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Description
The retinoid-X receptor (RXR) can form heterodimers with both the retinoic-acid
receptor (RAR) and vitamin D receptor (VDR). The RXR/RAR dimer is activated by ligand all
trans retinoic acid (ATRA), which culminates in gut-specific effector T cell migration. Similarly,
the VDR/RXR dimer binds 1,25(OH)2D3 to cause skin-specific effector T cell migration.

The retinoid-X receptor (RXR) can form heterodimers with both the retinoic-acid
receptor (RAR) and vitamin D receptor (VDR). The RXR/RAR dimer is activated by ligand all
trans retinoic acid (ATRA), which culminates in gut-specific effector T cell migration. Similarly,
the VDR/RXR dimer binds 1,25(OH)2D3 to cause skin-specific effector T cell migration.
Targeted migration is a potent addition to current vaccines, as it would induce activated T cell
trafficking to appropriate areas of the immune system and ensure optimal stimulation (40).
ATRA, while in use clinically, is limited by toxicity and chemical instability. Rexinoids
are stable, synthetically developed ligands specific for the RXR. We have previously shown that
select rexinoids can enhance upregulation of gut tropic CCR9 receptors on effector T cells.
However, it is important to establish whether these cells can actually migrate, to show the
potential of rexinoids as vaccine adjuvants that can cause gut specific T cell migration.
Additionally, since the RXR is a major contributor to VDR-mediated transcription and
epidermotropism (15), it is worth investigating whether these compounds can also function as
adjuvants that promote migration by increasing expression of skin tropic CCR10 receptors on T
cells.
Prior experiments have demonstrated that select rexinoids can induce gut tropic migration
of CD8+ T cells in an in vitro assay and are comparable in effectiveness to ATRA (7). The effect
of rexinoids on CD4+ T cells is unknown however, so the aim of this project was to determine if
rexinoids can cause gut tropic migration in CD4+ T cells to a similar extent. A secondary aim
was to investigate whether varying concentrations in 1,25-Dihydroxyvitamin D3 can be linked to
increasing CCR10 upregulation on Jurkat CD4+ T cells, with the future aim to combine 1,25
Dihydroxyvitamin D3 with rexinoids.
These hypotheses were tested using murine splenocytes for the migration experiment, and
human Jurkat CD4+ T cells for the vitamin D experiment. Migration was assessed using a
Transwell chemotaxis assay. Our findings support the potential of rexinoids as compounds
capable of causing gut-tropic migration in murine CD4+ T cells in vitro, like ATRA. We did not
observe conclusive evidence that vitamin D3 causes upregulated CCR10 expression, but this
experiment must be repeated with a human primary T cell line.
ContributorsDebray, Hannah Zara (Co-author) / Debray, Hannah (Co-author) / Blattman, Joseph (Thesis director) / Jurutka, Peter (Committee member) / Manhas, Kavita (Committee member) / Department of Psychology (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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Description
Glioblastoma multiforme (GBM) is a malignant, aggressive and infiltrative cancer of the central nervous system with a median survival of 14.6 months with standard care. Diagnosis of GBM is made using medical imaging such as magnetic resonance imaging (MRI) or computed tomography (CT). Treatment is informed by medical images and

Glioblastoma multiforme (GBM) is a malignant, aggressive and infiltrative cancer of the central nervous system with a median survival of 14.6 months with standard care. Diagnosis of GBM is made using medical imaging such as magnetic resonance imaging (MRI) or computed tomography (CT). Treatment is informed by medical images and includes chemotherapy, radiation therapy, and surgical removal if the tumor is surgically accessible. Treatment seldom results in a significant increase in longevity, partly due to the lack of precise information regarding tumor size and location. This lack of information arises from the physical limitations of MR and CT imaging coupled with the diffusive nature of glioblastoma tumors. GBM tumor cells can migrate far beyond the visible boundaries of the tumor and will result in a recurring tumor if not killed or removed. Since medical images are the only readily available information about the tumor, we aim to improve mathematical models of tumor growth to better estimate the missing information. Particularly, we investigate the effect of random variation in tumor cell behavior (anisotropy) using stochastic parameterizations of an established proliferation-diffusion model of tumor growth. To evaluate the performance of our mathematical model, we use MR images from an animal model consisting of Murine GL261 tumors implanted in immunocompetent mice, which provides consistency in tumor initiation and location, immune response, genetic variation, and treatment. Compared to non-stochastic simulations, stochastic simulations showed improved volume accuracy when proliferation variability was high, but diffusion variability was found to only marginally affect tumor volume estimates. Neither proliferation nor diffusion variability significantly affected the spatial distribution accuracy of the simulations. While certain cases of stochastic parameterizations improved volume accuracy, they failed to significantly improve simulation accuracy overall. Both the non-stochastic and stochastic simulations failed to achieve over 75% spatial distribution accuracy, suggesting that the underlying structure of the model fails to capture one or more biological processes that affect tumor growth. Two biological features that are candidates for further investigation are angiogenesis and anisotropy resulting from differences between white and gray matter. Time-dependent proliferation and diffusion terms could be introduced to model angiogenesis, and diffusion weighed imaging (DTI) could be used to differentiate between white and gray matter, which might allow for improved estimates brain anisotropy.
ContributorsAnderies, Barrett James (Author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / Stepien, Tracy (Committee member) / Harrington Bioengineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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Description
Climate change is one of the most pressing issues affecting the world today. One of the impacts of climate change is on the transmission of mosquito-borne diseases (MBDs), such as West Nile Virus (WNV). Climate is known to influence vector and host demography as well as MBD transmission. This dissertation

Climate change is one of the most pressing issues affecting the world today. One of the impacts of climate change is on the transmission of mosquito-borne diseases (MBDs), such as West Nile Virus (WNV). Climate is known to influence vector and host demography as well as MBD transmission. This dissertation addresses the questions of how vector and host demography impact WNV dynamics, and how expected and likely climate change scenarios will affect demographic and epidemiological processes of WNV transmission. First, a data fusion method is developed that connects non-autonomous logistic model parameters to mosquito time series data. This method captures the inter-annual and intra-seasonal variation of mosquito populations within a geographical location. Next, a three-population WNV model between mosquito vectors, bird hosts, and human hosts with infection-age structure for the vector and bird host populations is introduced. A sensitivity analysis uncovers which parameters have the most influence on WNV outbreaks. Finally, the WNV model is extended to include the non-autonomous population model and temperature-dependent processes. Model parameterization using historical temperature and human WNV case data from the Greater Toronto Area (GTA) is conducted. Parameter fitting results are then used to analyze possible future WNV dynamics under two climate change scenarios. These results suggest that WNV risk for the GTA will substantially increase as temperature increases from climate change, even under the most conservative assumptions. This demonstrates the importance of ensuring that the warming of the planet is limited as much as possible.
ContributorsMancuso, Marina (Author) / Milner, Fabio A (Thesis advisor) / Kuang, Yang (Committee member) / Kostelich, Eric (Committee member) / Eikenberry, Steffen (Committee member) / Manore, Carrie (Committee member) / Arizona State University (Publisher)
Created2023
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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

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
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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

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
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Description
A description of numerical and analytical work pertaining to models that describe the growth and progression of glioblastoma multiforme (GBM), an aggressive form of primary brain cancer. Two reaction-diffusion models are used: the Fisher-Kolmogorov-Petrovsky-Piskunov equation and a 2-population model that divides the tumor into actively proliferating and quiescent (or necrotic)

A description of numerical and analytical work pertaining to models that describe the growth and progression of glioblastoma multiforme (GBM), an aggressive form of primary brain cancer. Two reaction-diffusion models are used: the Fisher-Kolmogorov-Petrovsky-Piskunov equation and a 2-population model that divides the tumor into actively proliferating and quiescent (or necrotic) cells. The numerical portion of this work (chapter 2) focuses on simulating GBM expansion in patients undergoing treatment for recurrence of tumor following initial surgery. The models are simulated on 3-dimensional brain geometries derived from magnetic resonance imaging (MRI) scans provided by the Barrow Neurological Institute. The study consists of 17 clinical time intervals across 10 patients that have been followed in detail, each of whom shows significant progression of tumor over a period of 1 to 3 months on sequential follow up scans. A Taguchi sampling design is implemented to estimate the variability of the predicted tumors to using 144 different choices of model parameters. In 9 cases, model parameters can be identified such that the simulated tumor contains at least 40 percent of the volume of the observed tumor. In the analytical portion of the paper (chapters 3 and 4), a positively invariant region for our 2-population model is identified. Then, a rigorous derivation of the critical patch size associated with the model is performed. The critical patch (KISS) size is the minimum habitat size needed for a population to survive in a region. Habitats larger than the critical patch size allow a population to persist, while smaller habitats lead to extinction. The critical patch size of the 2-population model is consistent with that of the Fisher-Kolmogorov-Petrovsky-Piskunov equation, one of the first reaction-diffusion models proposed for GBM. The critical patch size may indicate that GBM tumors have a minimum size depending on the location in the brain. A theoretical relationship between the size of a GBM tumor at steady-state and its maximum cell density is also derived, which has potential applications for patient-specific parameter estimation based on magnetic resonance imaging data.
ContributorsHarris, Duane C. (Author) / Kuang, Yang (Thesis advisor) / Kostelich, Eric J. (Thesis advisor) / Preul, Mark C. (Committee member) / Crook, Sharon (Committee member) / Gardner, Carl (Committee member) / Arizona State University (Publisher)
Created2023
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Description
The most advanced social insects, the eusocial insects, form often large societies in which there is reproductive division of labor, queens and workers, have overlapping generations, and cooperative brood care where daughter workers remain in the nest with their queen mother and care for their siblings. The eusocial insects

The most advanced social insects, the eusocial insects, form often large societies in which there is reproductive division of labor, queens and workers, have overlapping generations, and cooperative brood care where daughter workers remain in the nest with their queen mother and care for their siblings. The eusocial insects are composed of representative species of bees and wasps, and all species of ants and termites. Much is known about their organizational structure, but remains to be discovered.

The success of social insects is dependent upon cooperative behavior and adaptive strategies shaped by natural selection that respond to internal or external conditions. The objective of my research was to investigate specific mechanisms that have helped shaped the structure of division of labor observed in social insect colonies, including age polyethism and nutrition, and phenomena known to increase colony survival such as egg cannibalism. I developed various Ordinary Differential Equation (ODE) models in which I applied dynamical, bifurcation, and sensitivity analysis to carefully study and visualize biological outcomes in social organisms to answer questions regarding the conditions under which a colony can survive. First, I investigated how the population and evolutionary dynamics of egg cannibalism and division of labor can promote colony survival. I then introduced a model of social conflict behavior to study the inclusion of different response functions that explore the benefits of cannibalistic behavior and how it contributes to age polyethism, the change in behavior of workers as they age, and its biological relevance. Finally, I introduced a model to investigate the importance of pollen nutritional status in a honeybee colony, how it affects population growth and influences division of labor within the worker caste. My results first reveal that both cannibalism and division of labor are adaptive strategies that increase the size of the worker population, and therefore, the persistence of the colony. I show the importance of food collection, consumption, and processing rates to promote good colony nutrition leading to the coexistence of brood and adult workers. Lastly, I show how taking into account seasonality for pollen collection improves the prediction of long term consequences.
ContributorsRodríguez Messan, Marisabel (Author) / Kang, Yun (Thesis advisor) / Castillo-Chavez, Carlos (Thesis advisor) / Kuang, Yang (Committee member) / Page Jr., Robert E (Committee member) / Gardner, Carl (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Cancer is a major health problem in the world today and is expected to become an even larger one in the future. Although cancer therapy has improved for many cancers in the last several decades, there is much room for further improvement. Mathematical modeling has the advantage of being able

Cancer is a major health problem in the world today and is expected to become an even larger one in the future. Although cancer therapy has improved for many cancers in the last several decades, there is much room for further improvement. Mathematical modeling has the advantage of being able to test many theoretical therapies without having to perform clinical trials and experiments. Mathematical oncology will continue to be an important tool in the future regarding cancer therapies and management.

This dissertation is structured as a growing tumor. Chapters 2 and 3 consider spheroid models. These models are adept at describing 'early-time' tumors, before the tumor needs to co-opt blood vessels to continue sustained growth. I consider two partial differential equation (PDE) models for spheroid growth of glioblastoma. I compare these models to in vitro experimental data for glioblastoma tumor cell lines and other proposed models. Further, I investigate the conditions under which traveling wave solutions exist and confirm numerically.

As a tumor grows, it can no longer be approximated by a spheroid, and it becomes necessary to use in vivo data and more sophisticated modeling to model the growth and diffusion. In Chapter 4, I explore experimental data and computational models for describing growth and diffusion of glioblastoma in murine brains. I discuss not only how the data was obtained, but how the 3D brain geometry is created from Magnetic Resonance (MR) images. A 3D finite-difference code is used to model tumor growth using a basic reaction-diffusion equation. I formulate and test hypotheses as to why there are large differences between the final tumor sizes between the mice.

Once a tumor has reached a detectable size, it is diagnosed, and treatment begins. Chapter 5 considers modeling the treatment of prostate cancer. I consider a joint model with hormonal therapy as well as immunotherapy. I consider a timing study to determine whether changing the vaccine timing has any effect on the outcome of the patient. In addition, I perform basic analysis on the six-dimensional ordinary differential equation (ODE). I also consider the limiting case, and perform a full global analysis.
ContributorsRutter, Erica Marie (Author) / Kuang, Yang (Thesis advisor) / Kostelich, Eric J (Thesis advisor) / Frakes, David (Committee member) / Gardner, Carl (Committee member) / Jackiewicz, Zdzislaw (Committee member) / Arizona State University (Publisher)
Created2016
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Description
There has been important progress in understanding ecological dynamics through the development of the theory of ecological stoichiometry. This fast growing theory provides new constraints and mechanisms that can be formulated into mathematical models. Stoichiometric models incorporate the effects of both food quantity and food quality into a single framework

There has been important progress in understanding ecological dynamics through the development of the theory of ecological stoichiometry. This fast growing theory provides new constraints and mechanisms that can be formulated into mathematical models. Stoichiometric models incorporate the effects of both food quantity and food quality into a single framework that produce rich dynamics. While the effects of nutrient deficiency on consumer growth are well understood, recent discoveries in ecological stoichiometry suggest that consumer dynamics are not only affected by insufficient food nutrient content (low phosphorus (P): carbon (C) ratio) but also by excess food nutrient content (high P:C). This phenomenon, known as the stoichiometric knife edge, in which animal growth is reduced not only by food with low P content but also by food with high P content, needs to be incorporated into mathematical models. Here we present Lotka-Volterra type models to investigate the growth response of Daphnia to algae of varying P:C ratios. Using a nonsmooth system of two ordinary differential equations (ODEs), we formulate the first model to incorporate the phenomenon of the stoichiometric knife edge. We then extend this stoichiometric model by mechanistically deriving and tracking free P in the environment. This resulting full knife edge model is a nonsmooth system of three ODEs. Bifurcation analysis and numerical simulations of the full model, that explicitly tracks phosphorus, leads to quantitatively different predictions than previous models that neglect to track free nutrients. The full model shows that the grazer population is sensitive to excess nutrient concentrations as a dynamical free nutrient pool induces extreme grazer population density changes. These modeling efforts provide insight on the effects of excess nutrient content on grazer dynamics and deepen our understanding of the effects of stoichiometry on the mechanisms governing population dynamics and the interactions between trophic levels.
ContributorsPeace, Angela (Author) / Kuang, Yang (Thesis advisor) / Elser, James J (Committee member) / Baer, Steven (Committee member) / Tang, Wenbo (Committee member) / Kang, Yun (Committee member) / Arizona State University (Publisher)
Created2014
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Description
In 1968, phycologist M.R. Droop published his famous discovery on the functional relationship between growth rate and internal nutrient status of algae in chemostat culture. The simple notion that growth is directly dependent on intracellular nutrient concentration is useful for understanding the dynamics in many ecological systems. The cell quota

In 1968, phycologist M.R. Droop published his famous discovery on the functional relationship between growth rate and internal nutrient status of algae in chemostat culture. The simple notion that growth is directly dependent on intracellular nutrient concentration is useful for understanding the dynamics in many ecological systems. The cell quota in particular lends itself to ecological stoichiometry, which is a powerful framework for mathematical ecology. Three models are developed based on the cell quota principal in order to demonstrate its applications beyond chemostat culture.

First, a data-driven model is derived for neutral lipid synthesis in green microalgae with respect to nitrogen limitation. This model synthesizes several established frameworks in phycology and ecological stoichiometry. The model demonstrates how the cell quota is a useful abstraction for understanding the metabolic shift to neutral lipid production that is observed in certain oleaginous species.

Next a producer-grazer model is developed based on the cell quota model and nutrient recycling. The model incorporates a novel feedback loop to account for animal toxicity due to accumulation of nitrogen waste. The model exhibits rich, complex dynamics which leave several open mathematical questions.

Lastly, disease dynamics in vivo are in many ways analogous to those of an ecosystem, giving natural extensions of the cell quota concept to disease modeling. Prostate cancer can be modeled within this framework, with androgen the limiting nutrient and the prostate and cancer cells as competing species. Here the cell quota model provides a useful abstraction for the dependence of cellular proliferation and apoptosis on androgen and the androgen receptor. Androgen ablation therapy is often used for patients in biochemical recurrence or late-stage disease progression and is in general initially effective. However, for many patients the cancer eventually develops resistance months to years after treatment begins. Understanding how and predicting when hormone therapy facilitates evolution of resistant phenotypes has immediate implications for treatment. Cell quota models for prostate cancer can be useful tools for this purpose and motivate applications to other diseases.
ContributorsPacker, Aaron (Author) / Kuang, Yang (Thesis advisor) / Nagy, John (Committee member) / Smith, Hal (Committee member) / Kostelich, Eric (Committee member) / Kang, Yun (Committee member) / Arizona State University (Publisher)
Created2014