• 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.
    • Biophysical factors associated with the marine growth and survival of Auke Creek, Alaska coho salmon (Oncorhynchus kisutch)

      Robins, Joshua Benjamin (2006-12)
      Correlation and stepwise regression analyses were used to investigate relationships between growth in four distinct marine habitats, marine survival, and biophysical indices for Auke Creek coho salmon, a coho salmon population in Southeast Alaska. Early marine growth of males and females were positively correlated, but neither was correlated with early marine growth of jacks. Regional biophysical indices had significant effects on early marine growth of jack, but not on early marine growth of adult coho salmon. Sea surface temperature and number of hatchery pink and churn salmon juveniles released had negative and positive effects on growth in strait habitat, respectively. Hatchery pink and churn salmon abundance and pink salmon catch in Northern Southeast Alaska were negatively related to the growth of Auke Creek coho salmon in the late ocean phase. The average length-at-return of males, but not females, was negatively related to the abundance of hatchery pink and chum salmon. Female and male size-at-return were positively correlated (r = 0.68) but within-year variation was less for females, indicating possible sex-specific differences in adult size requirements associated with reproductive success. Adult survival and jack return rate were significantly related to early marine growth of adults and jacks, respectively, indicating size-selective mortality. Hatchery pink and churn salmon abundance had positive effects on adult survival and jack return rate.
    • Biosorption of heavy metals by citrus fruit waste materials

      Patil, Santosh Bramhadev (2004-12)
      Conventionally used processes for removing heavy metals from wastewater are usually either expensive, such as ion exchange, or inefficient, such as precipitation. An innovative technique that is both efficient and economical is biosorption, in which living and dead biomass can act as biosorbents through physical-chemical processes like ion exchange and micro-precipitation. Pectin, a structural polysaccharide present in plant cell walls, is similar to alginate, a molecule that is often responsible for the high metal uptake by algae. Based on the structural similarity between alginate and pectin, it was expected that pectin rich bio-wastes may be as good a biosorbent material as brown algae. A comparison between different pectin-rich materials showed high stability and metal binding capacity of citrus peels. Sorption isotherms for citrus peels showed higher metal uptake capacity at pH 5 compared to pH 3. Kinetic studies revealed the time required to reach equilibrium for lemon fruit waste (0.177 mm) was 20 min while for larger particles the time increased to 30 min-60 min. For lemon fruit waste, the content and pKa values of acidic groups were determined by using a pKa spectrum technique. Isotherm modeling was carried out by using Langmuir isotherms and pH sensitive modeling.
    • Biosorption of lead by citrus pectin and peels in aqueous solution

      Balaria, Ankit (2006-05)
      Biosorption of heavy metal ions by different pectin rich materials such as waste citrus peels is emerging as a promising technique for metallic contaminant removal. While binding rate and capacity of citrus peels were previously investigated, there is a lack of mechanistic information about Pb-citrus pectin/peels interaction mechanisms. Present research focused on evaluating this binding mechanism by corroborating macroscopic studies with spectroscopic techniques. Citrus pectins of two different methoxylation degrees and orange peels were characterized using potentiometric titrations and Fourier transform infrared (FTIR) spectroscopy. Binding mechanisms were evaluated using molecular scale FTIR analyses. The effects of particle size, pH, co-ion presence, and background electrolyte concentrations were also investigated for biosorption of Pb by orange peels. Both citrus pectin and orange peels reached their sorption equilibrium within 45 minutes. The maximum uptake capacity for orange peels was found to be 2.32 mmol/g. Citrus peels have very similar FTIR spectra to citrus pectin, suggesting that they have similar functional groups and pectin can be used as a model for citrus peels. Furthermore, carboxylic acid groups were found to be responsible for binding of Pb by citrus pectin and orange peels.
    • Biotic and abiotic influences on the use of Arctic lakes by fish and loons

      Haynes, Trevor B.; Lindberg, Mark; Rosenberger, Amanda; Lopez, Andrés; Titus, Kimberly (2014-12)
      The particularly severe effects of climate change anticipated in the Arctic, accompanied by ongoing anthropogenic activities, necessitate proactive and knowledge-based management of the region's aquatic ecosystems. However, the paucity of information on the Arctic's aquatic environments hinders strategic or spatially-explicit management. In this dissertation, I examine the habitat use of poorly studied taxa of the Arctic Coastal Plain (ACP) of Alaska, including freshwater fishes and yellow-billed loons (Gavia adamsii). Distribution studies can be biased by false absences; therefore, I began by determining the detection probabilities of six fish species common to Arctic lakes for five gear types (Chapter 2). Variation in gear- and species-specific detection probability was considerable, suggesting a multi-method approach may be most effective for whole-assemblage sampling. Adjusting for detection probability, I then examine how occupancy probabilities of the six fish species were related to lake and landscape scale covariates (Chapter 3). Three large-bodied salmonid species were influenced by factors associated with the probability of fish colonizing lakes, including whether the lakes had a stream connection. Models for small-bodied fish indicated different strategies for persistence among species. Ninespine stickleback (Pungitius pungitius) were widespread and captured in lakes that freeze to the bottom, suggesting rapid dispersal after spring freshet (when snow and ice had melted rapidly and caused widespread flooding) and colonization of sink habitats. In contrast, Alaska blackfish (Dallia pectoralis) distributions reflect tolerance to harsh conditions, while the slimy sculpin's (Cottus cognatus) was indicative of its marine origin. Based on these patterns, I propose a model of primary controls on the distribution of fishes in ACP lakes. Severe winter conditions limit occupancy through extinction events, while lake occupancy in spring and summer is driven by directional migration (large-bodied species) and undirected dispersal (small-bodied species). To provide insight to the relevance of species-specific distributions of prey fish to yellow-billed loons (Gavia adamsii), I investigated loon diet on their breeding grounds using quantitative fatty acid signature analysis (Chapter 4). Tissues were collected from 26 yellow-billed loons (shortly after they had moved from coastal staging areas), nine fish species and two invertebrate groups. Results suggest that yellow-billed loons are eating high proportions of Alaska blackfish, broad whitefish (Coregonus nasus) and three-spined stickleback (Gasterosteus aculeatus). The prominence of blackfish in diets highlights the importance of this species' tolerance to winter conditions that permits its widespread availability during the early stages of loon nesting. Broad whitefish and three-spined stickleback are more likely to be encountered in coastal regions at this time, and their importance may reflect pre-nesting period diet, when loons are staging in coastal and brackish waters before lakes are ice free. Finally, I use the prior chapters to inform an investigation into lake occupancy dynamics of nesting yellowbilled loons and loon chicks (Chapter 5). From a total of four years of data (collected over nine years for nests and seven years for chicks), I examine landscape features that influence the distribution and breeding success of breeding loons on ACP lakes (>7 ha in area), including landscape and lake features, and fish prey occupancy. Over this time, nesting yellow-billed loons exhibited a relatively low (< 30%), but stable to increasing, lake occupancy. Local extinction and colonization rates were also relatively stable, suggesting the nesting population in this region may be near equilibrium. A decreasing rate of change in chick occupancy associated with concomitant increases in nesting occupancy implies density-dependence in chick production. The occupancy probability of a prey fish, least cisco (Coregonus sardinella), had a positive influence on the probability of colonization of unoccupied lakes by nesting loons. I confirm that lake size and lake depth were not only positively associated with nesting occupancy, but also with chick production. Large lakes had occupancy probabilities near one for nesting loons and chicks; this, along with the near equilibrium in breeding loon occupancy and the relative rarity of these large lakes over the landscape, suggests breeding habitat is limiting loon populations in this part of their range. Given the lack of data from the ACP on fish distributions and yellow-billed loons, my findings inform current management practices and provide foundation for future research.
    • 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.
    • Birch, Berries, And The Boreal Forest: Activities And Impacts Of Harvesting Non-Timber Forest Products In Interior Alaska

      Maher, Kimberley Anne C.; Juday, Glenn P.; Barber, Valerie; Gerlach, S. Craig; Watso, Annette (2013)
      Harvesting wild berries, firewood, and other non-timber forest products (NTFPs) from the boreal forest in Interior Alaska is a common activity amongst local residents. NTFPs are harvested for personal use, subsistence, and commercial purposes. While these activities contribute to informal household economies and livelihoods, harvest of NTFPs are not well documented in Alaska. Availability of these ecosystem services may be altered under changing management and climate regimes. This interdisciplinary dissertation takes a look at the activities and impacts of current NTFP harvesting practices. Survey results from a forest use survey provide insight into harvest activity in the Tanana Valley. Wild blueberries (38.5% of households with mean harvested amount of 7.7 quarts) and firewood (25.0% of households with a mean harvest amount of 4.7 cords) were reported harvested with greatest frequency, and harvesting activities were mostly concentrated around larger population centers. Interviews were conducted with personal use and subsistence NTFP harvesters from Interior Alaska. Participants enjoy harvesting from the forest, and that the importance of harvesting is a combination of both the intangible benefits from the activity and the tangible harvested items. Harvested NTFPs were seen as high-quality products that were otherwise unavailable or inaccessible. Birch syrup is a commercially available NTFP produced in Alaska by a small number of companies. Similar to maple syrup, producing birch syrup is a labor intensive process with marginal profits. Interviews were conducted with workers in the Alaskan birch syrup industry, who reported that they were seeking an alternative to the traditional employment. The effects from mechanical damage from tapping for spring sap on birch's vigor are of concern to birch syrup producers and natural resource managers. This study compared the annual increment growth of Alaskan birch trees, Betula neoalaskana, between tapped and untapped trees. No significant difference was detected from tapping, but annual variability in growth was strongly significant. A temperature index accounted for nearly two-thirds of the annual variability. Pairing this index with two climate scenarios, birch growth was extended out through the 21st century. As temperatures rise, birch in Interior Alaska are projected to face a critical threshold, which may limit or extinguish their ability to sustain growth and yield a sustainable sap resource. Integrating the survey, interview, and dendroclimatological data provides a richer picture of how NTFP harvesters actively use the forest and about the benefits derived. These findings can assist resource managers in balancing these needs with those of other forest uses on public land.
    • Bird use of arctic tundra habitats at Canning River Delta, Alaska

      Martin, Philip D. (1983-12)
      Seasonal patterns of abundance of shorebirds and Lapland Longspur were studied at the Canning River delta. Study plots with differing habitat characteristics were examined: upland, mesic, and lowland tundra, and coastal saline flats. Nesting density was greatest in the mesic plot, but the lowland received intense use by late summer transients; use of the saline habitat was consistently high. Cold weather in July, 1980 probably reduced prey availability. Aquatic habitats, especially polygon troughs, produced a high proportion of the adult insect biomass. Comparison of energetic requirements of birds with the energetic value of their prey supply suggests that food could have limited reproductive success. Availability of both aquatic and terrestrial insects may contribute to high breeding bird density in structurally diverse habitats. Heavy use of wet/flooded tundra by late summer migrants probably reflects abundance of midge (Diptera: chironomidae) larvae in pond sediments.
    • Birdcatchers

      Keenan, Brian M. (2007-05)
      The four short stories and novella of Birdcatchers explore the choices that people make or fail to make at moments when different ways of knowing and conducting themselves in their circumstances become possible. The narrator of the title story, for instance, struggles to deal with his isolation and loneliness in the wake of his wife's death; when the protagonist of 'Tunnel of Love' finds the delicate balance of his double life upset, he ultimately manages to reclaim a realistic connection with his lover and broader world. Regardless of the success or failure each character experiences, though, the stories suggest that in our lonely and isolated individual lives, the potential for meaningful connection-and maybe some measure of grace-does exist.
    • Birthing change: an ethnographic study of the Alaska Family Health & Birth Center in Fairbanks, Alaska

      Bennett, Danielle M. Redmond (2013-05)
      This study examines the practices of the Alaska Family Health & Birth Center in order to understand how midwives help clients navigate the process of pregnancy, birth, and the postpartum period with a high rate of success, as defined by a low cesarean rate, low mortality and morbidity, and high maternal satisfaction. How do the midwives prepare mothers to navigate the transformation and how do they address failure to progress during birth? This study analyzes birth as a rite of passage, which incorporates a culture's worldview and its practices. These outcomes are achieved by employing a positive, holistic view of the natural, physiological process, by using practices that support the physiological process and minimize intervention, and by keeping the space in which out-of hospital birth takes place. The fact that parents are choosing an alternative ritual for birth at an increasing rate nationwide reflects a change happening in American culture.
    • Bitter

      Johnson, August; Hill, Sean; Stanley, Sarah; Carr, Rich; Jones, Seth (2017-05)
    • Bitter crab disease studies: observations on seasonality, mortality, species susceptability and life history

      Love, David Champlain (1992-05)
      Incidence and average intensity of Bitter Crab Disease (BCD) in Auke Bay Tanner crabs CChionoecetes bairdi) were significantly greater during June through September of both 1989 and 1990 then during October through May. BCD is a chronic but fatal disease; crabs did not develop immunity and often died from secondary bacterial and ciliate infections. Total mortality exceeded incidence and was not significantly different between summer and winter seasons or between years. BCD appears to be host specific: red king crabs (Paralithodes camtschaticus) and Dungeness crabs (Cancer maaister) did not contract BCD post-injection. BCD amoeboid stages consistently caused disease in Tanner crabs when injected into the hemocoel, while dinospore stages did not. Waterborne challenges did not cause disease. BCD parasites did not occur intracellularly, remaining within the hemal and vascular systems. Parasites exited the host via gills and possibly esophagus. The life cycle of BCD dinoflagellates outside their hosts remains incompletely described.
    • 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.
    • Black phase: a novel of Alaskan alchemy

      Fannin, Addley C. (2016-12)
      Black Phase is a speculative fiction novel for a young adult audience, set in and around a fictional boarding school in modern-day southeast Alaska. Our protagonist is Mara Edenshaw, an ambitious young artist of Tlingit descent who survives a mysterious illness only to find herself the primary suspect in a string of bizarre vandalisms. Her search to clear her name leads her to Alvis Norling, a shy alchemist’s apprentice living on a nearby island with only his own creation for company: a doll-sized homunculus made from a combination his and Mara’s DNA. Thus Mara’s illness and the vandalisms proved to be linked and, as more clues arise connecting these events to the “sacred science” of alchemy, she and Alvis must work together to uncover the truth, which is intimately tied to the boarding school’s history as an assimilation tool under the Bureau of Indian Affairs and the secret atrocities that happened there in the name of science. Rooted in northern history, Alaska Native culture, traditional folklore and the lives of modern teens in the Last Frontier, Black Phase is appropriate for readers ages thirteen and up.
    • Blasting Bridges And Culverts: Water Overpressure And Vibration Effects On Fish And Habitat

      Dunlap, Kristen N.; Smoker, William; Timothy, Jackie; Kelley, John; Quinn, Terrance II (2009)
      Water overpressures and ground vibrations from blasting may injure or kill salmonid fish in streams and embryos in streambeds. Explosives are used to remove failing structures in remote areas of the Tongass National Forest that impair watershed function. The State of Alaska Department of Fish and Game standards limit blast induced water overpressures to 2.7 lb/in 2 (18.6 kPa) and streambed vibrations to 0.5 in/s (13 mm/s) when embryos are present. Researchers, however, have reported salmonid mortality from pressures only as low as 12.3 and 19.3 lbs/in2 (85 and 133 kPa) and embryo mortality from vibrations as low as 5.75 in/s (146 mm/s). I recorded in-stream overpressures and streambed vibrations with hydrophones and geophones at various distances from log bridge, log culvert, and metal culvert blasts. Peak water pressures (lb/in2) were directly related to cube-root scaled distances with an attenuation rate of -1.51. Peak particle velocities in gravel were directly related to square-root scaled distances (SRSD, ft/lb 1/2) with an attenuation rate of -0.75. Water pressures were less than 7.1 lb/in2 (49.0 kPa) in all but one blast, and streambed vibrations did not exceed 5.5 in/s in gravel streambeds. State standards should be revised to reflect reported mortality and these observations of blasts in streams.