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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- All Subjects: conservation
- All Subjects: Evolution
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
The Mexican gray wolf (Canis lupus baileyi) is a genetically distinct subspecies of the gray wolf (Canis lupus) that was driven to the brink of extinction as a result of human persecution. The wolf is listed as Endangered under the Endangered Species Act, and a recovery program is underway in Arizona and New Mexico to restore its population. However, the wolf is struggling to recover due to high mortality, which is a result of continued human hostility toward it. This thesis examines historical and current human attitudes toward the wolf and the implications that they have had on the extermination and recovery of the subspecies. An overview is given of wolf biology, the history of wolf extermination and recovery, and recent events relating to the recovery of the wolf. Negative impacts on ranching, hunting, and human safety are the main reasons for opposition toward wolves and wolf recovery; these concerns are analyzed, and solutions to them are proposed, with the goal of addressing them while fostering non-lethal coexistence with the wolf. In addition, opposition to wolves and wolf recovery is tied in with larger socio-political issues and is influenced by the representation of the wolf in culture; these issues in the context of wolves are also analyzed.
ContributorsLenk, Heather Nicole (Author) / Smith, Andrew (Thesis director) / Minteer, Ben (Committee member) / Brown, David E. (Committee member) / School of Life Sciences (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
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
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
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
Abstract The intent of this research is to understand what it means to be a journalist in the 21st century. As technology continues to advance at an accelerated pace, industries must adapt in order to sustain business and keep people employed. Journalism is a field that has struggled to find a way to monetize the services it provides with the overwhelming abundance of information that is now accessible for anyone on the Internet. As a result, journalism has expanded to become more than a source for news and information; it is an area of interest, topic of discussion, and connector for both consumers and producers to create, interact with, share, and engage in. The goals for this study are focused around three main research questions that aim to uncover differences in the journalism field today compared to 10-20 years ago, what skills and traits are required for students to become journalists in the 21st century, and how this data and information should affect journalism education. 1. How does the change from tradition mediums to digital change journalism jobs? 2. What skills and traits are required for students to become successful journalists? 3. How should this data affect journalism education? The research for this thesis was collected using a variety of methods including observation, interviews, and surveys from a sample data population of journalism students, recent journalism graduates, journalism professors and professionals from the Walter Cronkite School of Journalism and Mass Communication. While there are many ways to interpret and analyze why and how the journalism field has changed, most of the research uncovers what young journalists moving forward in the field can do to prepare for the changes they will face in the future. While striving to uncover what the most important traits for young journalists to have entering the journalism field today, the data showed the answer varied depending on the individual. Across all three categories of the data sample of students, graduates, and professionals/professors, honesty, curiosity, and hardworking were important traits needed to be successful in the journalism field. According to the sample of data recorded in the survey, writing was the number one skill journalists need to be successful in the 21st century. This study also revealed how the evolution of the journalism field allows opportunities for new ideas and innovation for journalism education. According to interviews with professors and professionals, journalism education should focus on a hands-on learning approach that spans across multiple disciplines like business, design, communication, technology, science, etc. Because it is important for journalists to be multi-disciplinary in their field, journalism schools must teach multi-disciplinary skills and allow for new ideas and creativity in media innovation.
ContributorsWong, Lauren Alaine (Author) / Silcock, Bill (Thesis director) / Gilger, Kristin (Committee member) / Blatt, Rebecca (Committee member) / Barrett, The Honors College (Contributor) / School of Sustainability (Contributor) / Walter Cronkite School of Journalism and Mass Communication (Contributor)
Created2015-05
Description
A literature review summarizing the current status of conservation efforts of the Mojave Desert tortoise (Gopherus agassizii) including a brief overview of the Endangered Species Act (ESA) and its applicability to this species' conservation. A genetic and physiological comparison of the morphologically similar Mojave species with the Sonoran (Gopherus morafkai) species proceeded by an analysis of if and how the ESA should apply to the Sonoran population. Analysis of current plans and interagency cooperations followed by a multi-step proposal on how best to conserve the Sonoran population of Desert tortoise.
ContributorsKulik, Elise Chikako (Author) / Kusumi, Kenro (Thesis director) / Tollis, Marc (Committee member) / Wilson Sayres, Melissa (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Biogeography is the study of the spatial distribution of the earth's biota, both in the present and the past. Traditionally, biogeographical studies have relied on a combination of surveys of existing populations, fossil evidence, and the geological record of the earth. However, with the advent of relatively inexpensive methods of DNA sequencing, it is now possible to use information concerning the genetic relatedness of individuals in populations to address questions about how those populations came to be where they are today. For example, biogeographical studies of HIV-I provide strong support for the hypothesis that this virus arose in Africa through a host switch from chimpanzees to humans and only began to spread to human populations located on other continents some 60 to 70 years ago (Sharp & Hahn, 2010).
ContributorsZheng, Wenyu (Author) / Taylor, Jesse (Thesis director) / Escalante, Ananias (Committee member) / Thieme, Horst (Committee member) / Barrett, The Honors College (Contributor)
Created2015-05
Description
We examined the evolutionary morphological responses of Drosophila melanogaster that had evolved at constant cold (16°), constant hot (25°C), and fluctuating (16° and 25°C). Flies that were exposed to the constant low mean temperature developed larger thorax, wing, and cell sizes than those exposed to constant high mean temperatures. Males and females both responded similarly to thermal treatments in average wing and cell size. The resulting cell area for a given wing size in thermal fluctuating populations remains unclear and remains a subject for future research.
ContributorsAdrian, Gregory John (Author) / Angilletta, Michael (Thesis director) / Harrison, Jon (Committee member) / Rusch, Travis (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Three populations of experimentally evolved Drosophila melanogaster populations made up of high temperature (H, constant 25 ᵒC), low temperature (C, constant 16 ᵒC) and temporal homogeneity (T, environment changes between 16 ᵒC and 25 ᵒC) were prepared and assayed to determine difference in citrate synthase activity. Between the three groups, the results were inconclusive: the resulting reaction rates in units of nmol min-1mgfly-1 were 81.8 + 20.6, 101 + 15.6, and 96.9 + 25.2 for the hot (H), cold (C), and temporally homogeneous (T) groups, respectively. We conclude that the high associated variability was due to a lack of control regarding the collection time of the experimentally evolved Drosophila.
ContributorsBelohlavek, David (Author) / Angilletta, Michael (Thesis director) / Francisco, Wilson (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2015-05