• 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.
    • Body condition and reproductive strategies of female lesser scaup in the boreal forest of Alaska

      DeGroot, Kristin A.; Lindberg, Mark; Barboza, Perry; Schmutz, Joel (2011-05)
      In many waterfowl species, body condition of breeding females can contribute to reproductive success by influencing factors such as egg size, clutch size and ability to incubate eggs. In turn, changes in female condition at the population level could affect population growth rates. Large-scale declines in populations of Lesser Scaup (Aythya affinis) raised concerns that poor female body condition was contributing to declines by reducing reproductive output. However, little was known about changes in body condition over time and about the contribution that stored body reserves make to egg production, especially in boreal forest regions where most scaup breed. My objectives were: 1) examine temporal changes in body condition of pre-breeding female lesser scaup on the Yukon Flats National Wildlife Refuge, Alaska and the relationship between body condition and breeding status; 2) examine the role of body reserves (protein and lipid) in egg production using stable isotope techniques. I found no evidence for a decline in female body condition as compared to historic measures. However, females that had entered rapid follicle growth (the early stages of egg production) were significantly fatter than birds that were not currently producing eggs. In addition, I found that female lesser scaup use both body reserves and dietary nutrients for production of egg yolk.
    • A breccia-centered ore and alteration model for the Copper Canyon alkalic Cu-Au porphyry deposit, British Columbia

      Twelker, Evan (2007-08)
      Similar to the nearby Galore Creek deposit, the Copper Canyon prospect of northwestern British Columbia is a porphyry-type copper-gold-silver occurrence associated with alkalic intrusive rocks of the Late Triassic-Early Jurassic Copper Mountain Suite. A reevaluation of the prospect geology shows that, of the previously recognized orthoclase and/or pseudoleucite porphyry syenite intrusions, mineralization is spatially and temporally associated with a single intrusive phase (unit i5) and biotite-garnet stockworks. Further, a newly defined unit of pre-mineralization magmatic-hydrothermal intrusive breccia occupies the core of the prospect and is a favorable host for much of the prospect mineralization. Prospect alteration can be divided into two distinct styles. Calc-potassic alteration consists of K-feldspar, Mg and Fe³-rich (An₂₀) biotite, andradite-rich garnet, hematite, magnetite, chalcopyrite, pyrite, and sphalerite (Zn₉₄₋₉₉, Fe₀.₅₋₂, Cd₀.₄₋₁)S and is associated with copper-gold-silver mineralization. Ankerite-sericite-pyrite (± fluorite, albite, anhydrite, pyrite, and trace covellite and bornite) alteration adjoins this core, hosting gold mineralization and insignificant copper. Sulfide-electrum and biotite geothermometry suggest fluid temperatures decreasing from the core (<̲S 550°C) to distal gold mineralization (<̲361°C). Distal gold mineralization is most likely the result of higher than typical sulfur activity and bisulfide transport of gold.
    • Breeding ecology and fasting tolerance of scaup and other ducks in the boreal forest of Alaska

      Martin, Kate H. (2007-08)
      Information on the breeding ecology of boreal forest ducks is lacking, despite management concern for species such as the lesser scaup (Aythya affinis), whose population has declined markedly since the 1980s. The mechanisms impacting population growth of scaup, and which component of their population dynamics is most affected, are unknown. Previous investigators hypothesized that food deprivation in the spring may reduce breeding success. My objectives were to: 1) examine reproductive parameters of lesser scaup and other ducks on the Yukon Flats in interior Alaska, and 2) measure the tolerance of captive scaup to fasting, in comparison to sympatric Northern shovelers (Anas clypeata) and American wigeon (Anas americana). Although breeding probability of paired females was assumed to be 1.0, the breeding probability of paired female scaup was between 0.12 (SE = 0.05, n=67) to 0.68 (SE = 0.08, n=37), and was positively related to body mass. These results suggest that managers may overestimate the productivity of boreal ducks using traditional survey methods. In addition, captive female scaup completely recovered from a loss of 11% body mass in only four days, suggesting that mass loss can be rapidly reversed, and may be able to obtain the body condition required for reproduction, if food supplies are adequate.
    • Breeding ecology of Smith's longspurs (Calcarius pictus) in the Brooks Range, Alaska

      Craig, Heather Rebekah; Powell, Abby; Kendall, Steve; O'Brien, Diane (2015-08)
      Alaska's Arctic ecosystem provides critical habitat for nesting songbirds. However, within this region climate change projections indicate a shrubbier future, as well as major shifts in summer weather patterns. The polygynandrous Smith's Longspur (Calcarius pictus) is a little known species that is closely tied to treeless tundra habitat in northern Alaska. I evaluated Smith's Longspur dispersal ability and annual survival rates using seven years of banding data, as well as breeding habitat requirements and reproductive success in two populations in the Brooks Range. Most adults (88%; n = 34) returned to nest in the same breeding neighborhood as previous years, and dispersal distance (x ± SE = 301 ± 70 m) did not differ between sexes. Only 4% of juvenile birds were resighted as adults and dispersal distance (x = 1674 ± 500 m; n = 6) was significantly greater for juveniles than for adults. From 674 capture-recapture histories, I evaluated annual survival and found that adult female survival (50-58%) was only slightly lower than for males (60-63%); juvenile survival was 41%, but was also paired with a low (13%) encounter probability. I examined nest-site selection patterns by comparing habitat measurements from 86 nests to paired random points within the nest area. Nests were typically found in open low shrub tundra and never among tall shrubs (height of tallest shrub x = 26.8 ± 6.7 cm). However, the only predictor of nest location I found was variation in willow height, which was slightly lower at nests than at random points. Daily nest survival rates were estimated from 257 nests and found to be relatively high (0.97-0.99) and consistent across years, and the best approximating model indicated that nest survival was negatively related to the numbers of days below freezing and season date. Despite dispersal ability and resilience to harsh conditions, Smith's Longspurs' response to climate change is unknown. The lack of sex-bias in dispersal and the low sex bias in survival, as well as the weak nest-site selection, may be attributed to the species' social mating system. Unlike most songbirds, multiple inter-mated individuals exist within each breeding neighborhood, altering social dynamics and likely demographic patterns. This is the first study to investigate the breeding biology of Smith's Longspurs at the western extent of their range and provides important conservation information as Arctic regions change.
    • Breeding ecology of whimbrels (Numenius phaeopus) in Interior Alaska

      Harwood, Christopher M.; Powell, Abby N.; Verbyla, David; Gill, Robert E. Jr. (2016-12)
      Whimbrels Numenius phaeopus breed in tundra-like habitats, both beyond treeline and within the boreal forest of interior Alaska. Despite their widespread distribution and designation as a species of conservation concern, their ecology has been particularly understudied in Alaska. During 2008--2012, I initiated the first dedicated study of Whimbrel breeding ecology in Alaska, and the first such study of any boreal-breeding shorebird in the state. Within a habitat mosaic of forest, woodlands, muskeg, scrub, and ponds within the floodplain of the Kanuti River in north-central Alaska, Whimbrels bred in the three largest (of nine) patches of discontinuous tussock tundra. These Whimbrels exhibited a compressed annual breeding schedule with the first birds arriving about 6 May and nests hatching about 17 June. Evidence for clustered and synchronous nesting, which may aid in predator defense, was equivocal. Most (69%) Whimbrels nested in mixed shrub-sedge tussock bog. I modeled nest-site selection at multiple spatial scales for 39 nests; however, the only variables important in the models were at the finest scale around the nest, namely that nests tended to be located on hummocks and exhibited lateral cover. Model results for nest survival of 67 nests over 4 years revealed a considerable difference in nest success (92% vs. 41%) at the two largest patches studied; this site effect was largely unexplained. To investigate Whimbrel ecology more broadly in the boreal biome, in 2013 I designed and conducted a Whimbrel-specific survey comprising 279 point counts within 28 transects along the road system of interior Alaska. I detected Whimbrels on just 32% of transects and 11% of count points. Although I detected Whimbrels at 3 sites where they had not been reported previously, I failed to detect them at several historically occupied sites. Dwarf shrub meadow was the most commonly observed habitat for all points visited. I modeled Whimbrel presence based on coarse habitat and avifaunal community features; no models were well supported. Between the local and regional surveys, my results tended to reinforce several widespread, but not necessarily investigated, descriptions about the breeding ecology of Whimbrels. My studies supported the premises that Whimbrels are patchily distributed on the landscape and often breed in clusters. Breeding of individuals and occupancy of some patches may be annually variable. Despite analyses of multiple habitat features at multiple spatial scales, I mostly observed a lack of specificity in where they bred among tundra-like patches, and where they nested specifically within such patches. This suggests that Whimbrels are tundra habitat generalists on their breeding grounds. Such phenotypic plasticity may be particularly adaptive in the dynamic, wildfire-prone landscape of interior Alaska.
    • Breeding ecology of white-winged scoters on the Yukon Flats, Alaska

      Safine, David Elliot (2005-08)
      Breeding bird surveys indicate a long-term decline in the numbers of scoters (Melanitta sp.) in North America. My objectives were to estimate survival of nests, ducklings, and adult female White-winged Scoters (Melanitta fusca) breeding on the Yukon Flats National Wildlife Refuge, Alaska, 2002-2004, within their primary breeding range. I measured habitat variables at nest sites and random sites in the study area to characterize nest habitat selection, and investigated breeding incidence with a laboratory analysis of circulating concentrations of the plasma yolk precursors vitellogenin (VTG) and very-low density lipoprotein (VLDL). The low hen and nest survival rates I observed combined with the substantial proportion of non-breeders on the breeding ground (up to 28%) may be responsible for the observed declines in abundance if annual survival rates are not high enough to maintain stable populations. Scoters avoided nesting in graminoid habitat, but nested in all other scrub or forested plant communities in proportion to their availability, selecting sites with more cover, higher variability of cover, and closer to edge and water than random sites. At the nest habitat scale, scoters are generalists, which may reduce the foraging efficiency of nest predators.
    • Bridging Arctic pathways: integrating hydrology, geomorphology and remote sensing in the North

      Trochim, Erin Dawn; Prakash, Anupma; Kane, Douglas; Romanovsky, Vladimir; Jorgenson, M. Torre (2015-12)
      This work presents improved approaches for integrating patterns and processes within hydrology, geomorphology, ecology and permafrost on Arctic landscapes. Emphasis was placed on addressing fundamental interdisciplinary questions using robust, repeatable methods. Water tracks were examined in the foothills of the Brooks Range to ascertain their role within the range of features that transport water in Arctic regions. Classes of water tracks were developed using multiple factor analysis based on their geomorphic, soil and vegetation characteristics. These classes were validated to verify that they were repeatable. Water tracks represented a broad spectrum of patterns and processes primarily driven by surficial geology. This research demonstrated a new approach to better understanding regional hydrological patterns. The locations of the water track classes were mapped using a combination method where intermediate processing of spectral classifications, texture and topography were fed into random forests to identify the water track classes. Overall, the water track classes were best visualized where they were the most discrete from the background landscape in terms of both shape and content. Issues with overlapping and imbalances between water track classes were the biggest challenges. Resolving the spatial locations of different water tracks represents a significant step forward for understanding periglacial landscape dynamics. Leaf area index (LAI) calculations using the gap-method were optimized using normalized difference vegetation index (NDVI) as input for both WorldView-2 and Landsat-7 imagery. The study design used groups to separate the effects of surficial drainage networks and the relative magnitude of change in NDVI over time. LAI values were higher for the WorldView-2 data and for each sensor and group combination the distribution of LAI values was unique. This study indicated that there are tradeoffs between increased spatial resolution and the ability to differentiate landscape features versus the increase in variability when using NDVI for LAI calculations. The application of geophysical methods for permafrost characterization in Arctic road design and engineering was explored for a range of conditions including gravel river bars, burned tussock tundra and ice-wedge polygons. Interpretations were based on a combination of Directcurrent resistivity - electrical resistivity tomography (DCR-ERT), cryostratigraphic information via boreholes and geospatial (aerial photographs & digital elevation models) data. The resistivity data indicated the presence/absence of permafrost; location and depth of massive ground ice; and in some conditions changes in ice content. The placement of the boreholes strongly influenced how geophysical data can be interpreted for permafrost conditions and should be carefully considered during data collection strategies.
    • Bridging the gap between pupping and molting phenology: behavioral and ecological drivers in Weddell seals

      Beltran, Roxanne Santina; Burns, Jennifer; Breed, Greg; Testa, J. Ward; O'Brien, Diane; Barnes, Brian (2018-08)
      In Antarctica, the narrow window of favorable conditions constrains the life history phenology of female Weddell seals (Leptonychotes weddellii) such that pupping, breeding, foraging, and molting occur in quick succession during summer; however, the carry-over effects from one life history event to another are unclear. In this dissertation, I characterize the phenological links between molting and pupping, and evaluate feeding behavior and ice dynamics as mechanistic drivers. First, I review the contributions of natural and sexual selection to the evolution of molting strategies in the contexts of energetics, habitat, function, and physiology. Many polar birds and mammals adhere to an analogous biannual molting strategy wherein the thin, brown summer feathers/fur are replaced with thick, white winter feathers/fur. Polar pinnipeds are an exception to the biannual molting paradigm; most rely on blubber for insulation and exhibit a single molt per year. Second, I describe the duration and timing of the Weddell seal molt based on data from 4,000 unique individuals. In adult females, I found that successful reproduction delays the molt by approximately two weeks relative to non-reproductive individuals. Using time-depth recorder data from 59 Weddell seals at the crucial time between pupping and molting, I report a striking mid-summer shallowing of seal dive depths that appears to follow a vertical migration of fishes during the summer phytoplankton bloom. The seals experience higher foraging success during this vertical shift in the prey distribution, which allows them to re-gain mass quickly before the molt. Across four years of study, later ice break-out resulted in later seal dive shallowing and later molt. In combination, the data presented in this dissertation suggest that molting, foraging, and pupping phenology are linked in Weddell seals and are affected by ice break-out timing.
    • Brucella suis type 4 in foxes and their role as reservoirs/vectors among reindeer

      Morton, Jamie Kay; Williamson, Francis S. L. (1989)
      Field and laboratory studies were conducted to test the hypotheses that (1) the reindeer/caribou organism, Brucella suis type 4, is incidentally transmitted to reindeer predators such as foxes but does not cause reproductive disease in them, and (2) infected predators such as foxes are terminal hosts and do not serve as reservoirs of infection for reindeer. In field collections, serologic prevalence of brucellosis was similar for male and female foxes (Vulpes vulpes and Alopex lagopus). B. suis type 4 was isolated from female Vulpes and Alopex. No association between reproductive status of foxes and brucellosis infections was observed. Serologic titers in Vulpes experimentally infected by oral exposure to Brucella suis type 4 were detected first by the standard tube and plate agglutination tests which were followed by the buffered Brucella antigen, rivanol, and complement fixation tests. Brucella suis type 4 was isolated from the feces 4 to 6 days post-exposure (PE) and from the oral cavity for as long as 3 weeks PE in Vulpes challenged with 10$\sp9$ or 10$\sp{11}$ colony forming units. Brucella suis type 4 was isolated frequently from regional lymph nodes in the head up to 18 weeks PE, and from only more distant nodes at 22 and 66 weeks PE. Organisms did not localize in the reproductive tract. Clinical effects of brucellosis in Vulpes experimentally-infected were not observed. Pathologic lesions were not detected in the male and non-gravid female reproductive tract. Due to breeding failure, effects of Brucella suis type 4 on the pregnant fox reproductive tract were not determined in experimental infections. Gross and microscopic pathology was limited to lymph nodes. Fox to fox transmission attributed to aerosols from products shed by infected foxes occurred readily. Transmission from Vulpes to lemmings (Dicrostonyx rubricatus) that were exposed to urine from infected fox occurred frequently. Transmission from infected Vulpes to two reindeer (Rangifer tarandus) occurred under conditions of close confinement. Ingestion of organisms passed mechanically in the fox feces was considered the probable source of infection. Fox saliva containing Brucella was also implicated in transmitting the organism through bites or aerosols.
    • Building Blocks Of Self -Organized Criticality

      Woodard, Ryan; Newman, David (2004)
      Why are we having difficulty developing economical nuclear fusion? How can a squirrel cause a statewide power blackout? How do correlations arise in a random complex system? How are these questions related? This thesis addresses these questions through a study of self-organized criticality (SOC). Among the systems that have been proposed as SOC are confined fusion plasmas, the Earth's magnetosphere and earthquake faults. SOC describes how large-scale complex behavior can emerge from small-scale simple interactions. The essence of SOC is that many dynamical systems, regardless of underlying physics, share a common nonlinear mechanism: local gradients grow until exceeding some critical gradient and then relax in events called avalanches. Avalanches range in size from very small to system-wide. Interactions of many avalanches over long times result in robust statistical and dynamical signatures that are surprisingly similar in many different physical systems. Two of the more well-known signatures are power law scaling of probability distribution functions (PDFs) and power spectra. Of particular interest in the literature for approximately a century are 1/f spectra. I studied the SOC running sandpile model and applied the results to confined and space plasmas. My tools were power spectra, PDFs and rescaled range ( R/S) analysis. I found that SOC systems with random external forcing store memory of previous states in their local gradients and can have dynamical correlations over very long time scales regardless of how weak the external forcing is. At time scales much longer than previously thought, the values of the slope of the power spectra, beta and the Hurst exponent, H, are different from the values found for white noise. As forcing changes, beta changes in the range 0.4 <math> <f> &lap;</f> </math> beta &le; 1 but the Hurst exponent remains relatively constant, H &ap; 0.8. The same physics that produces a 1/f spectrum at strong forcing produces a f -0.4 spectrum at weaker forcing. Small amounts of diffusive spreading added to the two dimensional SOC sandpile greatly decreases the frequency and maximum size of large transport events. More diffusion increases the frequency of large events to values much greater than for systems without diffusion.