Theses and Dissertations at Montana State University (MSU)
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Item Analysis of complex samples by mass spectrometry leads to insights into system dynamics(Montana State University - Bozeman, College of Letters & Science, 2021) Peach, Jesse Thomas; Chairperson, Graduate Committee: Brian Bothner; James Larson, Sutton Kanta, Eric Boltinghouse, Rebecca Mueller, Ganesh Balasubramanian, Mohammed Refai, Brent Peyton and Brian Bothner were co-authors of the article, 'Optimization of thermal small molecule and protein mass spectrometry analysis' submitted to the journal 'Analytical biochemistry' which is contained within this dissertation.; Rebecca Mueller, Dana Skorupa, Margaux Mesle, Sutton Kanta, Eric Boltinghouse, Bailey Sharon, Valerie Copie, Brian Bothner and Brent Peyton were co-authors of the article, 'Longitudinal meta-analysis of the Five Sisters Hot Springs in Yellowstone National Park reveals a dynamic thermoalkaline environment' submitted to the journal 'Environmental microbiology' which is contained within this dissertation.; Stephanie M. Wilson, Logan D. Gunderson, Lizzi Frothingham, Tan Tran, Seth T. Walk, Carl J. Yeoman, Brian Bothner and Mary P. Miles were co-authors of the article, 'Temporal metabolic response yields a dynamic biosignature of inflammation' submitted to the journal 'iScience' which is contained within this dissertation.Systems biology offers a holistic approach to biological science. In its most complete form, systems biology requires comprehensive data encompassing all of the parts or molecules across a set of hierarchical networks. To obtain and analyze the comprehensive and large datasets required for systems biology analysis, biologists have taken advantage of new technology and computational tools. Over the last few decades, advances in computational modeling and analysis technology has dramatically increased the efficacy of systems biology and the understanding of the natural world. However, systems biology is still an emerging discipline. The overwhelming scale of potential biological data that has yet to be described, coupled with interpretation and application obstacles, leaves much work to be accomplished. One aspect of systems biology that needs development is the interpretation and analysis of temporal biological data. Temporal data reveals more about biological phenomena than static data as biology is inherently dynamic. This dissertation explores the benefits of temporal profiling of complex samples to make time-resolved conclusions about complicated biological questions. Three research projects are the backbone of this document, with a chapter being devoted to each. Chapter 2 describes the development of a comprehensive method for extraction and mass spectrometry analysis of several different fractions from hot spring sediment. Chapter 3 delves into a multi-omics analysis tracking changes over the course of three years in a thermoalkaline spring system in Yellowstone National Park. It defines how specific extracellular small molecules correlate with microbial fitness. Specifically, how unique nitrogen and sulfur containing molecules in the sediment drive archaeal abundance and diversity. The final chapter introduces the concept of a 'dynamic biosignature', a set of metabolites that have similar responses to known biomarkers, in this case pro-inflammatory cytokines. A cohort of metabolites was identified that provided mechanistic insight into the inflammatory response. Overall, this dissertation provides examples of systems biology analysis and provides evidence that static, single time-point datasets fail to capture that which is the essence of biology - change.Item Temporal dynamics of Escherichia coli and the microbiome(Montana State University - Bozeman, College of Letters & Science, 2020) Martinson, Jonathan Nathan Vernon; Chairperson, Graduate Committee: Seth Walk; Seth T. Walk was a co-author of the article, 'Escherichia coli residency in the gut of healthy human adults' submitted to the journal 'EcoSal plus' which is contained within this dissertation.; Nicholas V. Pinkham, Garrett W. Peters, Hanybul Cho, Jeremy Heng, Mychiel Rauch, Susan C. Broadaway and Seth T. Walk were co-authors of the article, 'Rethinking gut microbiome residency and the enterobacteriaceae in healthy human adults' in the journal 'The ISME journal' which is contained within this dissertation.; Nicholas V. Pinkham and Seth T. Walk were co-authors of the article, 'Phenotypic predictors of Escherichia coli residency in the gut of healthy human adults' submitted to the journal 'Applied and environmental microbiology' which is contained within this dissertation.Over the past two decades, our understanding of the gut microbiome has increased dramatically. However, most studies involving healthy adults have relied almost exclusively on cross-sectional design, negating the changes occurring within an individual's microbiome through time. With this, we performed a small longitudinal study over a period of ~2 years with a cohort of 8 healthy adults. By sequencing the DNA encoding the 16S ribosomal RNA gene, we assessed the community level change in this cohort through time. Similar to previous findings, we found that using these methods there was remarkable stability through time with nearly 50% of the microbiome remaining the same throughout the study period in the participants. However, analysis of 16S ribosomal RNA sequences limits taxonomic resolution. By cultivating members of the Enterobacteriaceae, we found that turnover at the clone-level (below the species level) was common. Within the Enterobacteriaceae, Escherichia coli was the most numerically dominant species and most often observed as a long-term member of the gut (i.e. resident). Longitudinal analysis of Escherichia coli revealed that some phylogenetic groups within the species are more often long-term residents than other phylogroups. We next assessed the means by which the resident E. coli were capable of establishing and maintaining themselves in the gut. We found that residents were much more likely to produce antagonism (inhibition of other clones) than the E. coli that did not reside in the gut long-term.Item Deep Now & The Seed Bank Project(Montana State University - Bozeman, College of Arts & Architecture, 2018) Jones, Rachael Marne; Chairperson, Graduate Committee: Jeremy HatchThe Deep Now & The Seed Bank Project critically examines flaws in Western Society's tendency towards singular perceptual and singular analytical ways of constructing reality. The exhibition is built from cultural signifiers of both loss and hope, expanding on the belief that what we leave behind is an indication of the future. I am among one of the first generations to expect a future in flux, and in order to adapt, our methods of problem-solving need to expand to include both analytical and automatic thinking strategies. As a relatively new civilization that has expanded its influence globally, the instigation of metacognition between the head and the heart could ignite the fundamental psychological shift to understanding deep time within Western Society. Only with a sense of empathy, as well as deep humility for reconciling our place within the larger eco-system of the earth, will the future look brighter for future generations of all life forms. Looking at both analytical and automatic thinking patterns exhibited within Western Society's evolutionary trajectory, this paper posits that both are valid problem-solving strategies depending on context and flexibility. This involves understanding our reality as a construct, fabricated from both cognition and phenomenological experience. Accepting that this construct will demand flexibility in interpretation as the future changes insures a more cognizant relationship with our environment. Deep Now & The Seed Bank Project was formulated with a rich recognition of cultural signifiers that relate how the 20th and 21st century established Western Society's values as well as a self-consciousness of our era. Through flow state drawing processes, artefactual sculpture and ritualistic, reliquarizing seed banks, the work hopes to deviate from apocalyptic visions, while recognizing an eminent paradigmatic shift in the future of Western Society. The exhibition harks to focus clearly on the clues from the past to rebuild a more interconnected and sustainable intention for our projection into space and time.Item Live for a day - live for an age(Montana State University - Bozeman, College of Arts & Architecture, 2016) Kim, Soon; Chairperson, Graduate Committee: Dean AdamsHumanity has a limited amount of time. Life's brevity is what makes it beautiful. With unlimited time, we lose the beauty of the human experience. The same way an immortal cell becomes cancer, an immortal human loses their humanity. Things seem to matter more the less time we have. One's emotional state affects one's perception of time and leads to a heightened awareness that extends even to the body. Most of us focus too much on the past or worry too much about the future; we lose time because we fail to exist deeply in the present moment. Through my research on biological time and the human condition, painting, and personal experience, I delve into the themes of life and mortality with emphasis on time and identity coupled with organic cells and DNA sequences. I hope that my art inspires others to consider the heavy themes that often motivate my art such as the imminence of death, and with the knowledge of that reality, using the time you are given to the fullest.Item Common Ground(Montana State University - Bozeman, College of Arts & Architecture, 1991) Welch, Harry ScovilleMy recent work is a statement combining painting, sculpture, and architecture. The installation here in the Haynes Gallery consists of a painted network of panels and framework constructed out of materials collected from around the Bozeman area. The construction took place from September, 1990 to May, 1991 and was completed in my backyard studio in Bozeman. The structure was then dismantled piecemeal and moved to the Haynes Gallery where it was installed as my thesis exhibit. The installation is a reflection of my fascination with time and its affect on all things. The different painted areas of the installation present a theme of varying abstract studies with color, line, curve, and shape. These studies are fused to create a uniform piece representing both the organic and synthetic qualities of life. The walls are designed in part to represent unconventional billboards, graffiti smattered walls, and a notebook for my day-to-day thoughts. The construction serves as an area for me to explore my interests with the time process by acting as a large tack board for paint and found materials. These different materials are what I use to represent different colors on a picture plane, and when combined they become a sculptural form of architecture. This structure stands as a new form created from time worn parts, ready to undergo a new transformation.Item Duration estimates and behavioral measures as a function of sex and personality(Montana State University - Bozeman, College of Letters & Science, 1985) Warner, Donald JamesItem Spatial incubation of intuitive mitigation(Montana State University - Bozeman, College of Arts & Architecture, 2007) Robertson, Christopher Cole; Chairperson, Graduate Committee: Michael Everts; Steven Juroszek (co-chair)THESIS: Current engagement in public parks are “Open vague”, or “Specific” questioning how we are to use the space. In contract, “Open Specific” public spaces provide a more explicit opportunity providing users a choice of multiple intuitive responses. GOAL: Achieve Spatial Incubation by engaging in the intuitions for defined users. CONTEXT: Our culture is operating under the influence of a progressively growing technological developments such as ipods, cell phones, pda’s, and laptop computers. Within this pace superficial overlays of context form like a blanket causing a vagueness in our articulation of the external environment. Futhermore, when we rely on others to perform in favor of our best interest vagueness can persuade us individuals to believe responsible actions are taking place on issues that concern us, and in actuality these steps are not taking place. STRATEGY: ARCHITECTUALLY THREADING AN “OPEN SPECIFIC” PUBLIC SPACE. PROJECT SITE: Why the United Nations? Politically charged with a history of agenda, diversity, failing collaboration, status, and iconography: the site is currently exclusive in relationship to the public. This exclusivity includes a history of problems with diplomatic immunity, closed physical access to the archives library denying information context, security tight entrances, and inaccessible members. This backdrop intensifies a relationship between an archaic closed source operating model with the public and current open source model found in successful collaborative entities such as wikipedia, linux, and youtube. ARCHITECTURAL CONCLUSIONS: Incubating Intuition. Creating engagement of our intuitive interactions among the environment requires an intense study and sensitivity of both general, and specific user groups. The weaving that takes place among such groups of people in a political charged park atmosphere requires a sense of anticipatory response. In this case, the goal of architecture is not always to provide space, but to suggest interaction with calculated moves. This takes a humbled approach that may require the absolute understanding that our constructed architectural space may not be fullfilled until it is inhabited.Item A paradox of cinematic sight : exploring the ramifications of high-speed digital cinematography in science & natural history documentary(Montana State University - Bozeman, College of Arts & Architecture, 2010) Smith, Richard Francis Xavier; Chairperson, Graduate Committee: Ian van Coller.The immense popularity of science and natural history documentaries ensures the genres' influential role in shaping the viewer' relationship with the world. Many scholars and scientists have critiqued various aspects of the genre's overall construction as contributing to the maintenance of the separation between humans and nature. Beyond these structural critiques, there seems to be a more fundamental ideological consequence resulting from the relationship between the cinematic techniques used in creating science and natural history programming and the audience. The genre's dependence on new technologies of "seeing" is indicative of the underlying epistemology of the medium and suggests the importance of understanding ideological consequences of the cinematic apparatus itself. One of these new ways of "seeing" that is particularly useful for exploring the relationship between the cinematic apparatus and the audience is high-speed digital photography. An investigation of the historical origins of both the photograph and the cinema will show how high-speed photography is representative of the deeply ingrained epistemological foundations of these pictorial technologies. Photography's origins as a manifestation of scientific objectivity position the medium uniquely as a popularizer of scientific and factual information. Exploring the dynamic between the scientific profession and the lay public is integral to teasing apart how the genre of science and natural history documentary film affects the viewer. Photographic technologies privileged status as an unfiltered representation of physical truth lies at the center of the development of positivist science and the popularization of science and nature. Its privileged status derives from the denial of human subjectivity and the emphasis of mechanically mediated representations of the world. The cinematic apparatus' techno-scientific origins and its implicit promise to supplement our deficient perceptual abilities paradoxically functions to distance the viewer from the world it so acutely represents.