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Description
Cellular and molecular biologists often perform cellular assays to obtain a better understanding of how cells work. However, in order to obtain a measurable response by the end of an experiment, the cells must reach an ideal cell confluency. Prior to conducting the cellular assays, range-finding experiments need to be conducted to determine an initial plating density that will result in this ideal confluency, which can be costly. To help alleviate this common issue, a mathematical model was developed that describes the dynamics of the cell population used in these experiments. To develop the model, images of cells from different three-day experiments were analyzed in Photoshop®, giving a measure of cell count and confluency (the percentage of surface area covered by cells). The cell count data were then fitted into an exponential growth model and were correlated to the cell confluency to obtain a relationship between the two. The resulting mathematical model was then evaluated with data from an independent experiment. Overall, the exponential growth model provided a reasonable and robust prediction of the cell confluency, though improvements to the model can be made with a larger dataset. The approach used to develop this model can be adapted to generate similar models of different cell-lines, which will reduce the number of preliminary range-finding experiments. Reducing the number of these preliminary experiments can save valuable time and experimental resources needed to conduct studies using cellular assays.
ContributorsGuerrero, Victor Dominick (Co-author) / Guerrero, Victor (Co-author) / Watanabe, Karen (Thesis director) / Jurutka, Peter (Committee member) / School of Mathematical and Natural Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Acetylcholinesterase (AChE) inhibition by chemical toxicants such as organophosphates, nerve agents, and carbamates can lead to a series of adverse health outcomes including seizures, coma, and death. An adverse outcome pathway (AOP) is a framework that describes a series of biologically measurable key events (KEs) leading from some molecular initiating event (MIE) to an adverse outcome (AO) of regulatory significance, all developed and hosted in the AOP Wiki. A quantitative AOP (qAOP) is a mathematical model that predicts how perturbations in the MIE affect KEs based on the key event relationships (KERs) that define the AOP. The purpose of this thesis was to expand upon the KERs that define the AOP for AChE inhibition leading to neurodegeneration in order to better understand the effects of AChE inhibitors and the risks they pose to ecosystems, wildlife, and human health. In order to reduce the resources and time spent for chemical toxicity testing, a qAOP was developed based on the available quantitative data and models that supported the AOP. A literature review for the collection of qualitative evidence and quantitative data in support of the AOP was performed resulting in further expansion of the relationships between key events (KERs) through construction of additional KER description pages. A model evaluation was performed by comparing the qAOP model predictions with experimental data, with a subsequent sensitivity analysis of unknown parameters. The qAOP model simulates the MIE through its fifth KE (KE 5) and KE 7. Model predictions compared to experimentally measured data either under- or overpredicting multiple KEs warranting additional refinement such as a formal parameter optimization. Overall, more data amenable to qAOP model development are needed. To aid qAOP model development, the presentation of data in the AOPWiki may be improved by presenting the quantitative data in the AOP Wiki in a tabular format and allowing for the hosting of mathematical models or raw data. With these recommendations in mind, and through continued AOP construction in the AOP Wiki, new qAOP models will be developed, ultimately supporting chemical risk assessment and the mitigation of effects upon exposed individuals and wildlife populations.
ContributorsSinitsyn, Dennis (Author) / Watanabe, Karen (Thesis advisor) / Vinas, Natalia (Committee member) / Wirkus, Stephen (Committee member) / Arizona State University (Publisher)
Created2023
Description
Microbial diversity manifests differently in different ecological niches of the body, with greater diversity generally expected in the gut, given that different locations have unique roles to play in the digestive system. Most microbial research is conducted using fecal samples, meaning the resulting microbes come from various places all throughout the intestines and not specific locations. The Integrative Human Microbiome Project (HMP2), provides a unique opportunity to study microbiomes of both the rectum and ileum through the use of biopsy samples taken from both locations. Using the data provided the microbiome compositions of the rectum and ileum were able to be studied and analyzed to showcase how those microbes associated with clinical variables. Inflammatory bowel diseases are complex diseases that are heterogeneous at clinical, immunological, molecular, genetic, and microbial levels. While it is known that those affected by these diseases have microbiomes that differ from those with healthy guts, not much is known about which changes in the microbiome represent causes rather than effects from changes in health.
ContributorsVecchio, Kurt (Author) / Zhao, Yunpeng (Thesis advisor) / Wang, Yue (Committee member) / Jurutka, Peter (Committee member) / Arizona State University (Publisher)
Created2023
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.
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.
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