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Objective: Isoforms of insulin-like growth factor-1 (IGF-1) gene encodes different IGF-1 isoforms by alternative splicing, and which are known to play distinct roles in muscle growth and repair. These isoforms in humans exist as IGF-1Ea, IGF-1Eb and IGF-1Ec (the latter is also known as mechano-growth factor). We sought to determine whether mRNA expression of any of these isoforms is impaired in skeletal muscle of humans with obesity, and given that humans with obesity display reduced protein synthesis in muscle. Methods: We studied 10 subjects (3 females/7 males) with obesity (body mass index: 34 ± 1 kg/m2) and 14 subjects (6 females/8 males) that were lean (body mass index: 24 ± 1 kg/m2) and served as controls. The groups represented typical populations of individuals that differed (P < 0.05) in body fat (obese: 32 ± 2; lean: 22 ± 2) and insulin sensitivity (Matsuda insulin sensitivity index, obese: 5 ± 1; lean 11 ± 2). Total RNA was extracted from 20-30 mg of tissue from muscle biopsies performed after an overnight fast. Isolated RNA was used to perform cDNA synthesis. Real-time PCR was performed using predesigned TaqMan® gene expression assays (Thermo Fisher Scientific Inc) for IGF-1Ea (assay ID: Hs01547657_m1), IGF-1Eb (assay ID: Hs00153126_m1) and IGF-1Ec (assay ID: Hs03986524_m1), as well as ACTB (assay ID: Hs01060665_g1), which was used to adjust the IGF-1 isoform mRNA expression. Responses for mRNA expression were calculated using the comparative CT method (2-ΔΔCT). Results: IGF-1Eb mRNA expression was lower in the subjects with obesity compared to the lean controls (0.67 ± 0.09 vs 1.00 ± 0.13; P < 0.05) but that of IGF-1Ea (0.99 ± 0.16 vs 1.00 ± 0.33) or IGF-1Ec (0.83 ± 0.14 vs 1.00 ± 0.21) were not different between groups (P > 0.05). Conclusions: Among the IGF-1 mRNA isoforms, IGF-1Eb mRNA is uniquely decreased in humans with obesity. Lower IGF-1Eb mRNA expression in muscle of humans with obesity may explain the lower protein synthesis observed in these individuals. Furthermore, these findings may have direct implications for muscle growth and repair in humans with obesity.
ContributorsSon, John Lee (Author) / Katsanos, Christos (Thesis director) / Gu, Haiwei (Committee member) / College of Health Solutions (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The prevalence of obesity continues to increase in the United States, along with its risk for other associated cardiovascular and metabolic diseases. Several therapeutic methods are aimed at targeting and reducing obesity, now defined as a state of chronic, low-grade inflammation (in addition to BMI > 30 kg/m2). In an attempt to expand on these therapeutic methods, research on the concept of browning in white adipose tissue (WAT) and brown adipose tissue (BAT) is being conducted. Brown adipose tissue (BAT), and a newly discovered type of adipocyte, beige adipocytes, are heavily involved in thermogenesis with the use of uncoupling protein-1 (UCP-1). This paper focuses on the analysis of common browning genes, ATP-related genes, and metabolic genes in varying biological groups in mice (Chow/High-Fat Diet and Inguinal FAT and Perigonadal Fat) and in humans (Lean/Obese and Subcutaneous WAT (SC) and Omental WAT (OM)) using methods such as RT-PCR and immunohistochemistry. The data obtained shows an increase in browning in the leaner group, specifically in the subcutaneous fat. Further, browning is significantly reduced in the obese groups of subjects and mice tested, in addition to omental/perigonadal versus subcutaneous/inguinal fat depots. Interestingly, two key ATP genes, UCP-1 and COX4I1 are vastly elevated in the OM WAT, indicating that browning may not be as important in the OM, but rather may have a potential role in SC. This is contrary to prior research findings that attempt to exclude mice surrogates in future experimentation of the browning phenomenon. Further experimentation is needed to expand on the findings of this paper.
ContributorsGhannam, Hamza Ibrahim (Author) / De Filippis, Eleanna (Thesis director) / Katsanos, Christos (Committee member) / Hernandez, James (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-12
Description
Magnetic resonance imaging (MRI) data of metastatic brain cancer patients at the Barrow Neurological Institute sparked interest in the radiology department due to the possibility that tumor size distributions might mimic a power law or an exponential distribution. In order to consider the question regarding the growth trends of metastatic brain tumors, this thesis analyzes the volume measurements of the tumor sizes from the BNI data and attempts to explain such size distributions through mathematical models. More specifically, a basic stochastic cellular automaton model is used and has three-dimensional results that show similar size distributions of those of the BNI data. Results of the models are investigated using the likelihood ratio test suggesting that, when the tumor volumes are measured based on assuming tumor sphericity, the tumor size distributions significantly mimic the power law over an exponential distribution.
ContributorsFreed, Rebecca (Co-author) / Snopko, Morgan (Co-author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / WPC Graduate Programs (Contributor) / School of Accountancy (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
Prostate cancer is the second most common kind of cancer in men. Fortunately, it has a 99% survival rate. To achieve such a survival rate, a variety of aggressive therapies are used to treat prostate cancers that are caught early. Androgen deprivation therapy (ADT) is a therapy that is given in cycles to patients. This study attempted to analyze what factors in a group of 79 patients caused them to stick with or discontinue the treatment. This was done using naïve Bayes classification, a machine-learning algorithm. The usage of this algorithm identified high testosterone as an indicator of a patient persevering with the treatment, but failed to produce statistically significant high rates of prediction.
ContributorsMillea, Timothy Michael (Author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
This paper begins by exploring the prior research that has shown how eating a plant-based diet can affect the human body. Some of these effects include: improved mood, energy levels, gut health, alkalized urine pH, as well as, lowering the risk of hormonal imbalance, kidney stones, diabetes, cancer, and coronary artery disease. The worries that generally accompany eating a fully vegan diet, which include, malnutrition and protein deficiency, are also addressed in the background research. In attempt to build upon previous research, a weeklong experiment was conducted testing 3 different factors, which include: gut health, improved mood, and urine pH. Mood states were measured quantifiably using a POMS (profile of mood states) test. Gut health was measured using several factors, including consistency and frequency of bowel movements, as well as, GI discomfort. Two 24-hour urine samples were collected from each of the subjects to compare the pH of their urine before and after the study. The sample size of this study included 15 healthy, non-smoking, subjects, between 18-30 years of age. The subjects were split up into 3 stratified random samples, including, an omnivore control group, vegan control group, and experimental vegan group. The experimental vegans had eaten meat/eggs/dairy regularly for their whole lives before the start of the study, and had consented to eating a vegan diet for the entirety of one week. While the data from the control groups remained mostly constant as predicted, the results from the experimental group were shown to have a significantly better mood (P<0.05) after one week, as well as, a significantly higher urine pH (P < 0.025) than they did before the study. However, the experimental group did not show a significant change in stool frequency, consistency, or GI discomfort within one week. The vegan control group, which included subjects who had eaten a plant-based diet for 1-3 years, had much better gut health scores. This leads us to believe that the vegan gut microbiome takes much longer to transform into than just one week unlike urine pH and mood, which can take as little as one week. These findings warrant further investigation.
ContributorsMacias, Lindsey Kaori (Author) / Johnston, Carol (Thesis director) / Katsanos, Christos (Committee member) / Harrington Bioengineering Program (Contributor) / School of Nutrition and Health Promotion (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
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 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
Description
Free coenzyme A (CoASH) carries acyl groups for the tricarboxylic acid (TCA) cycle and fatty acid metabolism, and donates acyl groups for protein posttranslational modifications. Cellular de novo CoASH synthesis starts with a pantothenate kinase (PANK1-3) phosphorylating pantothenate (vitamin B5). Mutations in PANK2 cause a subtype of neurodegeneration with brain iron accumulation (NBIA). The PANKs have differential subcellular distribution and regulatory properties. However, the purpose of each PANK has remained obscure, with knockout mouse models presenting with mild phenotypes unless challenged with a high-fat diet. Based on PANK2’s known activation by palmitoylcarnitine, the PANK2-deficient cells were challenged with palmitic acid (PAL) added to glucose-containing media. The high nutrient mixture generated a surprising “starvation” profile of reduced proliferation, low ATP, AMPK activation, and autophagy upregulation in PANK2-deficient PAL-challenged cells. Further experiments showed that fatty acids accumulated and that PANK2-deficient cells had reduced respiration when provided with palmitoylcarnitine as a substrate, seemingly due to an impaired ability to oxidize fatty acids during PAL-induced Randle Cycle activation. Intriguingly, whole-cell CoASH levels remained stable despite the PAL-induced starvation phenotype, and increasing CoASH via PANK1β overexpression did not rescue the phenotype, demonstrating a unique role for PANK2 in fatty acid metabolism. Even though a direct CoASH deficiency was not detected, there were changes in short chain CoA-derivatives, including acetyl-CoA, succinyl-CoA, and butyryl-CoA, as well as evidence of impaired TCA cycle function. These impairments in both the TCA cycle and fatty acid oxidation implicate a role for PANK2 in regulating mitochondria CoA dynamics.
ContributorsNordlie, Sandra Maria (Author) / Kruer, Michael C (Thesis advisor) / Neisewander, Janet (Thesis advisor) / Padilla Lopez, Sergio (Committee member) / Katsanos, Christos (Committee member) / Arizona State University (Publisher)
Created2022
Description
This dissertation research project developed as an urgent response to physical inactivity, which has resulted in increased rates of obesity, diabetes, and metabolic disease worldwide. Incorporating enough daily physical activity (PA) is challenging for most people. This research aims to modulate the brain's reward systems to increase motivation for PA and, thus, slow the rapid increase in sedentary lifestyles. Transcranial direct current stimulation (tDCS) involves brain neuromodulation by facilitating or inhibiting spontaneous neural activity. tDCS applied to the dorsolateral prefrontal cortex (DLPFC) increases dopamine release in the striatum, an area of the brain involved in the reward–motivation pathways. I propose that a repeated intervention, consisting of tDCS applied to the DLPFC followed by a short walking exercise stimulus, enhances motivation for PA and daily PA levels in healthy adults. Results showed that using tDCS followed by short-duration walking exercise may enhance daily PA levels in low-physically active participants but may not have similar effects on those with higher levels of daily PA. Moreover, there was a significant effect on increasing intrinsic motivation for PA in males, but there were no sex-related differences in PA. These effects were not observed during a 2-week follow-up period of the study after the intervention was discontinued. Further research is needed to confirm and continue exploring the effects of tDCS on motivation for PA in larger cohorts of sedentary populations. This novel research will lead to a cascade of new evidence-based technological applications that increase PA by employing approaches rooted in biology.
ContributorsRuiz Tejada, Anaissa (Author) / Katsanos, Christos (Thesis advisor) / Neisewander, Janet (Committee member) / Sadleir, Rosalind (Committee member) / Buman, Matthew (Committee member) / Arizona State University (Publisher)
Created2023
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 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
Description
Over the past 20 years, the fields of synthetic biology and synthetic biosystems engineering have grown into mature disciplines, leading to significant breakthroughs in cancer research, diagnostics, cell-based medicines, biochemical production, etc. Application of mathematical modelling to biological and biochemical systems have not only given great insight into how these systems function, but also have lent enough predictive power to aid in the forward-engineering of synthetic constructs. However, progress has been impeded by several modes of context-dependence unique to biological and biochemical systems that are not seen in traditional engineering disciplines, resulting in the need for lengthy design-build-test cycles before functional prototypes are generated.In this work, two of these universal modes of context dependence – resource competition and growth feedback –their effects on synthetic gene circuits and potential control mechanisms, are studied and characterized. Results demonstrate that a novel competitive control architecture can be utilized to mitigate the effects of winner-take-all resource competition (a form of context dependence where distinct gene modules influence each other by competing over a shared pool of transcriptional/translational resources) in synthetic gene circuits and restore circuits to their intended function. Application of the fluctuation-dissipation theorem and rigorous stochastic simulations demonstrate that realistic resource constraints present in cells at the transcriptional and translational levels influence noise in gene circuits in a nonmonotonic fashion, either increasing or decreasing noise depending on the transcriptional/translational capacity.
Growth feedback on the other hand links circuit function to cellular growth rate via increased protein dilution rate during exponential growth phase. This in turn can result in the collapse of bistable gene circuits as the accelerated dilution rate forces switches in a high stable state to fall to a low stable state. Mathematical modelling and experimental data demonstrate that application of repressive links can insulate sensitive parts of gene circuits against growth-fluctuations and can in turn increase the robustness of multistable circuits in growth contexts.
The results presented in this work aid in the accumulation of understanding of biological and biochemical context dependence, and corresponding control strategies and design principles engineers can utilize to mitigate these effects.
ContributorsStone, Austin (Author) / Tian, Xiao-jun (Thesis advisor) / Wang, Xiao (Committee member) / Smith, Barbara (Committee member) / Kuang, Yang (Committee member) / Cheng, Albert (Committee member) / Arizona State University (Publisher)
Created2023