ix, 94 p. : ill. A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / This thesis examines the Long-Term Ecological Reflections at H.J. Andrews Experimental Forest, Oregon, a project that promotes creative inquiry at an ecological research station. I analyze how reflective writing contributes to a deeper understanding of ecosystem processes and fosters a closer connection to nature, referred to as "ecological awareness." I argue that the greatest ecological awareness comes from a combination of scientific and artistic ways of knowing as well as physical immersion in nature. I critically analyze the work of four writers: Jane Coffey, Vicki Graham, Freeman House, and Robin Kimmerer. These works create a strong connection to place for the reader and facilitate an understanding of the forest ecosystem through a discussion of scientific facts. They also create a sense of place through vivid and metaphorical language. These reflections will become an increasingly valuable mode of inquiry as the Andrews Forest develops a stronger writer-scientists interaction. / Committee in Charge: Dr. Louise V. Westling, Chair; Dr. Brendan Bohannan; Dr. Scott D. Bridgham

No description available.

<p> A novel mathematical model has been developed for biofilms and bioflocs. The model is based on the use of the effectiveness factor and the effect of cell density is included. The key assumption in the model is that cell density decreases in proportion to the substrate concentration within the biofilm or biofloc, reflecting lower rates of cellular metabolism. The equations given by the model were solved numerically for three types of reaction kinetics: Monod, Andrews (substrate inhibition), and multiple-Monod (twolimiting substrates), as well as for two geometries: a slab, as a representation of a biofilm and a sphere, as a representation of a biofloc. The simulations indicate that a decrease of the cell density in the biofilm and biofloc results in a decline of the effectiveness factor. Furthermore, the analytical solutions and approximate analytical versions of the effectiveness factor for the biofilm in two cell growth models: Monod and Andrews, have been derived. The effectiveness factors derived analytically are in agreement with those calculated numerically, and the approximate analytical versions are valid for the Thiele modulus greater than five. This new model was tested using operational data available in the literature, by including the effectiveness factor as a part of the design equations for an upflow anaerobic sludge blanket (UASB) reactor. </p> <p> For any biologically mediated transformation, it is critical to uniquely identify the parameters associated with microbial growth models. In this study, it is proved that the parameters of the integrated Andrews model are identifiable if the experimental data does not contain any random noise based on a criterion proposed by Beck and Arnold [1977]. When noise is present, the parameters may or may not be identifiable, depending on noise levels. A new approach has been developed based on the calculation of dimensionless sensitivity coefficients. Plotting these coefficients provides straightforward visualization of parameter identification. This method was used for quantitative evaluation of the noise level that can be associated with measurements, while still allowing parameter identification. It was demonstrated that an indirect cause of the parameter nonidentification of the integrated Andrews model is the linearization of the Andrews model at a low or high substrate concentration. Robinson [1985] obtained a similar result with the Monod model. </p> / Thesis / Master of Science (MSc)

Mat-forming ectomycorrhizal (EcM) fungi represent a prevalent constituent of many temperate forest ecosystems and create dramatic changes in soil structure and chemistry. EcM mat soil have been shown to have increased microbial respiration rates and have been hypothesized to harbor unique assemblages of fungi and bacteria. The objectives of this dissertation were to characterize and examine the fungal and bacterial communities associated with EcM mats in old-growth forests of the H.J. Andrews Experimental Forest located in the Oregon Cascades. Additionally, this work assessed the application of traditional, emerging, and novel molecular sampling techniques for determining microbial communities of environmental samples. This research investigated the microbial communities associated with two common EcM mat genera found in old-growth Douglas fir stands in the Pacific Northwest; Piloderma (Atheliales, Basidiomycota) and Ramaria (Gomphales, Basidiomycota). Soil samples were collected from Piloderma and Ramaria mats and surrounding non- mat soil for molecular analysis of nucleic acids. First, a comparative study was conducted to determine the most appropriate rDNA molecular sampling technique for microbial community characterization. Two next-generation sequencing methods, Roche 454 pyrosequencing and Illumina-based environmental sequencing, the latter developed by the author, were compared to a more traditional sequencing approach, i.e., Sanger sequencing of clone libraries. These findings informed the subsequent sampling of the fungal ITS and bacterial 16S rDNA fragment with 454 pyrosequencing to determine the microbial communities within mat and non-mat soils. Second, this work utilized a pyrosequencing approach to explore fungal community structure in EcM mat and non-mat soils. This work concluded that differences in microbial communities do exist between Piloderma mat, Ramaria mat, and non-mat soils, but the differences are largely quantitative with relatively few distinct taxonomic shifts in microbial constituents. Piloderma, Ramaria and Russula, in addition to being the dominant taxa found on mycorrhizal root tips, were found to be the most abundant taxa in bulk soils within their respective mat types or non-mat sample. The background fungal communities within the EcM mats in this study exhibited considerable taxonomic overlap with the exception of Piloderma vs. non-mat comparisons; Russula species dominated nonmat soils but tended to be excluded or significantly underrepresented in Piloderma mats. Lastly, this study explored the bacterial communities associated with Piloderma and Ramaria mats using lower- coverage 454-Jr pyrosequencing. Bacterial communities exhibited significant structure as a function of mat-type, soil horizon and pH, but this finding should be interpreted with respect to the nonrandom distribution of Piloderma-mats in the O- horizon and the Ramaria-mats in the A-horizon, and the tendancy for EcM mats to be more acidic than surrounding soils. Nonetheless, the total microbial (bacterial and fungal) community was typically dominated by the mat-forming taxa, or Russula, in the case of non-mat soils. While the presence of Piloderma mats did enrich or restrict some bacterial groups, soil pH was also found to be a significant driver of bacterial richness and taxonomic diversity. Fungal and bacterial richness were also found to be positively related to one another, regardless of soil horizon or EcM mat type. This work, taken together, contributes to the understanding of hyperdiversity and heterogeneity of microbial communities of temperate forest soils and highlights the potential for fungal and bacterial communities to be influenced by the presence of EcM mats. / Graduation date: 2012

Soil organic matter (SOM) is the terrestrial biosphere's largest pool of organic carbon (C) and is an integral part of C cycling globally. Soil organic matter composition typically can be traced directly back to the type of detrital inputs; however, the stabilization of SOM results as a combination of chemical recalcitrance, protection from microbial decomposition within soil structure, and organo-mineral interactions. A long-term manipulative field experiment, the Detrital Input and Removal Treatment (DIRT) Project, was established to examine effects of altering detrital inputs (above- vs. below-ground source, C and nitrogen (N) quantity, and chemical quality) on the stabilization and retention of SOM. Surface mineral soil was collected from two DIRT sites, Bousson (a deciduous site in western Pennsylvania) and H.J. Andrews (a coniferous site in the Oregon Cascade Mountains), to examine the influence of altering detrital inputs on decomposability and mean residence time of soil organic matter and different organic matter fractions. Soil organic matter was physically separated into light fraction (LF) and heavy fraction (HF) organic matter, by density fractionation in 1.6 g mL⁻¹ sodium polytungstate (SPT). Density fractionation in SPT resulted in the mobilization and loss of ~25% of total soil organic C and N during the physical separation and rinsing of fractions during recovery, which was also the most easily decomposed organic matter present in the bulk soil. At H.J. Andrews, this mobilized organic matter had a short mean residence time (MRT), indicating that it originated from fresh detrital inputs. In contrast, at Bousson, the organic matter mobilized had a long MRT, indicating that it originated from organic matter that had already been stabilized in the soil. Mean residence times of LF from Bousson varied widely, ~3 y from doubled litter and control plots and 78-185 y for litter removal plots, while MRT of HF was ~250 y and has not yet been affected by litter manipulations. Results from long term incubation of LF and HF material supported these estimates; respiration was greatest from LF of doubled litter and control plots and least from HF of litter removal plots. In contrast, MRT estimated for LF and HF organic matter from H.J. Andrews were similar to each other (~100 y) and were not affected by litter manipulation. These estimates were also supported by the incubation results; there was not a difference in cumulative respiration between detrital treatments or density fractions. The results from the coniferous site may be due to a legacy of historically large inputs of coarse woody debris on the LF and it may be decades before the signal of detrital manipulations can be measured. Alternatively, these highly andic soils may be accumulating C rapidly, yielding young HF ages and C that does not differ substantially in lability from coniferous litter-derived LF. The DIRT Project was intended to follow changes in soil organic matter over decades to centuries. As expected, manipulation of detrital inputs has influenced the lability and mean residence time of the light fraction before the heavy fraction organic matter; however, it will be on much more lengthy time scales that clear differences in organic matter stabilization in response to the alteration of detrital inputs will emerge. Soil CO₂ efflux is a compilation of CO₂ from many sources, including root respiration and the decomposition of different organic matter fractions, roots, and exudates. If the sources of CO₂ have different isotopic signatures, the isotope analysis of CO₂ efflux may reveal the dominant sources within the soil profile. In a short incubation experiment of density fractions from both sites, respired CO₂ reflected the isotopic signature of the organic matter fraction after 30 days, but was more enriched in ¹³C. Initially CO₂ was isotopically depleted in ¹³C relative to the organic matter fraction and the period of depletion related to the amount of easily degraded organic matter present at H.J. Andrews only. / Graduation date: 2006

Since its foundation between 1410 and 1414 the University of St Andrews has acquired what can be considered to be ‘artefacts of significance’. This somewhat nebulous phrase is used to denote items that have, for a variety of reasons, been deemed to have some special import by the University, and have been displayed or otherwise presented in a context in which this status has been made apparent. The types of artefacts in which particular meaning has been vested during the centuries under consideration include items of silver and gold (including the maces, sacramental vessels of the Collegiate Church of St Salvator, collegiate plate and relics of the Silver Arrow archery competition); church and college furnishings; artworks (particularly portraits); sculpture; and ethnographic specimens and other items described in University records as ‘curiosities’ held in the University Library from c. 1700-1838. The identification of particular artefacts as significant for certain reasons in certain periods, and their presentation and display, may to some extent reflect the University's values, preoccupations and aspirations in these periods, and, to some degree, its identity. Consciously or subconsciously, the objects can be employed or operate as signifiers of meaning, representing or reflecting matters such as the status, authority and history of the University, its breadth of learning and its interest and influence in spheres from science, art and world cultures to national affairs. This thesis provides a comprehensive examination of the growth and development of the University's holdings of 'artefacts of significance' from its foundation to the mid-19th century, and in some cases (especially portraits) beyond this date. It also offers insights into how the University viewed and presented these items and what this reveals about the University of St Andrews, its identity, which changed and developed as the living institution evolved, and the impressions that it wished to project.

Andrew Melville (1545-1622) was the leader of the Presbyterian wing of the Scottish Kirk between 1574 and 1607, and he and his colleagues were a perpetual irritant to James VI and I in his attempts to establish a royal and Episcopal dominance over the Kirk. Yet much of Melville’s reputation has been based on the seventeenth-century Presbyterian historical narratives written by the likes of James Melville (Andrew’s nephew) and David Calderwood. These partisan accounts formed the basis of modern historiography in Thomas M’Crie’s monumentally influential Life of Andrew Melville. Modern historians broadly agree that Melville’s portrayal as a powerful and decisive church leader in these narratives is greatly exaggerated, and that he was at best an influential voice in the Kirk who was quickly marginalised by the adult James VI. However, only James Kirk has commented at any length on Melville’s other role in Jacobean Scotland—that of developing and reforming the Scottish universities. Melville revitalised the near-defunct Glasgow University between 1574 and 1580, and from 1580 to 1607 was principal of St Mary’s College, St Andrews, Scotland’s only divinity college. He was also rector of the University of St Andrews between 1590 and 1597. This thesis provides a detailed account of Melville’s personal role in the reform and expansion of the Scottish universities. This includes an analysis of his direct work at Glasgow, but focuses primarily on St Andrews, using the untapped archival sources held there and at the Scottish National Library and Archives to create a detailed picture of the development of the University after the Reformation. This thesis also evaluates the intellectual content of Melville’s reform programme, both as it developed during his time in Paris, Poitiers and Geneva, and as we see it in action in St Andrews.

In an initial research proposal of December 1969, the scientists of the Coniferous Forest Biome (CFB), an ecosystem study centered in the Pacific Northwest and part of the larger International Biological Programme (IBP), expressed optimism that computer simulations and systems modeling could transform empirical knowledge of the carbon, water, and nutrient flows turned into viable forest management practice. The CFB's strategy aimed to use projections of the computer simulations and data from field study to constantly check and direct each other, resulting in a flexible, refined, and accurate understanding of forest ecosystems, as well as a reliable guide to forest management. To what extent did the CFB's research program, centered on a total system model, complete its cycle of field study, modeling, and validation? Despite the innovative strategies of the CFB modelers, ecosystem modeling lost its preeminent status among the goals of the CFB, due to different interpretations of the purpose and philosophy of ecosystem modeling and the practical limitations of administering a large research program. Instead, small field-based studies during the CFB yielded a number of ground-breaking discoveries. Although they diverged from the modeling objectives, these areas of fieldwork emerged from questions the forest's functions and cycling processes that the modeling efforts of the CFB required. Focusing on the work of CFB participants from Oregon State University and the USDA Forest Service in the H. J. Andrews Experimental Forest, this thesis addresses the relationship between the marginalization of the modeling objectives and the rising centrality of field-based forest studies in the CFB from 1969 to 1980. Given the ongoing legacy of CFB research at the Andrews Long-Term Ecological Research (LTER) site and the later implications of CFB findings in debates over forest policy and management, this thesis also seeks to evaluate the Coniferous Forest Biome as a whole and discuss the role of modeling and field work within large ecological research endeavors more generally. / Graduation date: 2006

This essay is an attempt to show how certain elements, or techniques of history writing, can be used in creative non-fiction. It uses three major sources of theory. First, there is Charlotte Canning and Thomas Postlewait’s view on “the five themes of historiography,” which are indispensable for researching history: time, space, archive, identity, and narrative. The essay primarily focuses on narrative, because it is connected to representations of human lives, and as such contributes to meaning- creation. Second, the essay employs Hayden White’s concept of the historian’s working process and the notions of chronicle, story, mode of emplotment, mode of argument and ideological implications. Third is the method developed by Thomas Andrews and Flannery Burke of the five C’s of historical thinking: change over time, causality, context, complexity and contingency. Although these are separate theories, the essay shows how they can be complementary and help in the development of memoir writing, which is here my creative work, A Family Memoir in Essays, in particular the essays entitled “Trimdiniekis,” “Brasiliana,” and “A Sertaneja”.

The parallels between the works of Geoffrey Chaucer and Henry Fielding are very striking. Both authors produced some of the greatest works in English literature, yet very little scholarly investigation has been done regarding these two in relationship with one another. In this work I explore the characters of Chaucer’s Parson and Parson Adams, assessing their strengths and weaknesses through pastoral guides by Gregory the Great and George Herbert, while drawing additional conclusions from John Dryden. I examine the episodic, theatrical nature of both authors’ works, along with the inclusion of fabliau throughout. Finally, I look at the shared motif of knight-errant in the works of both authors and the motion employed throughout the tales as travel narratives. By examining these authors’ works, I contend that Fielding masterfully employs many of Chaucer’s literary techniques in his own tales, crafting them to work specifically for the eighteenth-century novel and its audience.