Matching Items (112)
Description
The mutual inhibition between synthetic gene circuits and cell growth produces growth feedback in the host-circuit system. Previous studies have demonstrated that the growth feedback has an marked impact on the molecular dynamics of the host-circuit system. However, the complexity of the growth feedback effect is not fully understood. A theoretical framework was developed to study the dynamics of the coupling between growth feedback and synthetic gene circuits. The study’s results reveal three major points about the impact of growth feedback. First, a nonlinear emergent behavior mediated by growth feedback. The unexpected behavior depends on the dynamic ribosome allocation between gene circuit expression and host cell growth. Second, the emergence and loss of unexpected qualitative states on the host-circuit system generated by ultrasensitive growth feedback. Third, the growth feedback-induced cooperativity behavior in synthetic gene modules competing for resources. In addition, growth feedback attenuated the winner-takes-all rules on resource competition between the two self-activating modules. These results demonstrate that growth feedback plays an important role in the host-circuit system’s molecular dynamics. Characterizing general principles from the effect of growth facilitates the ability to minimize or even harness unexpected gene expression behaviors derived from the effect of growth feedback.
ContributorsMelendez-Alvarez, Juan Ramon (Author) / Tian, Xiaojun (Thesis advisor) / Wang, Xiao (Committee member) / Kuang, Yang (Committee member) / Arizona State University (Publisher)
Created2022
Description
This thesis project is a first-grade curriculum that is tailored for schools with school gardens. The curriculum contains worksheets and activities for the students, making it easier for teachers to take care of the school garden while also playing a part in fighting food injustice. The curriculum has 4 subjects: Math, Language Arts, Science, and Nutrition Education.
ContributorsShah, Hirni (Author) / McGregor, Joan (Thesis director) / Lee, Rebecca (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor) / School of Social Transformation (Contributor)
Created2023-05
Description
The purpose of this thesis is to determine whether Tai Chi Qigong or Health Information podcasts are more effective for improving mental health and sleep outcomes for midlife women with mobility impairments. No other studies have been done to investigate whether Tai Chi can be more effective for sleep, depressive symptoms, and anxiety for midlife women with mobility impairments specifically. Overall, it was found that midlife women with mobility impairments experienced better sleep when they focused on health information podcasts in comparison to Tai Chi. Change in anxiety and depressive symptoms were negligible.
ContributorsRastkhiz, Tara (Author) / Carvallo, Joanna (Co-author) / Lee, Rebecca (Thesis director) / Rodney, Joseph (Committee member) / Santana, Robert (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor) / Department of Psychology (Contributor)
Created2023-05
Description
The purpose of this thesis is to determine whether Tai Chi Qigong or Health Information podcasts are more effective for improving mental health and sleep outcomes for midlife women with mobility impairments. No other studies have been done to investigate whether Tai Chi can be more effective for sleep, depressive symptoms, and anxiety for midlife women with mobility impairments specifically. Overall, it was found that midlife women with mobility impairments experienced better sleep when they focused on health information podcasts in comparison to Tai Chi. Change in anxiety and depressive symptoms were negligible.
ContributorsCarvallo, Joanna (Author) / Rastkhiz, Tara (Co-author) / Lee, Rebecca (Thesis director) / Joseph, Rodney (Committee member) / Santana, Robert (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / School of Molecular Sciences (Contributor)
Created2023-05
Description
Diisobutylene maleic acid, or DIBMA, offers a novel approach to integral membrane protein extraction without requiring the use of detergent. This copolymer extracts the protein along with the surrounding lipids, creating native nanodiscs. This method of solubilization is the preferred method, as traditional detergent solubilization can possibly alter the structural and functional integrity of the membrane protein. DIBMA solubilization, on the other hand, is able to create a more stable environment for the integral membrane protein, while allowing purification through commonly used chromatography methods similar to established detergent solubilization protocols. In this project, we study the ability of DIBMA to isolate the integral membrane protein, chloroplast ATP synthase, without the use of detergents.
ContributorsBalachandran, Kavya (Author) / Fromme, Petra (Thesis director) / Yang, Jay-How (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / College of Health Solutions (Contributor)
Created2023-05
Description
The representation of a patient’s characteristics as the parameters of a model is a key component in many studies of personalized medicine, where the underlying mathematical models are used to describe, explain, and forecast the course of treatment. In this context, clinical observations form the bridge between the mathematical frameworks and applications. However, the formulation and theoretical studies of the models and the clinical studies are often not completely compatible, which is one of the main obstacles in the application of mathematical models in practice. The goal of my study is to extend a mathematical framework to model prostate cancer based mainly on the concept of cell-quota within an evolutionary framework and to study the relevant aspects for the model to gain useful insights in practice. Specifically, the first aim is to construct a mathematical model that can explain and predict the observed clinical data under various treatment combinations. The second aim is to find a fundamental model structure that can capture the dynamics of cancer progression within a realistic set of data. Finally, relevant clinical aspects such as how the patient's parameters change over the course of treatment and how to incorporate treatment optimization within a framework of uncertainty quantification, will be examined to construct a useful framework in practice.
ContributorsPhan, Tin (Author) / Kuang, Yang (Thesis advisor) / Kostelich, Eric J (Committee member) / Crook, Sharon (Committee member) / Maley, Carlo (Committee member) / Bryce, Alan (Committee member) / Arizona State University (Publisher)
Created2021
Description
Synthetic biology (SB) has become an important field of science focusing on designing and engineering new biological parts and systems, or re-designing existing biological systems for useful purposes. The dramatic growth of SB throughout the past two decades has not only provided us numerous achievements, but also brought us more timely and underexplored problems. In SB's entire history, mathematical modeling has always been an indispensable approach to predict the experimental outcomes, improve experimental design and obtain mechanism-understanding of the biological systems. \textit{Escherichia coli} (\textit{E. coli}) is one of the most important experimental platforms, its growth dynamics is the major research objective in this dissertation. Chapter 2 employs a reaction-diffusion model to predict the \textit{E. coli} colony growth on a semi-solid agar plate under multiple controls. In that chapter, a density-dependent diffusion model with non-monotonic growth to capture the colony's non-linear growth profile is introduced. Findings of the new model to experimental data are compared and contrasted with those from other proposed models. In addition, the cross-sectional profile of the colony are computed and compared with experimental data. \textit{E. coli} colony is also used to perform spatial patterns driven by designed gene circuits. In Chapter 3, a gene circuit (MINPAC) and its corresponding pattern formation results are presented. Specifically, a series of partial differential equation (PDE) models are developed to describe the pattern formation driven by the MINPAC circuit. Model simulations of the patterns based on different experimental conditions and numerical analysis of the models to obtain a deeper understanding of the mechanisms are performed and discussed. Mathematical analysis of the simplified models, including traveling wave analysis and local stability analysis, is also presented and used to explore the control strategies of the pattern formation. The interaction between the gene circuit and the host \textit{E. coli} may be crucial and even greatly affect the experimental outcomes. Chapter 4 focuses on the growth feedback between the circuit and the host cell under different nutrient conditions. Two ordinary differential equation (ODE) models are developed to describe such feedback with nutrient variation. Preliminary results on data fitting using both two models and the model dynamical analysis are included.
ContributorsHe, Changhan (Author) / Kuang, Yang (Thesis advisor) / Wang, Xiao (Committee member) / Kostelich, Eric (Committee member) / Tian, Xiaojun (Committee member) / Gumel, Abba (Committee member) / Arizona State University (Publisher)
Created2021
Description
Since the 20th century, Arizona has undergone shifts in agricultural practices, driven by urban expansion and crop irrigation regulations. These changes present environmental challenges, altering atmospheric processes and influencing climate dynamics. Given the potential threats of climate change and drought on water availability for agriculture, further modifications in the agricultural landscape are expected. To understand these land use changes and their impact on carbon dynamics, our study quantified aboveground carbon storage in both cultivated and
abandoned agricultural fields. To accomplish this, we employed Python and various geospatial libraries in Jupyter Notebook files, for thorough dataset assembly and visual, quantitative analysis. We focused on nine counties known for high cultivation levels, primarily located in the lower latitudes of Arizona. Our analysis investigated carbon dynamics across not only abandoned and actively cultivated croplands but also neighboring uncultivated land, for which we estimated the extent. Additionally, we compared these trends with those observed in developed land areas.
The findings revealed a hierarchy in aboveground carbon storage, with currently cultivated lands having the lowest levels, followed by abandoned croplands and uncultivated wilderness. However, wilderness areas exhibited significant variation in carbon storage by county compared to cultivated and abandoned lands. Developed lands ranked highest in aboveground carbon storage, with the median value being the highest. Despite county-wide variations, abandoned croplands generally contained more carbon than currently cultivated areas, with adjacent wilderness lands containing even more than both. This trend suggests that cultivating croplands in the region reduces aboveground carbon stores, while abandonment allows for some replenishment, though only to a limited extent. Enhancing carbon stores in Arizona can be achieved through active restoration efforts on abandoned cropland. By promoting native plant regeneration and boosting aboveground carbon levels, these measures are crucial for improving carbon sequestration. We strongly advocate for implementing this step to facilitate the regrowth of native plants and enhance overall carbon storage in the region.
ContributorsGoodwin, Emily (Author) / Eikenberry, Steffen (Thesis director) / Kuang, Yang (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2024-05
Description
Glioblastoma Multiforme is a prevalent and aggressive brain tumor. It has an average 5-year survival rate of 6% and average survival time of 14 months. Using patient-specific MRI data from the Barrow Neurological Institute, this thesis investigates the impact of parameter manipulation on reaction-diffusion models for predicting and simulating glioblastoma growth. The study aims to explore key factors influencing tumor morphology and to contribute to enhancing prediction techniques for treatment.
ContributorsShayegan, Tara (Author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution & Social Change (Contributor)
Created2024-05
Description
ABSTRACTWith the National Aeronautics and Space Administration (NASA) Psyche Mission, humans will soon have the first opportunity to explore a new kind of planetary body: one composed mostly of metal as opposed to stony minerals or ices. Identifying the composition of asteroids from Earth-based observations has been an ongoing challenge. Although optical reflectance spectra, radar, and orbital dynamics can constrain an asteroid’s mineralogy and bulk density, in many cases there is not a clear or precise match with analogous materials such as meteorites. Additionally, the surfaces of asteroids and other small, airless planetary bodies can be heavily modified over geologic time by exposure to the space environment. To accurately interpret remote sensing observations of metal-rich asteroids, it is therefore necessary to understand how the processes active on asteroid surfaces affect metallic materials. This dissertation represents a first step toward that understanding. In collaboration with many colleagues, I have performed laboratory experiments on iron meteorites to simulate solar wind ion irradiation, surface heating, micrometeoroid bombardment, and high-velocity impacts. Characterizing the meteorite surface’s physical and chemical properties before and after each experiment can constrain the effects of each process on a metal-rich surface in space. While additional work will be needed for a complete understanding, it is nevertheless possible to make some early predictions of what (16) Psyche’s surface regolith might look like when humans observe it up close. Moreover, the results of these experiments will inform future exploration beyond asteroid Psyche as humans attempt to understand how Earth’s celestial neighborhood came to be.
ContributorsChristoph, John Morgan M. (Author) / Elkins-Tanton, Linda (Thesis advisor) / Williams, David (Committee member) / Dukes, Catherine (Committee member) / Sharp, Thomas (Committee member) / Bell III, James (Committee member) / Arizona State University (Publisher)
Created2023