Matching Items (147)
Filtering by
- All Subjects: Biology
- Genre: Masters Thesis
- Creators: Arizona State University
Description
Dryland ecosystems are integral to the global agricultural system and play an important role in soil carbon (C) storage. Despite their importance, drylands are currently facing many challenges including climate-change induced rainfall variability and soil degradation. These challenges are predicted to have effects on the soil microbial communities in drylands. Compost, an organic soil amendment, is a land management strategy that has been proposed to increase soil C storage as well as improve soil conditions in drylands, specifically in restoration and agricultural sites where degradation has affected soil properties like microbial biomass and respiration. Compost additions and rainfall variability may interact to affect soil moisture, an important catalyst for microbial activity. Assessing microbial activity responses under compost applications and variable moisture will aid in understanding how land management strategies will be affected by climate change in the future. This study investigates how soil microbial activity from a degraded dryland restoration site is affected by different compost applications amounts and variable soil moistures. A laboratory incubation study was conducted in a controlled environmental chamber for 60 days. Soils were amended with different treatments of compost (0, 0.35, and 0.70 g cm -2) and water pulses (5, 10, and 15 mm) in a full factorial design. Each treatment received the same cumulative amount of water throughout the incubation, but pulses were administered in different frequencies (every 5, 10, and 15 days). Soil respiration and soil water content were measured daily, and microbial biomass was measured at the end of the incubation to assess treatment effects on microbial activity. Microbial respiration and soil water content increased with increasing compost additions and water pulse sizes. Microbial biomass did not have consistent increases with compost additions or water pulse size. Cumulative microbial respiration was highest with the large-infrequent pulse size and smallest with the small-frequent pulse size. These results suggest that microbial activity and carbon dynamics in soils where compost amendments are used will respond to future changes in precipitation variability. The results of this study can aid in understanding how microbial activity is influenced by compost applications, which will be critical in making informed management decisions in the context of climate change.
ContributorsAmari, Katherine Nicole (Author) / Throop, Heather L (Thesis advisor) / Ball, Becky A (Committee member) / Blankinship, Joseph C (Committee member) / Gherardi, Laureano A (Committee member) / Cueva Rodriguez, Alejandro H (Committee member) / Arizona State University (Publisher)
Created2021
Description
Adaptive therapy utilizes competitive interactions between resistant and sensitive cells by keeping some sensitive cells to control tumor burden with the aim of increasing overall survival and time to progression. The use of adaptive therapy to treat breast cancer, ovarian cancer, and pancreatic cancer in preclinical models has shown significant results in controlling tumor growth. The adaptive therapy model comes from the integrated pest management agricultural strategy, predator prey model, and the unique intra- and inter-tumor heterogeneity of tumors. The purpose of this thesis is to analyze and compare gemcitabine dose response on hormone refractory breast cancer cells retrieved from mice using an adaptive therapy strategy with standard therapy treatment. In this study, we compared intermittent (drug holiday) adaptive therapy with maximum tolerated dose therapy. The MCF7 resistant cell lines to both fulvestrant and palbociclib were injected into the mammary fat pads of 8 weeks old NOD/SCID gamma (NSG) mice which were then treated with gemcitabine. Tumor burden graphs were made to track tumor growth/decline during different treatments while Drug Dose Response (DDR) curves were made to test the sensitivity of the cell lines to the drug gemcitabine. The tumor burden graphs showed success in controlling the tumor burden with intermittent treatment. The DDR curves showed a positive result in using the adaptive therapy treatment method to treat mice with gemcitabine. Due to some fluctuating DDR results, the sensitivity of the cell lines to gemcitabine needs to be further studied by repeating the DDR experiment on the other mice cell lines for stronger results.
ContributorsConti, Aviona Christina (Author) / Maley, Carlo (Thesis advisor) / Blattman, Joseph (Committee member) / Anderson, Karen (Committee member) / Arizona State University (Publisher)
Created2022
Description
Bouteloua eriopoda (Torr.) Torr., also known as black grama, is a perennial bunchgrass native to arid and semiarid ecosystems in the southwestern region of North America. As a result of anthropogenic climate change, this region is predicted to increase in aridity and experience more frequent extreme drought and extreme wet years. This change in precipitation will no doubt affect black grama; however, few studies have investigated how the specific structural components of this grass will respond. The purpose of this study was to examine the effects of years since start of treatment and annual precipitation amount on tiller and stolon densities, and to test for interaction between the two predictor variables. Additionally, the effects of annual precipitation on ramets and axillary buds were investigated. By using 36 experimental plots that have been receiving drought, irrigated, or control treatments since 2007, tiller density was the most responsive component to both annual precipitation amount and years since start of treatment. Years since start of treatment and annual precipitation amount also had a statistically significant interaction, meaning the effect of precipitation amount on tiller density differs depending on how many years have passed since treatments began. Stolon density was the second-most responsive component; the predictor variables were found to have no statistically significant interaction, meaning their effects on stolon density are independent of one another. Ramet density, ramets per stolon, and axillary bud metabolic activity and density were found to be independent of annual precipitation amount for 2021. The results indicate that multiple-year extreme wet and multiple-year extreme dry conditions in the Southwest will both likely reduce tiller and stolon densities in black grama patches. Prolonged drought conditions reduced tiller and stolon production in black grama because of negative legacies from previous years. Reduced production during prolonged wet conditions could be due to increased competition between adjacent plants.
ContributorsSutter, Bryce Madison (Author) / Sala, Osvaldo E (Thesis advisor) / Makings, Elizabeth (Committee member) / Wojciechowski, Martin F (Committee member) / Arizona State University (Publisher)
Created2022
Description
It is well characterized that exposure to air pollutants is deleterious to human health. However, there is currently a gap in studying the effects of long term, low levels of exposure to pollution. The central objective of this study was to determine the effect(s) of environmental pollutants on health in the companion dog. This study used the vast Health and Life Experience Survey, Environment survey, Health Conditions survey, and Cancer Conditions survey from the Dog Aging Project as well as publicly available pollution data from the Environmental Protection Agency. These data along with a composite exposure measure, generated to accurately capture average exposure, were used to assess and model how exposure to environmental pollutants can affect reported health and disease. Overall, higher levels of exposure were found to be associated with a higher number of reported diseases. This study also included paired deoxyribonucleic acid (DNA) methylation data for a subset of dogs to investigate possible molecular mechanisms behind these observed associations. It was found that differential DNA methylation is not only associated with exposure to environmental pollutants but also that these changes mimic observed age-related changes. Due to companion dogs sharing their environment with humans, our findings may be applicable to human health. Continuing investigations into how poor air quality causes detrimental effects to health and disease will be especially valuable for more vulnerable populations.
ContributorsBrassington, Layla (Author) / Snyder-Mackler, Noah (Thesis advisor) / Promislow, Daniel (Committee member) / Jin, Kelly (Committee member) / Arizona State University (Publisher)
Created2022
Description
In Hawaiʻi, native macroalgae or “limu” are of ecological, cultural, and economic value. Invasive algae threaten native algae and coral that serve a key role in the reef ecosystem. Spectroscopy can be a valuable tool for species discrimination, while simultaneously providing insight into chemical processes occurring within photosynthetic organisms. The spectral identity and separability of Hawaiian macroalgal taxonomic groups and invasive and native macroalgae are poorly known and thus were the focus of this study. A macroalgal spectroscopic library of 30 species and species complexes found in Hawaiʻi was created. Spectral reflectance signatures were aligned with known absorption bands of division-specific photosynthetic pigments. Discriminant analysis was used to explore if taxonomic groups of algae and native versus invasive algae were separable. Discriminant analyses resulted in high overall classification accuracies. Algae were correctly classified based on taxonomic divisions 96.5% of the time and by species 83.2% of the time. Invasive versus native algae was correctly classified at a rate of 93% and higher. Analyses suggest there is spectral separability of algal taxonomic divisions and native-invasive status, which could have significant implications for coastal management. This study lays the groundwork for testing spectral mapping of native and invasive algal species using current airborne and forthcoming spaceborne imaging spectroscopy.
ContributorsFuller, Kimberly (Author) / Asner, Gregory P (Thesis advisor) / Vaughn, Nicholas (Committee member) / Martin, Roberta E (Committee member) / Arizona State University (Publisher)
Created2022
Description
Writing speculative fiction is a valuable method for exploring the potential societal transformations elicited by advances in science and technology. The aim of this project is to use speculative fiction to explore the potential consequences of precision medicine for individuals’ daily lives. Precision medicine is a vision of the future in which medicine is about predicting, and ultimately preventing disease before symptoms arise. The idea is that identification of all the factors that influence health and contribute to disease development will translate to better and less expensive healthcare and empower individuals to take responsibility for maintaining their own health and wellness. That future, as envisioned by the leaders of the Human Genome Project, the Institute for Systems Biology, and the Obama administration’s Precision Medicine Initiative, is assumed to be a shared future, one that everyone desires and that is self-evidently “better” than the present. The aim of writing speculative fiction about a “precision medicine” future is to challenge that assumption, to make clear the values underpinning that vision of precision medicine, and to leave open the question of what other possible futures could be imagined instead.
ContributorsVenkatraman, Richa (Author) / Brian, Jennifer (Thesis advisor) / Maienschein, Jane (Thesis advisor) / Hurlbut, James (Committee member) / Arizona State University (Publisher)
Created2022
Exploring the Relationship Between Depression and Graduate School Among Life Sciences Ph.D. Students
Description
Depression is one of the top mental health concerns among biology graduate students and has contributed to the “graduate student mental health crisis” declared in 2018. Prominent science outlets have called for interventions to improve graduate student mental health, but few studies have examined the relationship between depression and graduate school among life sciences Ph.D. students. In this coupled set of qualitative interview studies, 50 life sciences Ph.D. students from 28 institutions across the United States were interviewed. The first study explored how research and teaching affect depression in Ph.D. students and how depression in turn also affects students’ experiences in graduate school. Using inductive coding, four overarching aspects of graduate school that influenced student depression were highlighted, (1) structure in teaching and research, (2) positive and negative reinforcement, (3) success and failure, and (4) social support and isolation. The second study explored depression as a concealable stigmatized identity (CSI) by examining (1) to what extent and why graduate students revealed their depression to faculty advisors, graduate students, and undergraduate researchers, and (2) the consequences or benefits that they perceive are associated with revealing one’s depression through a hybrid approach of deductive and inductive coding. Graduate students most commonly revealed their depression to other graduate students; however, most were reluctant to share their depression with undergraduate researchers. These qualitative interview studies provide insights into creating more inclusive life science graduate programs for students with depression.
ContributorsWiesenthal, Nicholas John (Author) / Cooper, Katelyn M (Thesis advisor) / Brownell, Sara E (Committee member) / Maienschein, Jane (Committee member) / Arizona State University (Publisher)
Created2022
Description
Mast cells, components of the immune system, promote allergic symptoms such as itching, sneezing, and increased intestinal motility. Although mast cells have a detrimental role in allergies, they might have unrecognized physiological functions. Indeed, mast cells have been reported to protect against lethal envenomation. I hypothesized that mast cells have a protective role in the defense against toxins. Because toxin-induced diarrheal diseases are one of the top five causes of mortality in children worldwide (induced by cholera toxin, for example), I tested the role of mast cells in sensing relevant dietary toxins. My goals were to a) establish an in vitro model of mast cell activation using foodborne toxins and b) determine the mast cell transcriptional programs induced by these toxins. To establish the in vitro model, I generated mast cells from murine bone marrow precursors and cultured them in mast cell-specific media for 5 weeks. Mature mast cells were then stimulated with toxins from phylogenetically distinct origins. I found that, surprisingly, no toxin was able to induce significant cell death, even after 24h of culturing, suggesting that mast cells are resistant to the toxic effects of these compounds. To assess mast cell activation, I quantified the levels of TNF-α 6h after toxin exposure. None of the toxins were able to induce TNF-α production by mast cells, suggesting that toxins might not induce inflammation in mast cells. However, I found that mast cells induced expression of activation-related transcripts like Il1b, Tpsab1, Alox5, Egr1, Tnfa and Hdc in response to cholera toxin, when compared with controls. Mast cells stimulated with retrorsine induced the expression of Tph1, Alox5, Il1b and Hdc. Deoxynivalenol induced Ltc4, Il6, Tpsab1, Tnfa, Hdc, and Alox5 while okadaic acid induced Il6, Tnfa, Tph1, Alox5, Egr1, Il1b and Hdc expression. Aconitine only induced Il6, Hdc, and Tpsab1. Lastly, Ochratoxin A induced expression of Il1b, Il6, Tpsab1, Egr1 and Hdc. Altogether, these results suggest that mast cells directly sense and respond to food toxins, which was unknown. How exactly mast cells contribute to toxin defenses will be crucial to investigate as they impact both toxin-induced and inflammatory diseases.
ContributorsGalarza, Mayka (Author) / Borges Florsheim, Esther (Thesis advisor) / Lucas, Alexandra (Committee member) / Mana, Miyeko (Committee member) / Arizona State University (Publisher)
Created2023
Description
Riparian ecosystems comprise less than 2% of the landscape in the arid western U.S. yet provide habitat and resources to over half of arid-land wildlife species, including a broad diversity of anurans (frogs and toads). I surveyed anurans using passive acoustic monitoring to capture spring advertisement calls in wilderness area tributaries of the Verde River, Arizona, USA. In the spring and summer of 2021 and 2022, 13-29 autonomous recording units (ARUs) were deployed along perennial, intermittent, and ephemeral reaches across eight headwater streams. I characterized stream reaches based on the percent of pool, riffle, run, and side channel habitat within 100 meters of each ARU. I quantified substrate, discharge at 95% exceedance probability, flow width, and canopy cover at each site. To relate anuran occupancy and relative habitat use to environmental and hydrological variables, I evaluated acoustic data using single-species occupancy and Royle-Nichols and N-mixture (relative habitat use) models. Four species were detected in this study: canyon treefrog (Hyla arenicolor), red-spotted toad (Anaxyrus punctatus), Woodhouse’s toad (Anaxyrus woodhousii), and non-native American bullfrog (Lithobates catesbeianus), with canyon treefrog being the most ubiquitous species observed. Occupancy of canyon treefrog was greater at perennial and intermittent sites compared to ephemeral sites, and presence of pool was the most important driver of canyon treefrog occupancy and relative habitat use. Notably, this study did not detect several species with historical records in the middle Verde River watershed, including Arizona toad (Anaxyrus microscaphus) and Northern leopard frog (Lithobates pipiens). Given climate change-related flow declines and intensifying demands for water in the Southwest, maintaining stream flows that provide consistent and suitable hydroregimes for anuran breeding and larval development is of increasing importance. Determining habitat use and flow regimes necessary to support anuran populations can aid in prioritization of conservation actions related to water management and predict how changes in water availability may impact stream-breeding anurans.
ContributorsHuck, Margaret (Author) / Bateman, Heather L (Thesis advisor) / Albuquerque, Fabio S (Thesis advisor) / Lewis, Jesse S (Committee member) / Arizona State University (Publisher)
Created2023
Modeling Spatial Competition and Adaptive Therapy Protocols in Three-Dimensional Vascularized Tumors
Description
In contrast to traditional chemotherapy for cancer which fails to address tumor heterogeneity, raises patients’ levels of toxicity, and selects for drug-resistant cells, adaptive therapy applies ideas from cancer ecology in employing low-dose drugs to encourage competition between cancerous cells, reducing toxicity and potentially prolonging disease progression. Despite promising results in some clinical trials, optimizing adaptive therapy routines involves navigating a vast space of combina- torial possibilities, including the number of drugs, drug holiday duration, and drug dosages. Computational models can serve as precursors to efficiently explore this space, narrowing the scope of possibilities for in-vivo and in-vitro experiments which are time-consuming, expensive, and specific to tumor types. Among the existing modeling techniques, agent-based models are particularly suited for studying the spatial inter- actions critical to successful adaptive therapy. In this thesis, I introduce CancerSim, a three-dimensional agent-based model fully implemented in C++ that is designed to simulate tumorigenesis, angiogenesis, drug resistance, and resource competition within a tissue. Additionally, the model is equipped to assess the effectiveness of various adaptive therapy regimens. The thesis provides detailed insights into the biological motivation and calibration of different model parameters. Lastly, I propose a series of research questions and experiments for adaptive therapy that CancerSim can address in the pursuit of advancing cancer treatment strategies.
ContributorsShah, Sanjana Saurin (Author) / Daymude, Joshua J (Thesis advisor) / Forrest, Stephanie (Committee member) / Maley, Carlo C (Committee member) / Arizona State University (Publisher)
Created2023