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Description
Many factors are at play within the genome of an organism, contributing to much of the diversity and variation across the tree of life. While the genome is generally encoded by four nucleotides, A, C, T, and G, this code can be expanded. One particular mechanism that we examine in this thesis is modification of bases—more specifically, methylation of Adenine (m6A) within the GATC motif of Escherichia coli. These methylated adenines are especially important in a process called methyl-directed mismatch repair (MMR), a pathway responsible for repairing errors in the DNA sequence produced by replication. In this pathway, methylated adenines identify the parent strand and direct the repair proteins to correct the erroneous base in the daughter strand. While the primary role of methylated adenines at GATC sites is to direct the MMR pathway, this methylation has also been found to affect other processes, such as gene expression, the activity of transposable elements, and the timing of DNA replication. However, in the absence of MMR, the ability of these other processes to maintain adenine methylation and its targets is unknown.
To determine if the disruption of the MMR pathway results in the reduced conservation of methylated adenines as well as an increased tolerance for mutations that result in the loss or gain of new GATC sites, we surveyed individual clones isolated from experimentally evolving wild-type and MMR-deficient (mutL- ;conferring an 150x increase in mutation rate) populations of E. coli with whole-genome sequencing. Initial analysis revealed a lack of mutations affecting methylation sites (GATC tetranucleotides) in wild-type clones. However, the inherent low mutation rates conferred by the wild-type background render this result inconclusive, due to a lack of statistical power, and reveal a need for a more direct measure of changes in methylation status. Thus as a first step to comparative methylomics, we benchmarked four different methylation-calling pipelines on three biological replicates of the wildtype progenitor strain for our evolved populations.
While it is understood that these methylated sites play a role in the MMR pathway, it is not fully understood the full extent of their effect on the genome. Thus the goal of this thesis was to better understand the forces which maintain the genome, specifically concerning m6A within the GATC motif.
To determine if the disruption of the MMR pathway results in the reduced conservation of methylated adenines as well as an increased tolerance for mutations that result in the loss or gain of new GATC sites, we surveyed individual clones isolated from experimentally evolving wild-type and MMR-deficient (mutL- ;conferring an 150x increase in mutation rate) populations of E. coli with whole-genome sequencing. Initial analysis revealed a lack of mutations affecting methylation sites (GATC tetranucleotides) in wild-type clones. However, the inherent low mutation rates conferred by the wild-type background render this result inconclusive, due to a lack of statistical power, and reveal a need for a more direct measure of changes in methylation status. Thus as a first step to comparative methylomics, we benchmarked four different methylation-calling pipelines on three biological replicates of the wildtype progenitor strain for our evolved populations.
While it is understood that these methylated sites play a role in the MMR pathway, it is not fully understood the full extent of their effect on the genome. Thus the goal of this thesis was to better understand the forces which maintain the genome, specifically concerning m6A within the GATC motif.
ContributorsBoyer, Gwyneth (Author) / Lynch, Michael (Thesis director) / Behringer, Megan (Committee member) / Geiler-Samerotte, Kerry (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
As the prevalence and awareness of Autism Spectrum Disorder (ASD) increases, so does the variety of treatment options for primary symptoms (social interaction, communication, behavior) and secondary symptoms (anxiety, hyperactivity, GI problems, and insomnia). Various treatments, from Adderall to Citalopram to Flax Seed Oil promise relief for these symptoms. However, very little research has actually been done on some of these treatments. Additionally, the research that has been done fails to compare these treatments against one another in terms of symptom relief. The Autism Treatment Effectiveness Survey, written by Dr. James Adams, director of the Autism/Asperger's Research Program at ASU, and graduate student/program coordinator Devon Coleman, aims to fill this gap. The survey numerically rates medications based on benefit and adverse effects, in addition to naming specific symptoms that are impacted by the treatments. However, the survey itself was retrospective in nature and requires further evidence to support its claims. Therefore, the purpose of this research paper is to evaluate evidence related to the results of the survey. After the performing an extensive literature review of over 70 different treatments, it appears that the findings of the Autism Treatment Effectiveness Survey are generally well supported. There were a few minor discrepancies regarding the primary benefitted symptom, but there was not enough of a conflict to discount the information from the survey. As research is still ongoing, conclusions cannot yet be drawn for Nutritional Supplements, although the current data looks promising.
ContributorsAnderson, Amy Lynn (Author) / Adams, James (Thesis director) / Coleman, Devon (Committee member) / School of Nutrition and Health Promotion (Contributor) / W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This paper emphasizes how vital prosthetic devices are as tools for both congenital and acquired amputees in order to maximize this population's level of societal productivity, but several issues exist with the current technological focus of development by the prosthetic industry that creates unnecessary hurdles that amputees must surpass in order to truly benefit from these tools. The first major issue is that these devices are not readily available to all amputees. The astronomical cost of most prosthetic devices is a variable that restricts low income amputee populations from obtaining these vital tools regardless of their level of need, thus highlighting the fact that amputees who are not financially stable are not supported in a fashion that is conducive to their success. Also, cost greatly affects children who suffer from a missing appendage due to the fact that they are in constant need of prosthetic replacement because of physical growth and development. Another issue with the current focus of the prosthetic industry is that it focuses on acquired amputees because this population is much larger in comparison to congenital amputees and thus more lucrative. Congenital amputees' particular needs are often entirely ignored in terms of prosthetic innovation. Finally, low daily utilization is a major issue amongst the amputee population. Several variables exist with the use of prosthetic devices that cause many amputees to decide against the utilization of these tools, like difficulty of use and lack of comfort. This paper will provide solutions to cost, discrimination, issues in development, and daily utilization by emphasizing on how lowering the cost through alternative designs and materials, transitioning the focus of technological development onto the entire amputee population rather than targeting the most lucrative group, and advancing the design in a fashion to which promotes daily utilization will provide the largest level of societal support, so that the amputee population as a whole can maximize their level of productivity in a manner that will allow this group to conquer the hardships that are introduced into their lives due to a missing appendage.
ContributorsO'Connor, Casey Charles (Author) / Popova, Laura (Thesis director) / Graff, Sarah (Committee member) / Department of Psychology (Contributor) / School of Social Work (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Osteoporosis is a medical condition that leads to decreased bone mineral density, resulting in increased fracture risk.1 Research regarding the relationship between sleep and bone mass is limited and has primarily been studied in elderly adults. While this population is most affected by osteoporosis, adolescents are the most proactive population in terms of prevention. The purpose of this study was to evaluate the relationship between sleep efficiency and serum osteocalcin in college-aged individuals as a means of osteoporosis prevention. Thirty participants ages 18-25 years (22 females, 8 males) at Arizona State University were involved in this cross-sectional study. Data were collected during one week via self-recorded sleep diaries, quantitative ActiWatch, DEXA imaging, and serum blood draws to measure the bone biomarker osteocalcin. Three participants were excluded from the study as outliers. The median (IQR) for osteocalcin measured by ELISA was 11.6 (9.7, 14.5) ng/mL. The average sleep efficiency measured by actigraphy was 88.3% ± 3.0%. Regression models of sleep efficiency and osteocalcin concentration were not statistically significant. While the addition of covariates helped explain more of the variation in serum osteocalcin concentration, the results remained insignificant. There was a trend between osteocalcin and age, suggesting that as age increases, osteocalcin decreases. This was a limited study, and further investigation regarding the relationship between sleep efficiency and osteocalcin is warranted.
ContributorsMarsh, Courtney Nicole (Author) / Whisner, Corrie (Thesis director) / Mahmood, Tara (Committee member) / School of International Letters and Cultures (Contributor) / School of Nutrition and Health Promotion (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Adenosine triphosphate (ATP) is the driving force of the human body which allows individuals to move freely. Metabolism is responsible for its creation, and research has indicated that with training, metabolism can be modified to respond more efficiently to aerobic stimulus. During an acute bout of exercise, cardiac output increases to maintain oxygen supply to the body. Oxidative muscle fibers contract to move the body for prolonged periods of time, creating oxidative stress which is managed by the mitochondria which produce the ATP that supplies the muscle fiber, and as the body returns to its resting state, oxygen continues to be consumed in order to return to steady state. Following endurance training, changes in cardiac output, muscle fiber types, mitochondria, substrate utilization, and oxygen consumption following exercise make adaptations to make metabolism more efficient. Resting heart rate decreases and stroke volume increases. Fast twitch muscle fibers shift into more oxidative fibers, sometimes through mitochondrial biogenesis, and more fat is able to be utilized during exercise. The excess postexercise oxygen consumption following exercise bouts is reduced, and return to steady state becomes quicker. In conclusion, endurance training optimizes metabolic response during acute bouts of aerobic exercise.
ContributorsWarner, Erin (Author) / Nolan, Nicole (Thesis director) / Cataldo, Donna (Committee member) / School of Nutrition and Health Promotion (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
University students currently lack sufficient knowledge and resources needed to support healthy eating patterns and nutrition. Comparison of the number of registered dietitians that are available to all students, along with the number of wellness events that are held at each university within the Pacific-12 conference will help determine which schools are best able to support their students' needs. Data was collected using a Google forms survey sent via email to wellness directors of each of the universities in the Pac-12 conference. Eight out of the twelve schools in the conference responded to the survey. The average number of dietitians available to all students (regardless of athlete status) was found to be 1.43 dietitians. Of the schools that responded, the University of Colorado, Boulder, has the most resources dedicated to student nutrition wellness with three dietitians available for all undergraduate students, free dietitian services, and approximately 150 wellness events each year. The success of available nutrition wellness resources was inconclusive as schools did not provide the information regarding student utilization and attendance. Future university promoted nutrition wellness programs should increase the number of affordable dietitians and total wellness events, as well as promote student health services through social media platforms to improve student nutrition knowledge and usage of resources.
ContributorsCurtin, Anne Clare (Author) / Dixon, Kathleen (Thesis director) / McCoy, Maureen (Committee member) / School of Nutrition and Health Promotion (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This study examines Glamour magazine to determine the messages the publication sends to its readers and to evaluate if such messages align with modern feminist goals. The articles of Glamour's 12 issues from the year of 2016 are analyzed using a framework adapted from previous research on women's magazines. Articles are coded as either positive (feminist, anti-traditional, promotes equality) or negative (anti-feminist, traditional, promotes inequality). Distinct content themes (appearance, dating, home, self-development, career development, politics/world issues, and entertainment) are also examined individually. After the presentation of data, I examine my findings through a feminist lens to determine the nature of the messages being sent to women through the magazine's editorial content, followed by an assessment of the value of women's magazines and how they could potentially shape the beliefs and roles of a 2017 woman. It is found that about half of the articles in Glamour could be considered as having feminist messages, with strong themes of personal choice, individual empowerment, and political involvement or activism in these articles and throughout the magazine. The content also has many blatantly feminist messages, including consistent use of the word itself. Another 40% of the articles are found to be neutral (no clear message to reader), and the remaining are negative. The sexism inherent in these negative articles is critically examined. Finally, the main takeaways of the findings and their ramifications are discussed from both a media consumer and a media producer perspective, with arguments for why it is important to be critical of a magazine's editorial content.
ContributorsAllnatt, Libby Paige (Author) / Pucci, Jessica (Thesis director) / Dove-Viebahn, Aviva (Committee member) / School of Social Transformation (Contributor) / Department of Psychology (Contributor) / Walter Cronkite School of Journalism and Mass Communication (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Spousal loss is a common, significant life event that can negatively affect multiple facets of individual health and psychological adjustment. Social support is one factor that is shown to improve adjustment following spousal loss, but much less is known regarding which facet of social support is most predictive of positive adjustment outcomes following spousal loss. This study examined the course of changes in mental health and well-being following spousal loss and which facets of social support are associated with better outcomes following spousal loss. Latent growth curve modeling was applied to data from 265 widowed individuals, ages 65 and older, across four assessments (baseline, and 6-, 18-, and 48- months following spousal loss). I examined the following research questions: (1) adjustment following spousal loss will follow a trajectory of an increase in depressive symptoms and anxiety and decrease in well-being with a leveling-off over time, with between-person differences, and (2) emotional support and instrumental support given will lead to more positive adjustment outcomes over time. Depressive symptoms followed the hypothesized trajectory but anxiety and well-being showed relative stability before and after spousal loss. Instrumental support was the most beneficial facet of social support, such that receiving more instrumental support was associated with lower levels of depressive symptoms and anxiety 6-months following spousal loss. Giving more instrumental support led to an increase in well-being following spousal loss. Instrumental support given and received led to increases in well-being as a function of spousal loss. The discussion focuses on whether and how these findings can help to identify ways through which support and help can be given to individuals to improve adjustment to spousal loss and fully recover.
ContributorsSullivan, Colleen Elizabeth (Author) / Infurna, Frank (Thesis director) / Luthar, Suniya (Committee member) / Davis, Mary (Committee member) / Department of Psychology (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Effortful Control (EC) is a person's ability to self-regulate when presented with an environmental stimulus (Rothbart, et al., 2003). It has been well-established that high levels of EC are associated with multiple positive social and academic outcomes in adolescence (Spinrad et al., 2009). Research suggests that parents have a strong impact on numerous child outcomes, such as EC, through both genetic and environmental pathways. Past research has also examined how parents diagnosed with psychopathology contribute to maladaptive outcomes in their children, including poor regulation, through both genetic and environmental processes (Ellis, et al., 1997). However, less is known about the longitudinal effects of parent dysfunction on the child's environment and regulatory abilities and potential mediators of those effects. The current study tested the hypotheses that parent Alcohol Use Disorder (AUD) would specifically predict early adversity, biological mother conscientiousness, and child EC longitudinally and that early adversity and biological mother conscientiousness would predict child EC. Participants were from a longitudinal study of familial alcoholism (N = 195). Regression analyses indicated that parent AUD was not specifically associated with child EC or with biological mother conscientiousness. However, parent AUD was related to higher levels of early adversity. Additionally, biological mother conscientiousness was associated with higher levels of child EC and early adversity was associated with lower levels of child EC when controlling for earlier EC. Given these findings, future research should test mediation models in which parent AUD predicts child EC indirectly through early adversity.
ContributorsRuof, Ariana Kelsey (Author) / Chassin, Laurie (Thesis director) / Elam, Kit (Committee member) / Davis, Mary (Committee member) / Department of Psychology (Contributor) / Sanford School of Social and Family Dynamics (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Forty collegiate gymnasts were recruited for a nutrition and health study. Participants must have been at least eighteen years old at Arizona State University (ASU) in the club or team gymnastics program. The Institutional Review Board (IRB) reviewed and accepted my survey in order to hand out to the gymnasts. The ASU club and team coach and the ASU study team also approved my survey. As soon as the survey was approved, it was emailed to all of the gymnasts. ASU gymnasts were surveyed on nutritional knowledge and personal health. Subjects answered a quiz on nutrient needs and serving sizes. Personal questions consisted of height, weight, injuries, body image, and typical meal plans. Gymnasts were given a $10 compensation to increase the participation. We found that only 16% of gymnasts surveyed scored a 70% or higher on their nutritional knowledge. Although these gymnasts do not have adequate knowledge, the majority consume a healthy diet. Diets included fruits, vegetables, protein-rich foods, and few high fat and sugary foods. Four of the gymnasts had one or fewer injuries in the past two years, although, four gymnasts also had three or more injuries. No correlation was found between diet and injuries. There was also no correlation between the gymnast's nutritional knowledge and their health.
ContributorsKugler, Natalie K. (Author) / Levinson, Simin (Thesis director) / Berger, Christopher (Committee member) / School of Nutrition and Health Promotion (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12