• Biochemical and microbiological assessments of dried Alaska pink salmon, red salmon and Pacific cod heads

      Biceroglu, Huseyin; Smiley, Scott; Crapo, Charles; Bechtel, Peter J. (2012-05)
      Fish heads are generally considered as unsuitable byproducts for human consumption in the United States. The initial objective was to compare the moisture content and water activity levels on dried pink salmon (Oncorhynchus gorbuscha) and dried red salmon (O. nerka) using different temperature and time integration. The secondary objective was to compare shelf life characteristics, rancidity and mold growth, between dried pink dried salmon and dried Pacific cod (Gadus macrocephalus) heads stored for up to 180 days at the ambient temperature (21°C) for East African seafood markets. The third objective was to assess the antioxidant effects for frozen and dried pink salmon heads stored for up to 60 days. In a preliminary experiment, dried red salmon heads were found unsuitable due to the water activity levels above 0.6. The critical moisture contents were detected around 10% for pink salmon heads and were around 15% for Pacific cod heads to reduce water activity levels below 0.6 in these products. The applicable drying temperatures of 50°C lasting over 50 hours for pink salmon heads and 50°C for over 24 hours followed by 30°C for over 24 hours for Pacific cod heads were found optimal. Dried Pacific cod heads showed shelf stability as a potential dried seafood product. Frozen pink salmon heads had 60 days shelf life, while heads with antioxidant glazing retarded oxidation levels (p <0.05). The antioxidant treatment in dried pink salmon heads kept oxidation levels lower than the acceptable limit up to 60 days. This study provided essential information to improve the utilization of these Alaskan seafood byproducts.
    • 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.
    • Biochemistry of diatom photosynthetic membranes and pigment-protein complexes

      Martinson, Tracey Ann; Plumley, F. Gerald (1996)
      Diatoms are an ecologically important group of algae in both marine and freshwater systems, but in spite of their significance little is known about the structure of their photosynthetic apparatus. This is due in part to the lack of a highly purified, oxygen-evolving thylakoid membrane preparation. Since thylakoid membranes purified from diatoms using methods developed for green plants did not evolve oxygen, a new procedure was developed for use with diatoms. An oxygen-evolving thylakoid membrane preparation is crucial for the study of photosynthetic pigment-protein complexes from these algae because the stability of the Photosystem I (PS I) and Photosystem II reaction centers was shown to be greatly reduced in thylakoid preparations that did not retain electron transport activity. As a result of the instability of PS I in some thylakoid preparations, a novel chlorophyll-binding complex was isolated that contained only the PsaA polypeptide. The isolation of this complex should prove useful in elucidating the structure of the PS I reaction center in all plants. Immunological and N-terminal protein sequencing methods were used to identify several photosynthetic proteins in the purified thylakoid preparation. These results provided evidence for posttranslational modification of two light-harvesting polypeptides (LHCPs) as well as of the PsaB subunit of the PS I reaction center core. Posttranslational modification of LHCPs and/or of PsaB has not been observed in green plants. In contrast to green plants, PS I in diatoms has been shown to be located in the inner thylakoid membranes. It was hypothesized that proteolytic processing of the C-terminus of PsaB in diatoms may be necessary for the PS I holocomplex to be present in the inner membranes, and that this processing may be responsible for the instability of PS I in purified diatom thylakoids. The existence of a functional, highly purified, and extensively characterized thylakoid preparation from diatoms will promote our understanding of the photosynthetic apparatus in these algae.
    • Biochemistry of diatom photosynthetic membranes and pigment-protein complexes

      Martinson, Tracey A. (1996-05)
      Diatoms are an ecologically important group of algae in both marine and freshwater systems, but in spite of their significance little is known about the structure of their photosynthetic apparatus. This is due in part to the lack of a highly purified, oxygen evolving thylakoid membrane preparation. Since thylakoid membranes purified from diatoms using methods developed for green plants did not evolve oxygen, a new procedure was developed for use with diatoms. An oxygen-evolving thylakoid membrane preparation is crucial for the study of photosynthetic pigment-protein complexes from these algae because the stability of the Photosystem I (PS I) and Photosystem II reaction centers was shown to be greatly reduced in thylakoid preparations that did not retain electron transport activity. As a result of the instability of PS I in some thylakoid preparations, a novel chlorophyll-binding complex was isolated that contained only the PsaA polypeptide. The isolation of this complex should prove useful in elucidating the structure of the PS I reaction center in all plants. Immunological and N-terminal protein sequencing methods were used to identify several photosynthetic proteins in the purified thylakoid preparation. These results provided evidence for posttranslational modification of two light-harvesting polypeptides (LHCPs) as well as of the PsaB subunit of the PS I reaction center core. Posttranslational modification of LHCPs and/or of PsaB has not been observed in green plants. In contrast to green plants, PS I in diatoms has been shown to be located in the inner thylakoid membranes. It was hypothesized that proteolytic processing of the C-terminus of PsaB in diatoms may be necessary for the PS I holocomplex to be present in the inner membranes, and that this processing may be responsible for the instability of PS I in purified diatom thylakoids. The existence of a functional, highly purified, and extensively characterized thylakoid preparation from diatoms will promote our understanding of the photosynthetic apparatus in these algae.
    • 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.
    • Biodegradation Of Petroleum And Alternative Fuel Hydrocarbons In Moderate To Cold Climate

      Horel, Agota Anna (2009)
      Microbial degradation of hydrocarbon fuels contaminating soil in the Arctic and subarctic environment is a relatively slow process. Nevertheless, due to transportation and logistical limitations in rural Alaska, biodegradation might be the best and cheapest contaminant removal option. The aim of this thesis was to investigate the environmental effects on biodegradation by naturally occurring microorganisms for some innovative hydrocarbon fuels and to determine the overall fate of hydrocarbons in soil, including degradation by fungi and bacteria, volatilization, and transport in the soil. Three major types of fuels were investigated in small scale microcosms and larger soil columns: conventional diesel as a control substance, synthetic diesel (arctic grade Syntroleum) and different types of fish oil based biodiesel. The environmental conditions investigated included different soil types (sand and gravel), different temperatures (constant 6�C, 20�C, and fluctuating between 6 and 20�C), moisture levels (from 2% to 12% GWC), fuel concentrations (from 500 to 20,000 mg fuel/kg soil) and nutrient dosages (0 or 300 mg N/kg soil). Microbial response times and growth phases were also investigated for different inoculum types. Conditions of 20�C, 300 mg N/kg soil, sand, ?4000 mg of fuel/kg soil and ?4% GWC were favorable for bioremediation, with a short lag phase lasting from one day to less than a week, and pronounced peaks of daily CO 2 production between week 2 and 3. At suboptimal conditions, all phases were extended and slow, however at low temperatures steady metabolization continued over a longer time. The relative importance of fungal and bacterial remediation varied between fuel types. Diesel fuel degradation was mainly due to bacterial activities while fish biodiesel degradation occurred largely by mycoremediation. For Syntroleum both bacterial and fungal remediation played key roles. Volatilization contributed up to 13% to overall contaminant removal. In soil columns, degradation was slower than in microcosms, due to an uneven concentration profile of contaminants, nutrients and oxygen with depth. In general, biodegradation showed promising results for soil remediation and the alternate fuel types were more biodegradable compared with conventional diesel fuel.
    • Bioenergetic and economic impacts of humpback whale depredation at salmon hatchery release sites

      Chenoweth, Ellen M.; Atkinson, Shannon; McPhee, Megan; Criddle, Keith; Friedlaender, Ari; Heintz, Ron; Straley, Janice (2018-08)
      Since 2008, humpback whales have been documented depredating hatchery-produced juvenile salmon, a novel prey, at points of their release in Southeast Alaska. The objectives of this dissertation are to determine the spatial distribution, seasonal distribution, and frequency of humpback whale foraging at release sites, determine whether whale presence is affecting the economic productivity of hatchery operations, and compare the bioenergetic benefits for whales feeding on juvenile salmon at hatchery release sites relative to typical prey. Five hatchery release sites were monitored over six years during the spring release season for whale presence/absence, numbers, and behaviors. Linear models were used to determine that for coho salmon, cohorts with frequent humpback whale presence had lower marine survival than cohorts with less or no humpback whale presence, but this was not seen for chum or Chinook salmon. Over six years, these sites lost an estimated 23% of revenue from coho salmon totaling almost a million dollars per year in addition to increased rearing costs to mitigate whale predation. A process model was developed to compare the net energy gain for humpback whales foraging on krill, herring and juvenile salmon. Whales were found to feed profitably on krill and chum salmon where they occurred in dense enough distributions and on herring when large coordinated groups impeded the escape of prey. Coho salmon typically distributed too diffusely for humpback whales to recuperate the full energetic costs of engulfment, indicating that behaviors such as bubble net feeding may be essential for increasing prey aggregation to an energetically profitable level, or humpback whales may be feeding to mitigate energetic losses. As intraspecific competition increases due to recovery and or changes to prey resources, generalist humpback whales may expand feeding to exploit new and less profitable prey resources.
    • Biogeochemical tracers of change in Pacific walruses past and present

      Clark, Casey; Horstmann, Lara; Misarti, Nicole; Konar, Brenda; Severin, Ken; Lemons, Patrick (2019-05)
      Reduced sea ice and projected food web shifts associated with warming of the Arctic have raised concerns about the future of Arctic species. Pacific walruses (Odobenus rosmarus divergens) use sea ice as a platform for molting, giving birth, and resting between foraging bouts. Exactly how sea ice loss will affect walruses is difficult to predict, due to a lack of information about regional ecosystems and their responses to climate change. The objectives of the research in this dissertation were to 1) examine how walrus diet changed in response to shifting sea ice conditions over the last 4,000 years, with the goal of generating predictions about how current and future ice loss may affect the walrus population; 2) make it easier to directly compare the results of retrospective and contemporary stable isotope studies of walruses; and 3) generate new tools to assist wildlife managers in monitoring the walrus population in an uncertain future. Stable carbon and nitrogen isotope ratios of walrus bone collagen indicated that diet was similar during previous intervals of high and low sea ice; however, diet variability among individual walruses was greater when sea ice cover was low, suggesting decreased abundance of preferred mollusk prey. Modern walrus diet was different from both previous high and low ice intervals, meaning that food webs in the Arctic are still in a state of flux, or that recent changes are novel within the last 4,000 years. Tissue-specific stable isotope discrimination factors were generated for walrus muscle, liver, skin, and bone collagen to improve comparisons between retrospective and contemporary studies of walrus diet. Additionally, lipid normalization models were parameterized for walrus skin and muscle, thereby making future walrus stable isotope research more feasible by reducing analytical costs and allowing the use of non-lethal sample collection. Finally, a novel technique for estimating the age at onset of reproductive maturity using concentrations of zinc and lead in the teeth of female walruses was established. This new approach has the potential to become a powerful tool for monitoring the walrus population and may be applicable to other species. Use of this technique on archived specimens may make it possible to examine changes in wildlife population dynamics across thousands of years.
    • Biogeochemistry of a glaciated fjord ecosystem: Glacier Bay National Park, Alaska

      Reisdorph, Stacey; Weingartner, Thomas; Mathis, Jeremy; Hood, Eran; Danielson, Seth; Aguilar-Islas, Ana (2015-05)
      The burning of fossil fuels, coupled with land use and deforestation practices, has resulted in CO₂ being emitted into the atmosphere. As much as one third of the anthropogenic, or man-made, CO₂ that ends up in the atmosphere is absorbed by the oceans and has led to increases in marine dissolved inorganic carbon (DIC) concentrations and a decrease in ocean pH, a process referred to as ocean acidification (OA). Increased concentrations of DIC can reduce saturation states (Ω) with respect to biologically important calcium carbonate minerals, such as aragonite. However, CO₂ may not be the only factor in seasonal changes to calcium carbonate saturation states. With this project I was interested in understanding how glacial runoff impacts the seasonal changes to the marine biogeochemistry in a glaciated fjord. In addition to CO₂, glacial meltwater is low in alkalinity (TA) and may impact the seasonal biogeochemistry of the marine system, as well as how it influences the duration, extent, and severity of OA events in an Alaskan glacial fjord, Glacier Bay National Park (GLBA). Through this study, I found that glacial runoff heavily impacts aragonite saturation states, with the main drivers of Ω (DIC and TA) varying seasonally. In GLBA low Ω values were well correlated with the timing of maximum glacial discharge events and most prominent within the two regions where glacial discharge was highest. The influence of glaciers is not limited to just TA as runoff is also low in macronutrients due to a lack of leaching from the soil and rocky streambeds. This has the potential to greatly impact the efficiency and structure of the marine food web within GLBA, the lowest level of which can be estimated using net community production (NCP). Changes within the lowest level of the food web, as a result of seasonal OA events, may lead to bottom-up effects throughout the food web, though this project focused only on production and respiration signals within the lowest level. We estimated regional NCP values for each sampling season and found the highest NCP rates (~54 to ~81 mmoles C m⁻² d⁻¹) between the summer and fall of 2011, with the most marine influenced lower part of the bay experiencing the greatest production. As the climate continues to warm, further glacial volume loss will likely lead to additional modifications in the carbon biogeochemistry of GLBA. Understanding the dynamics that drive seasonal changes in Ω, NCP, and the associated air-sea CO₂ fluxes within glacially influenced Alaskan fjords can provide insights into how deglaciation may affect carbon budgets and production in similar fjords worldwide.
    • Biological impacts and recovery from marine disposal of metal mining waste

      Kline, Edward R. (1998)
      Waste from coastal, metal mining operations may be disposed of in the ocean. Studies were conducted using tailings and wastewater (effluent) from a proposed gold mine that is located near Juneau, Alaska, USA. The ability of invertebrates to colonize tailings after obliteration by submarine tailings disposal (STD) was assessed through a field experiment. Trays of tailings and reference sediment were placed on the sea floor and retrieved over a 22 month period. The taxonomic composition, abundance, and biomass of invertebrates that colonized tailings and reference sediment were similar. Therefore, recolonization of invertebrates after obliteration by STD should not be inhibited by the presence of these tailings as a bottom substrate. In a laboratory study, the toxicity of effluent from the milling process was compared for early life stage fish and crustaceans. Common reference species and species that are indigenous to southern Alaska were exposed to effluent. The relationship between effluent concentration and organism response was established for immobilization, paralysis, and death. For each response, the sensitivity of the reference species bracketed that of the indigenous species. An overall ranking of species sensitivity could not be made because it depended on the response that was compared. The source of effluent toxicity was determined for one of the reference species, a crustacean. A simulated effluent was created to duplicate the ionic composition of the actual effluent. Toxicity was compared in effluent, effluent with increased salinity, simulated effluent, and solutions with adjusted concentrations of ions. Calcium was in excess in the effluent, relative to seawater, and was isolated as the source of toxicity. Sodium deficiency in the effluent, relative to seawater, reduced calcium toxicity.
    • 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.
    • 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.