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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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
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
This is a creative thesis project on the topic of the third party logistics industry, and the improvements that are possible through the implementation of goods to person technologies. The scope of the project entails the relationship between Company X, which is a third party logistics provider, and Company Y, a major toy retailer. This thesis identifies current trends for the third party logistics industry such as rising operating costs and average savings achieved through these business relationships. After identifying the negative trends that Company X is vulnerable to such as high human resources costs, and cost of quality issues. Given the findings derived from industry data, a final recommendation was settled on to improve productivity and ultimately reduce the use of temporary labor for Company X. The implementation of a goods to person technology solution provides the opportunity to reduce hours of operation, man hours, as well as direct and indirect costs such as labor. Research has proven that firms operating in the retail industry rely heavily on temporary labor to handle the seasonal demand brought by the holidays, thus this recommendation could be applied to a variety of operations. The data compiled throughout this thesis have major implications for the third party logistics industry and achieving long term profitability in operations management.
ContributorsFonseca, Tanner (Author) / Printezis, Antonios (Thesis director) / Kellso, James (Committee member) / Department of Supply Chain Management (Contributor) / School of Sustainability (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
This research looks at a group of students from Tumaini Children's Home in Nyeri, Kenya. The purpose of this paper is to explore why this particular group of students is so academically successful. Quantitative research was taken from the average 2013 test scores of Tumaini students who took the Kenyan Certificate of Primary Education (KCPE) exam in comparison to the scores of students who are not residing in the orphanage. Qualitative research involves interviews from those students who live in Tumaini and interviews from adults who are closely connected to the orphanage. The purpose is to understand why the students are performing so well academically and what support they have created for themselves that allows them to do so.
ContributorsTooker, Amy Elizabeth (Author) / Puckett, Kathleen (Thesis director) / Cocchiarella, Martha (Committee member) / Barrett, The Honors College (Contributor) / Division of Teacher Preparation (Contributor)
Created2014-12
Description
Supply Chain Management has many fundamental principles that can be applied to all businesses to improve efficiency and create more transparency, this in turn, encourages collaboration and fosters healthy professional relationships. Using the fundamental principles of supply chain management, I evaluated the Veterans Administration(VA) hospital in regards to their provided treatment for Post-traumatic Stress Disorder(PTSD) to look for places where efficiency can be improved. I analyzed the problem in relation to Supply Chain Management, PTSD, and design in order to create a more complete solution. Once these areas were addressed, I proposed a solution that included creating a separate clinic for PTSD treatment that addressed the current issues in regards to treatment at the VA hospital. My goal was to improve space efficiencies and design a treatment environment that is more evolved and conducive to veterans suffering from PTSD. Though the creation of one PTSD clinic will not be able to completely change the system, it can be a step in the right direction to bring about the change that needs to occur within the VA medical system.
ContributorsGriffin, Kailey Anne (Author) / Brandt, Beverly (Thesis director) / Davila, Eddie (Committee member) / Damore-Minchew, Elizabeth (Committee member) / Barrett, The Honors College (Contributor) / W. P. Carey School of Business (Contributor) / The Design School (Contributor)
Created2014-05
Description
This article summarizes exploratory research conducted on private and public hospital systems in Australia and Costa Rica analyzing the trends observed within supply chain procurement. Physician preferences and a general lack of available comparative effectiveness research—both of which are challenges unique to the health care industry—were found to be barriers to effective supply chain performance in both systems. Among other insights, the ability of policy to catalyze improved procurement performance in public hospital systems was also was observed. The role of centralization was also found to be fundamental to the success of the systems examined, allowing hospitals to focus on strategic rather than operational decisions and conduct value-streaming activities to generate increased cost savings.
ContributorsBudgett, Alexander Jay (Author) / Schneller, Eugene (Thesis director) / Gopalakrishnan, Mohan (Committee member) / Barrett, The Honors College (Contributor) / Department of Supply Chain Management (Contributor) / Department of English (Contributor)
Created2015-05
Description
The Latino population is the fastest growing minority group in the United States (U.S Census Bureau, 2003). Such a rapidly changing demographic stresses the importance of implementing strategies into the community social framework to accommodate for cultural and language differences. This research paper seeks to answer: what factors influence the sense of community among Latino families in Phoenix? The following questions will help to assess the dynamic relationship between sense of community and literacy 1) what is the perceived importance of literacy among Latino families living in Phoenix? 2) How is language development reflected among the family dynamics within a predominantly collectivist culture? It is hypothesized that both collectivism and literacy are the main influences on sense of community among this population.
ContributorsBennett, Julie (Author) / Glenberg, Arthur (Thesis director) / Restrepo, Laida (Committee member) / Barrett, The Honors College (Contributor) / School of Politics and Global Studies (Contributor) / School of International Letters and Cultures (Contributor)
Created2015-05
Description
The rationale behind this thesis is grounded in nearly two years of experience interning at UTC Aerospace Systems (UTAS). I was able to gain a wide exposure to different facets of the supply chain management organization during my time as an intern, from strategic sourcing and commodity management, to tactical procurement and supplier development. In each of these respective areas, I observed a variety of initiatives that did not reach their full potential because employees were not provided the tools for success. One of these areas in particular is the New Product Introduction (NPI) process management, in which there is not a standard process for program managers to follow from start to finish. I saw this as an opportunity to hone in the scope of my thesis research and experience at UTAS to improve a process and provide standard work and tools for it to be consistently executed. The current state process is not formalized \u2014 it merely tracks certain metrics that are not necessarily applicable to the overall health of the program because they do not monitor the progress of the program. This resulted in heavy costs incurred from inadequate planning, a skewed timeline, and customer frustration. The aim of the desired state NPI process is to gather cross-functional expertise and weigh in, adhere to a strict entry to market timeline, and increase customer satisfaction, all while minimizing costs incurred throughout the life of the program. The dominant output of this project will be a cross-functional flow chart of the process for each group to follow and standard work and tools to support the process across a variety of NPI program applications.
ContributorsThorn, Taylor Aiko Marie (Author) / Brown, Steven (Thesis director) / Arrigoni, Gregory (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / Department of Supply Chain Management (Contributor) / W. P. Carey School of Business (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