Alaska, as part of this work, combined with records from other projects and publications, are included followed by a description of a new species I discovered, Caurinus tlagu Sikes & Stockbridge 2013 (Mecoptera, Boreidae, Caurininae).
    • The behavior of tellurium during copper ore processing at the American Smelting and Refining Company (Tucson, AZ)

      Josephson, Amy E.; Hayes, Sarah M.; Newberry, Rainer J.; Trainor, Thomas P. (2016-08)
      Essentially all tellurium (Te), an element used in solar panels and other high technology devices, is recovered as a byproduct of copper mining. Recent increases in demand have sparked questions of long-term supplies of Te (crustal abundance ~3 μg∙kg-1). As part of a larger study investigating Te resources, this project examines the behavior of Te during Cu ore mining, smelting, and refining at the American Smelting and Refining Company (Tucson, AZ) as a first step toward optimizing Te recovery. Mass balance calculations estimate that only 4 ± 1% of the Te in the ore reports to the Cu anodes, while 60 ± 30%, 0.8 ± 0.2% and 5.8 ± 0.4% is lost in the tailings, slag, and dust, respectively. The uncertainties reported are the standard deviation of analytical measurements, but due to heterogeneity of Te distribution in the ore, the actual uncertainty is likely higher. Microprobe data shows that Te in the concentrate is mainly present as telluride minerals, but substitution into sulfides most likely also occurs. X-ray fluorescence (XRF) mapping showed that Te is collocated with S in the raw anode slimes, pressed anode slimes, and doré furnace soda slag. X-ray absorption spectroscopy (XAS) was used to examine Te speciation in anode slimes. It was found that Te oxidizes during the Cu ore smelting process, with 44% Te4+ in the flash furnace SO₂ filter. Te also showed 32% Te4+ in the raw and pressed anode slimes. The doré furnace soda slag and dust filter showed the most oxidation of Te at 57% Te4+ and 60% Te6+ respectively. These results indicate several points in the extraction process that could be examined further to determine if additional Te might be recovered from the overall process.
    • Behavior, physiology, biological age, and cultural role of long-lived Bering Sea seabirds

      Young, Rebecca C.; Kitaysky, Alexander S.; Chapin, F. Stuart; Carothers, Courtney L.; Haussmann, Mark F. (2014-05)
      This dissertation focuses on the intersection of behavior, physiology, and biological age. Biological age is a measure of an organism's progress through life, and it incorporates chronological age as well as the actions of environment and innate quality at the individual level. We estimate biological age using telomere length as a biomarker. Telomere degradation in relation to oxidative stress links it directly to purported proximate mechanisms of aging under the free radical theory of aging. Short telomeres, or telomere loss, have been related to ecological indicators of lowered fitness. Our work focuses on aging in the thick-billed murre (Uria lomvia), a long-lived seabird breeding in the Bering Sea. Seabirds exemplify the "slow-lived" paradigm; they have long lifespans, low reproductive rates, and high adult survival. First we address the relationship between chronological age and telomere length in the thick-billed murre. We found longer telomeres in chicks than in adults, and longer telomeres in adult females than in adult males. Then we examine biological age, telomere length, in relation to physiology and behavior of murres equipped with a recording device to monitor foraging behavior. Chapter two describes the physiological and reproductive investment of these murres in relation to their biological age, while chapter three addresses the habitat and prey choices made by these birds in relation to sex, biological age, and environment. Behaviorally murres remain healthy into their old ages, with physiological diving capacity similar or improved in old birds. Stress patterns demonstrate that when conditions are good, older birds are more stressed, but experience buffers their stress levels under poor conditions. The fourth chapter of this thesis deals with seabirds as part of the larger socio-ecological system that includes the indigenous people living on the Pribilof Islands. The Priblovians value seabirds, but are members of periphery communities troubled by a poor economy and disconnected from a past that was tightly coupled to the natural world. Development requires active management by local stakeholders to reconnect with cultural and economic resources (like seabirds) and to make the communities more sustainable and resilient.
    • Benefits of using marginal opportunistic wildlife behavior data: Constraints and applications across taxa – a dominance hierarchy example relevant for wildlife management

      Jochum, Kim (2008-03-20)
      This study is a new approach on collecting, handling and examining wildlife behavior data across mammal species in order to provide new and unique conclusions from efficient data collection schemes. Sophisticated dominance hierarchy patterns and the ability of individual recognition are well described in many large mammals such as monkeys and cetaceans through the effort of detailed long-term studies. Their implications are well known as important topics regarding management strategies, especially for endangered species. However worldwide, for other large mammals, e.g. bears, detailed long-term wildlife behavior studies are virtually not available. This is due to the inaccessibility and inefficient observation abilities for many animal species in the wild, especially long-term studies. Up to now, it is believed that long-term studies are necessary to describe the existence of social structures like dominance hierarchies and individual perception abilities reliably and to present results in a sophisticated ‘significant’ manner. To accomplish more detailed behavior investigations on species where we lack such long-term data, here a new approach to this discipline ‘behavior modeling’ is presented, concentrating on the use of marginal opportunistic samples. This statistical approach has never been conducted to behavior analysis so far. Marginal behavior data for six species were investigated and c
    • Benzene as an indoor air pollutant in Fairbanks, Alaska

      Ricker, Janet Elaine (2000-08)
      Benzene is a known carcinogen found in gasoline, automobile exhaust, cigarette smoke, and organic solvents. Previous studies suggest that sources of chemicals within the home are the major factors influencing personal exposure to benzene. Indoor air was sampled for benzene in order to determine the concentrations present in Fairbanks homes, and to indentify what factors might be associated with higher concentrations. Sampling sites were limited to homes with attached garages and with no smokers in the household. A wide range of benzene concentrations was observed in the eight homes sampled. The highest concentration was about 70 ppbv, and the concentration in most homes was at or above 4 ppbv. The primary source of benzene appears to be gasoline, most likely from small engines (such as lawnmowers) stored in the attached garage. More sites, including homes with attached garages that contain various numbers of small engines, need to be sampled to confirm these conclusions.
    • Bioanalytical Development Of Charged Cyclodextrin Capillary Electrokinetic Chromatography And Microperfusion Sampling To Study Endogenous D-Serine And L-Glutamate Efflux In Brain

      Kirschner, Daniel L.; Greene, Thomas (2009)
      A multitude of studies have revealed specific biological mechanisms that contribute to D-amino acid action and regulation in the mammalian central nervous system. The remarkable increase in our understanding of D-amino acid function and distribution in mammals is in many ways a result of the development of sensitive enantioselective separation strategies that allow for quantification in real biological samples. In capillary electrokinetic chromatography (cEKC) the most powerful chiral resolving agents are anionic cyclodextrins (CDs), yet these have not previously been investigated for chiral bioanalysis of amino acids. The focus of this dissertation research was to investigate for the first time the feasibility of and application of anionic cyclodextrins as resolving agents in bioanalytical chiral separations of amino acids. This dissertation encompasses (1) the development of a new bioanalytical separation utilizing capillary electrophoresis laser induced fluorescence (CE-LIF) with sulfated-beta-cyclodextrin for analysis of D-serine (D-ser) and L-glutamate (L-glu) in mammalian brain, (2) the first synthesis and characterization of 6 members of a new family of single isomer sulfoalkyl cyclodextrins, (3) initial studies on chiral analysis of amino acids using single isomer sulfoalkyl CDs, and (4) development and application of a novel microperfusion sampling approach for acute brain slices and coupling of this method to the developed chiral CE-LIF for studying magnitude and timing of D-ser and L-glu efflux from acute hippocampus in response to modeled cerebral ischemia. The results of these studies demonstrate that (1) anionic CDs are powerful chiral selectors for amino acids and can be applied for sensitive bioanalysis of D-amino acids including D-ser, D-glu, and D-asp in brain samples; (2) single isomer sulfoalkyl CDs can be synthesized by regioselective reaction chemistry; (3) single isomer sulfoalkyl CDs are excellent resolving agents for amino acid analysis and may be valuable for bioanalytical chiral applications; and (4) microperfusion sampling coupled to CE-LIF can be used to analyze dynamic changes in the magnitude and timing of neurochemical efflux from single acute hippocampus slices exposed to modeled ischemia. Results of these latter studies suggest that D-ser and L-glu efflux occurs simultaneously in acute hippocampus with similar timing but differing magnitudes.
    • Biochemical study of a PSI-LHCI complex and molecular study of fcp genes in the diatom Cylindrotheca fusiformis

      Zhang, Hua; Plumley, Gerard; Boyer, Bert; Duffy, Lawrence K. (2002-08)
      A photosystem I-light-harvesting complex I (PSI-LHCI) was isolated from oxygen-evolving thylakoids of the diatom Cylindrotheca fusiformis. The circular dichroism (CD) spectrum of the complex resembled the photosystem I (PSI) complex of green plants. A single 77K fluorescence emission was observed at 715 nm. The excitation spectrum confirmed that both chlorophyll c and carotenoids were energetically coupled to chlorophyll a. The complex contained PSI reaction center proteins (PsaA/B, the PSI accessory subunit PsaC, and nine light-harvesting complex (LHC) apoproteins including an 18kD and a 17.5kD protein. Photosystem II core polypeptides were not detected by immuno- or silver staining. Taken together, the CD, fluorescence, and protein data indicate that at least nine LHC apoproteins can be specifically associated with PSI in this diatom. Twenty fcp gene sequences that encode fucoxanthin-chlorophyll a/c light-harvesting proteins (FCPs) and three encoded proteins that are similar to a 17.5kD FCP, but it was not possible to conclusively confirm that any of these genes encode proteins associated LHCI.
    • Biocomplexity Of Nonsorted Circles In The Low Arctic, Alaska

      Kade, Anja N.; Walker, Donald (2006)
      The vegetation and soils in many arctic tundra regions are influenced by the distribution of nonsorted circles, unique patterned-ground features that dot the well-vegetated tundra landscape. They are flat to dome-shaped, bare soil patches 0.5 to 3 m across and lack a border of stones. Localized soil disturbance due to cryogenic processes creates unusual micro-environments with unique plant communities, slow soil development and deep active layers. The contrast between barren nonsorted circles and the well-vegetated stable tundra provides an ideal opportunity to examine the complex linkages among vegetation, soil and disturbance through cryogenic processes, offering insight into how the tundra system operates. The central goal of this thesis is to understand the complex linkages of the nonsorted-circle system along a natural climate gradient on the North Slope in the Alaskan arctic tundra at different scales, ranging from plot level to regional changes. This thesis examines the interactions among vegetation, soil and cryogenic regime by treating the nonsorted circles within the stable tundra as a single complex system. The thesis presents a formal description and analysis of the plant communities on and off nonsorted circles along the climatic gradient using Braun-Blanquet classification approach. The thesis also studies the physical effects of vegetation, soil organic mat and snow cover on the microclimate of nonsorted circles and the stable tundra along the same climate gradient. The influence of vegetation on cryogenic processes is examined experimentally by manipulating the plant canopy on nonsorted circles. When compared to the stable tundra, nonsorted circles have minimal vegetation cover, resulting in warm soil temperatures and deep thaw depths in summer and allowing for increased ice-lens formation during freeze-up. The resulting frost heave and needle-ice formation at the soil surface maintain the bare surfaces of the circles through soil disturbance. Cryogenic processes dominate the system at the northern sites, while the warmer climate towards the south allows for thick vegetation mats on and off the nonsorted circles, suppressing cryogenic processes. The strength of the interactions among vegetation, soil and cryogenic regime may change under a warming arctic climate, possibly leading to the local disappearance of nonsorted circles.
    • The biodegradation of oil and the dispersant Corexit 9500 in Arctic seawater

      McFarlin, Kelly Marie; Leigh, Mary Beth; Perkins, Robert; Braddock, Joan; Hueffer, Karsten; Prince, Roger (2017-05)
      As oil and gas production continues in the Arctic, oil exploration and shipping traffic have increased due to the decline of Arctic sea ice. This increased activity in the Arctic Ocean poses a risk to the environment through the potential release of oil from cargo ships, oil tankers, pipelines, and future oil exploration. Understanding the fate of oil is crucial to understanding the impacts of a spill on the marine ecosystem. Previous oil biodegradation studies have demonstrated the ability of Arctic and sub-Arctic microorganisms to biodegrade oil; however, the rate at which oil degrades and the identity of indigenous oil-degrading microorganisms and functional genes in Arctic seawater remain unknown. In addition to oil, it is also important to understand the fate and effects of chemicals potentially used in oil spill response. Corexit 9500 is a chemical dispersant that is pre-approved for use in sub-Arctic seawater and is likely the dispersant of choice for spill responders in Arctic offshore environments. Currently no literature exists concerning the biodegradation of Corexit 9500 in Arctic seawater. Here we investigate the fate of oil, chemically dispersed oil, and the chemical dispersant, Corexit 9500, in laboratory mesocosms containing freshly collected Arctic surface seawater. The objectives of these experiments were to calculate the extent and rate of biodegradation (based on GC/MS & LC/MS/MS analysis) and to identify bacteria (determined using 16S rRNA gene sequencing) and genes (based on GeoChip 5.0 microarray) potentially involved in the biodegradation process. Indigenous microorganisms degraded both fresh and weathered oil, in both the presence and absence of Corexit 9500, with oil losses ranging from 36-41% within 28 days and 46-61% within 60 days. The biodegradation of the active components of Corexit 9500, which are dioctyl sodium sulfosuccinate (DOSS) and non-ionic surfactants, was also measured after 28 days. Biodegradation of DOSS was 77% in offshore seawater and 33% in nearshore seawater. Non-ionic surfactants were non-detectable after 28 days. Taxa known to include oil-degrading bacteria (e.g. Oleispira, Polaribacter, and Colwellia) and oilbiodegradation genes (e.g. alkB) increased in relative abundance in response to both oil and Corexit 9500. These results increase our understanding of oil and dispersant biodegradation in the Arctic and suggest that some bacteria may be capable of biodegrading both oil and Corexit 9500. We also sought to understand baseline abundances of taxa known to include oildegrading bacteria and functional genes involved in oil biodegradation in an offshore oil lease area. Aerobic oil-degradation genes (based on GeoChip 5.0 microarray) and taxa (determined using 16S rRNA gene sequencing) known to include oil-degrading bacteria were identified in seawater from the surface, middle, and bottom of the water column. Bacterial community structure differed significantly by depth (surface water vs. bottom water), while the relative abundance of major functional gene categories did not differ with depth. These findings support previous observations that two different water masses contribute to a stratified water column in the summer open-water season of the oil lease area, but indicate that potential function is fairly similar with depth. These results will contribute to understanding the potential for oil biodegradation throughout the Arctic water column and the fundamental microbial ecology of an offshore oil lease area. Together, these mesocosm experiments and in situ studies address important data gaps concerning the fate of spilled oil and Corexit in Arctic seawater. These results provide novel insight into the ability of Arctic bacteria to biodegrade crude oil and Corexit 9500, and suggest similarities between Arctic and temperate deep-sea environments in regards to taxa and functional genes that respond to oil and Corexit.
    • Biologically relevant secondary metabolites of Vaccinium uliginosum: bioassay-directed natural products identification of anti-neuroninflammatory agents in the Alaska bog blueberry

      McGill, Colin (2010-05)
      Dietary blueberry supplementation has demonstrated numerous health benefits including improved learning and memory in aging and neurodegenerative models, neuroprotection from ischemic events, anti-diabetic properties, and modulation of multiple inflammatory cascades. Despite previous research on antioxidant components prevalent in blueberries, no adequate explanation for a molecular mechanism for the benefits of blueberry supplementation has been proposed. Vaccinium uliginosum, the Alaska bog blueberry, possesses higher concentrations of antioxidant components than commercial varietals, and exhibits a greater oxygen radical scavenging capacity, making it an excellent candidate for the identification of biologically relevant secondary metabolites. An approach of bioassay-directed natural products identification was utilized to identify compounds in the Alaska bog blueberry responsible for the inhibition of both a magnesium-dependent neutral sphingomyelinase and NADPH oxidase in TNF-[alpha]-induced SH-SY5Y human neuroblastomas. Five relevant metabolites were identified: ß-sitosterol (1), ursolic acid (2), 3-0-(4-hydroxyphenylcarboxylic acid) 4-0-(ß-D-glucopyranosyl) gallic acid (3), malic acid (4), and 2,3-dihydroxybutane-1,2,3,4-tetracarboxylic acid (5). Neither compounds 3 or 5 had been previously described as a natural product in the literature. The identification of these compounds in the Alaska bog blueberry provides new explanations as to the benefits of blueberry consumption and offers new avenues of research for nutraceutical treatment of neuroinflammation.
    • Biophysical characterization of class II major histocompatibility complex (MHCII) molecules

      Osan, Jaspreet Kaur; Ferrante, Andrea; Kuhn, Thomas; Podlutsky, Andrej; Chen, Jack (2020-05)
      Class II Major Histocompatibility Complex (MHCII) molecules are transmembrane glycoproteins expressed on the surface of antigen-presenting cells (APCs). APCs engulf pathogens and digest pathogenic proteins into peptides, which are loaded onto MHCII in the MHCII compartment (MIIC) to form peptide-MHCII complexes (pMHCII). These pMHCII are then presented to CD4+ T cells on the surface of APCs to trigger an antigen-specific immune response against the pathogens. HLA-DM (DM), a non-classical MHCII molecule, plays an essential role in generating kinetically stable pMHCII complexes which are presented to CD4+ T cells. When a few peptides among the pool of the peptide repertoire can generate the efficient CD4+ T cell response, such peptides are known as immunodominant. The selection of immunodominant epitopes is essential to generate effective vaccines against pathogens. The mechanism behind immunodominant epitope selection is not clearly understood. My work is focused on investigating various factors that help in the selection of immunodominant epitopes. For this purpose, peptides derived from H1N1 influenza hemagglutinin protein with known CD4+ T cell responses have been used. We investigated the role of DM-associated binding affinity in the selection of immunodominant epitopes. Our analysis showed that the presence of DM significantly reduces the binding affinity of the peptides with low CD4+ T cell response and inclusion of DM-associated IC50 in training MHCII algorithms may improve the binding prediction. Previous studies have shown that there is an alternate antigen presentation depending on antigen protein properties. Here, we showed that the immunodominant epitope presentation is dependent on the pH and length of the peptides. To study the MHCII in its native form, we assembled full-length MHCII in a known synthetic membrane model known as nanodiscs. We noted that, based on the lipid composition, assembly of the MHCII differs. Preliminary binding studies with this tool showed that there might be a difference in the binding based on the type of the nanodisc. Collectively, our results showed that the immunodominant epitope selection is a complex process that is driven by various biochemical features.
    • Biotic Pest Damage Of Green Alder (Alnus Fruticosa ): Susceptibility To A Stem Disease (Valsa Melanodiscus) And Functional Changes Following Insect Herbivory

      Rohrs-Richey, Jennifer K.; H. Mulder, Christa P. (2010)
      Since the late 1990s, researchers have been predicting that a warming climate will lead to higher levels of plant disease damage. This appears to be the current trend in the boreal region; however, the level of complexity inherent to plant-pest interactions makes it difficult to make predictions across plant-pest systems. This study focuses on a boreal shrub in Alaska, Alnus fruticosa, which is currently a host to several insect and fungal pest species that are either already at epidemic status or have recently achieved epidemic status on other Alnus species in Alaska. Against the backdrop of a warming boreal forest, the overall aim of my study was to evaluate the response of A. fruticosa to two types of pest damage: the stem canker disease Valsa melanodiscus (anamorph Cytospora umbrina) and defoliation damage from insect leaf chewers. Our results indicate that, despite pest-related damage to the sapwood or leaf area, alders have physiological mechanisms in place to maintain homeostasis or recovery following disease damage. At the leaf-level, alders adjusted photosynthesis and stomatal conductance to cope with disease, despite decreased water transport and down-regulated light-response. At the ramet level, alders coordinated rates of water loss, hydraulic conductance, and maintenance leaf water balance following partial defoliation. These physiological host responses are not part of classical disease triangles, yet these types of host responses are likely to affect disease outcome in certain plant-pest systems and could potentially determine the trajectory of disease development.
    • Birding Data for Costa Rica

      Huettmann, Falk (2009)
      These data describe 703 species with geo-referencing information (latitude longitude) for 42 locations in Costa Rica. They are taken from the species lists presented in B. Lawson (2009; A bird-finding guide to Costa Rica. Comstock Publishing Associates and Cornell University Press. ISBN 978-0-8014-7584-9). This database is based on extensive fieldwork by B. Lawson and as described in his book. Here, these extensive species list data got geo-referenced via Google Maps. The resulting database described here consist of 4,829 rows and 8 columns (Page No,Site No,Site Name, latitude, longitude, SpeciesNo,SpeciestoExpect,Source) and is 969KB in size. The following locations were sampled: Arenal Volcano National Park, Bosque de Paz Biological Reserve and Lodge, Bosque del Rio Tigre, Braulio Carrillo National Park, Cabo Blanco Absolute Nature Reserve, Cano Negro National Refuge, Carara National Park, Cerro de la Muerte, Diria National Park, El Copal Biological Reserve, El Rodeo (University for Peace), Esquinas Rainforest Lodge, Irazu Volcano National Park, Kekoldi Hawk Watch, Km 70 (route 2), La Ensenada Wildlife Refuge, La Paz Waterfal Gardens, La Selva Biological Station, Laguna del Lagarto Lodge, Lankester Gardens, Las Alturas, Las Cruces Biological Station, Las Heliconias Lodge, Manuel Antonio National Park, Marenco Beach and Rainforest Lodge, Monteverde Cloud Forest Reserve, Oro Verde Biological Reserve, Palo Verede National Park, Poas Volcano National Park, Rancho Naturalista, Rara Avis Rainforest Lodge, Rincon de la Vieja National Park, Rio Negro, San Gerardo de Dota, Santa Rosa National Park, Selva Bananito Lodge, Talari Mountain Lodge, Tapanti National Park, The Coastline, The University of Costa Rica, Tortuguero National Park, Virgen del Socorro.
    • Black bear denning ecology and habitat selection in interior Alaska

      Smith, Martin E.; Follmann, Erich; Dean, Fred; Hechtel, John; Bowyer, Terry (1994-12)
      To identify conflicts between existing black bear (Ursus americanus) management and human activity on Tanana River Flats, Alaska, we monitored 27 radio-collared black bears from 1988-1991. We compared denning chronology, den characteristics, den-site selection, and habitat selection across sex, age, and female reproductive classes. Mean den entry was 1 October and emergence was 21 April, with females denned earlier and emerging later than males. Marshland and heath meadow habitats were avoided, and willow-alder was selected for den-sites. Eighty-three percent of dens were excavated, 100% contained nests, 18% were previously used, and 29% had flooded. Black bears selected black spruce-tamarack and birch-aspen significantly more, and marshland and heath meadow significantly less than available. Marshland and birch-aspen were used significantly more in spring than autumn. Marshland was used less than available by all bears in all seasons. Special habitat or den-site requirements are not critical for management of Tanana River Flats black bears.
    • Blood organochlorines, immune function and health of free-ranging northern fur seal pups (Callorhinus ursinus)

      Beckmen, Kimberlee Beth; Blake, John E. (1999)
      This study examined organochlorine (OC) contaminant levels in blood and milk along with immune function and health of northern fur seals ( Callorhinus ursinus) from St. George Island, Alaska. This portion of the Pribilof Islands breeding stock has undergone a long-term decline between 4 and 6% per year for unknown reasons. To examine the possible role of neonatal OC exposure on health, two cohorts of pups (69 total) and 33 matched periparturient dams were captured for blood and milk sample collection. From the second cohort of 49 neonates, 43 were re-sampled 29 to 51 days later. OCs were extracted from whole blood and milk to identify 15 polychlorinated biphenyl (PCB) congeners and 4 metabolites of dichloro-diphenyl-trichloroethane by high performance liquid chromatography. Peripheral blood lymphocytes were isolated and cryopreserved for in vitro lymphoproliferative immunoassays. These cellular function assays, along with complete blood cell counts, growth rates and survival through the early developmental period, were used as indicators of health status. Humoral immune function was assessed by in vivo antibody responses to tetanus vaccination. Mean blood levels of PCBs were higher in neonate samples than in pups one to two months old. Seven of the eight congeners detected in blood were higher (lipid weight) in neonate blood than in dam blood or milk. First-born neonates were exposed to higher levels of OCs from ingested milk and had higher blood levels of OCs than neonates of older, multiparous dams. Higher OC exposure in neonates was correlated to higher blood OC levels and poorer lymphoproliferative responses as well as lowered serum. retinol and thyroxine. Higher proportions of pups born to old dams developed tetanus antibodies compared to the pups of young dams. Higher OC exposure and poor immune responses in first-born pups may indicate a higher risk of secondary morbidity and mortality than for pups born to multiparous dams but an affect on growth rate or survival to midway through the nursing period was not detected. Evidence of substantial OC contaminant exposure at a critical period of development for the immune system must be considered as a potential contributing factor to reduced post-weaning survival.
    • Blood profile of grizzly bears in central and northern Alaska

      Brannon, Robert D. (1983-05)
      Blood from 151 grizzly bears (Ursus arctos) captured between 1973 and 1982 in the Brooks Range, Alaska, and the Alaska Range was examined for 7 hanatological, 24 serum chemistry, and 6 protein electrophoretic determinations. Differences in these characteristics between samples collected one hour apart indicate a response to stress during capture. Location differences in leukocyte count, erythrocyte count, hemoglobin, hematocrit, and cortisol suggest that Alaska Range bears were more stressed by capturing than Brooks Range bears. Sodium, creatinine, and urea nitrogen were negatively correlated with capture date, suggesting varied diet reinstatement and regained renal function as time from den emergence increased. Calcium, phosphorous, and alkaline phosphatase were negatively correlated with age, reflecting increased osteoblast activity and bone formation in young bears. Males had higher values than females for erythrocyte count, hematocrit, glucose, creatinine, calcium, phosphorous, and alkaline phosphatase, while glutamic-oxalacetic and glutamic-pyruvic transaminases were higher in females.