Barrett, The Honors College Thesis/Creative Project Collection
Barrett, The Honors College at Arizona State University proudly showcases the work of undergraduate honors students by sharing this collection exclusively with the ASU community.
Barrett accepts high performing, academically engaged undergraduate students and works with them in collaboration with all of the other academic units at Arizona State University. All Barrett students complete a thesis or creative project which is an opportunity to explore an intellectual interest and produce an original piece of scholarly research. The thesis or creative project is supervised and defended in front of a faculty committee. Students are able to engage with professors who are nationally recognized in their fields and committed to working with honors students. Completing a Barrett thesis or creative project is an opportunity for undergraduate honors students to contribute to the ASU academic community in a meaningful way.
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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
This creative project consists of three short stories with a common theme of release, letting go, and exhalation. Nymphal Instar is a story about Tommy, a young boy, and his encounter with his uncle, a troubled man who has just returned from war. The story explores the idea of growth and maturation, and the ability to move past and let go of trauma. A Cat Goes Away is about a young man, Richard, who is required to simultaneously deal with the loss of his cat and the suicide attempts of his sister. He also runs into his sister's ex-husband and is forced to deal with him. The story explores the difficulty in recognizing one's own emotions and the importance of knowing the difference between what one can change and what one cannot. Since Diagnosis is a story about Kate, a woman who has just been diagnosed with cancer and who is unable to tell her loved ones. The story explores acceptance and the idea that letting go can allow one to live more fully. Though the three stories are disparate in their characters and events, they share a commonality in their endings and in the final realizations of the characters. There is a focus on the importance of breath and breathing, and the essentiality of acceptance and release.
ContributorsMyers, Alan Yutaka (Author) / McNally, T. M. (Thesis director) / Irish, Jenny (Committee member) / School of International Letters and Cultures (Contributor) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Many bacteria actively import environmental DNA and incorporate it into their genomes. This behavior, referred to as transformation, has been described in many species from diverse taxonomic backgrounds. Transformation is expected to carry some selective advantages similar to those postulated for meiotic sex in eukaryotes. However, the accumulation of loss-of-function alleles at transformation loci and an increased mutational load from recombining with DNA from dead cells create additional costs to transformation. These costs have been shown to outweigh many of the benefits of recombination under a variety of likely parameters. We investigate an additional proposed benefit of sexual recombination, the Red Queen hypothesis, as it relates to bacterial transformation. Here we describe a computational model showing that host-pathogen coevolution may provide a large selective benefit to transformation and allow transforming cells to invade an environment dominated by otherwise equal non-transformers. Furthermore, we observe that host-pathogen dynamics cause the selection pressure on transformation to vary extensively in time, explaining the tight regulation and wide variety of rates observed in naturally competent bacteria. Host-pathogen dynamics may explain the evolution and maintenance of natural competence despite its associated costs.
ContributorsPalmer, Nathan David (Author) / Cartwright, Reed (Thesis director) / Wang, Xuan (Committee member) / Sievert, Chris (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
"The Problem of Hope: Literary Tragedy in Mid-Twentieth Century American Fiction" examines Arthur Miller's Death of a Salesman, Ralph Ellison's Invisible Man, and Sylvia Plath's The Bell Jar through the lens of tragedy. This thesis delves into how conflicts between internal and external identities can create a tragic individual, what kinds of success count toward achievement of the "American Dream," and whether the tragic "common man" is the socially normative one or the socially disenfranchised one. It raises a three-dimensional theoretical approach to American tragedy and, most importantly, considers the significance of tragic hope for American literature. This paper questions the construction of American identities across class, race, and gender according to social scripts. It seeks to uncover what forces these scripts exert on American cultural myths and rereads those myths through tragedy to explore Miller's idea of a noble common man. By moving from Miller to Ellison to Plath, this thesis traces the undercurrents of tragedy through some of the most identity-focused novels of mid-twentieth century American fiction to see how the overarching American narrative changed from 1940 to 1969 as the US underwent significant social changes domestically and image changes abroad. Ultimately, this paper concludes that tragedy in mid-twentieth century American fiction points toward a new idea of American success as a success that occurs beyond social scripts.
ContributorsMedeiros, Amy Marie (Author) / Holbo, Christine (Thesis director) / Sadowski-Smith, Claudia (Committee member) / Department of English (Contributor) / W. P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Prince Shendi is a novella set in the semi-fictional continent of Great Africa, specifically in a proud and prosperous region called Serengeti. Our story follows the thrilling adventure of Serengeti's king-to-be, the young and naive Shendi. When Kovalu, the mighty king of Serengeti and Shendi's father, passes away due to old age, Shendi is thrust into the gauntlet of responsibility in an early and unprepared state. After a short foray as the amateur king heavily assisted by the tenured members of Serengeti's Plain Council, Shendi encounters disaster that results in the death of an important council representative and the young king's temporary exile from Serengeti. The journey produced by his one hundred day exile takes Shendi through an arid wasteland, a teeming jungles, a mystic desert, and every terrain in between before his return. Along the way, Shendi unravels the details of a prophecy that means the end of the peaceful and prosperous life his lion kin and other Serengeti dwellers had known for centuries. This prophecy held him at the center of it as the catalyst and ultimately it would be up to Shendi and his actions to stop the ancient evil at work from killing all the lions of his pride and plunging all of Serengeti into a desolate and dismal state. Will Shendi overcome the primal evil looking to dominate the land of Great Africa forevermore? And if so, what will become of him afterwards? Prince Shendi was written over the course of 2015 and early 2016 by Lucas Revelle, a student at Arizona State University studying Exercise and Wellness as well as a student of Barrett, the Honors College. The story was directed, advised, and edited by Honors Fellow Dr. Aviva Dove-Viebahn along with help from the project's 2nd reader, Rebecca Viles.
ContributorsRevelle, Lucas Benjamin (Author) / Dove-Viebahn, Aviva (Thesis director) / Viles, Rebecca (Committee member) / School of Nutrition and Health Promotion (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Two primary contexts for the adaptive evolution of bright coloration are competition for mates (i.e. mate choice) and avoiding predator attacks (i.e. warning coloration). Bright animal coloration can be iridescent, in which the surface appears to change color with changing viewing or illumination angle. Bright animal coloration can also be produced by pigments, which do not appear to change color with changing viewing or illumination angle. The Pipevine Swallowtail, Battus philenor, is unique in having both sexual signals and warning coloration that include iridescent and pigment components, both of which are variable in color. The aim of our study was to examine the role genes play in producing this variation, providing us a sense of potential indirect benefits of female choice. We tested the hypothesis that color variation has a genetic component. We predicted that in a full-sib analysis there should be greater variation in the coloration of the sexual and warning signal among families than within families. We reared B. philenor under standard laboratory conditions and analyzed heritability using a full-sib analysis. We collected reflectance measurements for components of the sexual and warning signal iridescence using a spectrophotometer and used CLR (color analysis software) to extract brightness, hue, and chroma values. We used a multivariate ANOVA (IBM SPSS, v. 21) to analyze the warning signal variation, and a generalized linear mixed model (IBM SPSS, v. 21) to analyze the sexual versus warning signal variation in males. A significance value of 0.05 was used for both analyses. Our results indicated a genetic component to coloration, implicating indirect benefits in B. philenor female mate bias. Further research on bright coloration in B. philenor indicates that there may also be direct benefits of female mate choice.
ContributorsOlzer, Rachel Maureen (Co-author) / Raymundo, Andrew (Co-author) / Pegram, Kimberly (Co-author) / Rutowski, Ronald (Co-author, Thesis director) / Pratt, Stephen (Committee member) / Papaj, Daniel (Committee member) / Barrett, The Honors College (Contributor) / School of Social Transformation (Contributor) / School of Social Sciences (Contributor)
Created2014-12
Description
Abstract "Empty Horizons": A Creative Writing Piece Max Harmon "Empty Horizons" is a creative writing piece composed of two different short stories sharing a common narrator. The first story "Can you dig it?" details a trip the narrator takes to South Dakota to go hunting shortly before starting college. On the trip the narrator contemplates certain aspects of his life and the events of the story serve as a vehicle to explore the narrator's mindset as an eighteen year old about to start a new phase in his life. The second story "Toads, Sharks and Beautiful Encounters with Uncertainty" takes place during the summer before the narrator begins his last semester in college as he attends the funeral of his recently deceased grandmother in Hawaii. During the trip to Hawaii, the narrator meets a girl his age and they are able to bond with each other over feelings of loss and uncertainty. In this story the narrator explores his feelings about life with college graduation on the horizon and comes to terms with some of the anxieties that have been plaguing him since the start of college. By detailing these two distinct and important time periods in the narrator's life the reader is able to gain a sense of understanding in regards to the narrator's own process of beginning life as an adult.
ContributorsHarmon, Max Doyle (Author) / Soares, Rebecca (Thesis director) / Popova, Laura (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2014-12
Description
The title means nothing because the stories have little in common, aside from the fact that I wrote them. The common theme of anxiety was unintentional, though it is prevalent in the stories, poetry and my life. Each story is written from a different style, with a different interest in mind. The poetry that breaks up the stories is mine, and also free of common bonds. People whom I love inspired some of them; others stem from people with whom I was (or still am) angry. Some of them are just me trying to write poetry like other successful poets, who seem to know something I don't. I wrote this set of stories and poems because I wanted to see if I could do it. I wanted to challenge myself in a new medium (two new mediums really, if you separate literature and poetry). I wanted to prove to myself that I could do it, if I really set my mind to it. I wanted to have some wealth of words, which I could record myself reading. Overall, I hope that you enjoy these stories and words. I wrote them to entertain myself, and they seem to do that pretty well. If you don't like them, stop reading. If you do like them, keep reading and tell everyone you know about this collection. I'm proud of my work here, so anything beyond that is icing on my cake.
ContributorsRagatz, Zachariah Edward (Author) / Scott, Jason Davids (Thesis director) / Espinosa, Micha (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / School of Film, Dance and Theatre (Contributor)
Created2015-05
Description
Mammals with a habitually orthograde trunk posture possess a more anterior foramen magnum than mammals with non-orthograde trunk postures. Russo & Kirk (2013) also found that bipedal orthograde mammals possess a more anteriorly placed foramen magnum than those that are just habitually orthograde. This finding has allowed us to use foramen magnum position as a predictor of trunk posture in early hominins. This prompts more research of how the other landmarks on the cranial base move in relation to this shift in foramen magnum positioning. I collected landmark data on images of 125 mammalian basicrania spanning 41 species that differed in trunk posture. Using Procrustes and Principal Components Analysis (PCA), I attempted to evaluate the effects of trunk posture on basicranial morphology, primarily focusing on the placement of the carotid and jugular foramina. The results supported Russo and Kirk's finding of a more anterior foramen magnum placement in orthograde mammals; in addition, the results displayed correlations between foramen magnum position and carotid foramen position among primates and diprotodonts.
ContributorsPena, Angela (Author) / Kimbel, William (Thesis director) / Schwartz, Gary T. (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2015-05
Description
The seven interconnected short stories of Miserablists spring from a reality created by its protagonist and ostensible author: Paul Marston, a persistently melancholy undergraduate who tries to exorcise the ghost of a past love by adapting the story into a screenplay for a film entitled Miserablists. What happens to our identity, Paul asks, in post-narrative selfhood—that is, when the meaningful narratives we’ve told ourselves about others and ourselves collapse?
In other stories (wherein Paul tries—and often fails—to figure himself a secondary character), the tangled lives of his immediate social circle unravel, overlap, and disintegrate amidst the decaying milieu of the Scene and the maddening sprawl of Phoenix. A brief sampling of happenings: Sophie confronts ideological qualms with capitalism by way of a summer gig selling knives to depressed housewives; Brett nearly burns a house down on the Fourth of July; hallucinogenic kombucha is foisted upon a hapless Alex; black mold overtakes Paul’s residence; etc.
The core text is followed by an afterword supposedly written by (the perhaps psychotic) Saul P. Thomas Marton, Ph.D. and acts as an academic analysis of the nonexistent film adaption of Miserablists. There, Marton places Marston’s work in conversation with many influential critical text and works of fiction that shaped the formation of Miserablists (including Roland Barthes’ Lover’s Discourse, Slavoj Žižek’s The Plague of Fantasies, and Alain Robbe-Grillet’s Last Year at Marienbad).
In other stories (wherein Paul tries—and often fails—to figure himself a secondary character), the tangled lives of his immediate social circle unravel, overlap, and disintegrate amidst the decaying milieu of the Scene and the maddening sprawl of Phoenix. A brief sampling of happenings: Sophie confronts ideological qualms with capitalism by way of a summer gig selling knives to depressed housewives; Brett nearly burns a house down on the Fourth of July; hallucinogenic kombucha is foisted upon a hapless Alex; black mold overtakes Paul’s residence; etc.
The core text is followed by an afterword supposedly written by (the perhaps psychotic) Saul P. Thomas Marton, Ph.D. and acts as an academic analysis of the nonexistent film adaption of Miserablists. There, Marton places Marston’s work in conversation with many influential critical text and works of fiction that shaped the formation of Miserablists (including Roland Barthes’ Lover’s Discourse, Slavoj Žižek’s The Plague of Fantasies, and Alain Robbe-Grillet’s Last Year at Marienbad).
ContributorsWebb, Zachariah Kaylar (Author) / Gilfillan, Daniel (Thesis director) / Garrison, Gary (Committee member) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05