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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

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.
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
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Description
The purpose of this study is to analyze the stereotypes surrounding four wind instruments (flutes, oboes, clarinets, and saxophones), and the ways in which those stereotypes propagate through various levels of musical professionalism in Western culture. In order to determine what these stereotypes might entail, several thousand social media and

The purpose of this study is to analyze the stereotypes surrounding four wind instruments (flutes, oboes, clarinets, and saxophones), and the ways in which those stereotypes propagate through various levels of musical professionalism in Western culture. In order to determine what these stereotypes might entail, several thousand social media and blog posts were analyzed, and direct quotations detailing the perceived stereotypical personality profiles for each of the four instruments were collected. From these, the three most commonly mentioned characteristics were isolated for each of the instrument groups as follows: female gender, femininity, and giggliness for flutists, intelligence, studiousness, and demographics (specifically being an Asian male) for clarinetists, quirkiness, eccentricity, and being seen as a misfit for oboists, and overconfidence, attention-seeking behavior, and coolness for saxophonists. From these traits, a survey was drafted which asked participating college-aged musicians various multiple choice, opinion scale, and short-answer questions that gathered how much they agree or disagree with each trait describing the instrument from which it was derived. Their responses were then analyzed to determine how much correlation existed between the researched characteristics and the opinions of modern musicians. From these results, it was determined that 75% of the traits that were isolated for a particular instrument were, in fact, recognized as being true in the survey data, demonstrating that the stereotypes do exist and seem to be widely recognizable across many age groups, locations, and levels of musical skill. Further, 89% of participants admitted that the instrument they play has a certain stereotype associated with it, but only 38% of people identify with that profile. Overall, it was concluded that stereotypes, which are overwhelmingly negative and gendered by nature, are indeed propagated, but musicians do not appear to want to identify with them, and they reflect a more archaic and immature sense that does not correlate to the trends observed in modern, professional music.
ContributorsAllison, Lauren Nicole (Author) / Bhattacharjya, Nilanjana (Thesis director) / Ankeny, Casey (Committee member) / School of Life Sciences (Contributor) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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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

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
Only in the world of acting can an individual be denied a job simply on the basis of their appearance, and in my thesis, I sought to explore alternatives to this through the concept of nontraditional casting and casting against "type", which included the presentation of a full-length production of

Only in the world of acting can an individual be denied a job simply on the basis of their appearance, and in my thesis, I sought to explore alternatives to this through the concept of nontraditional casting and casting against "type", which included the presentation of a full-length production of the musical "Once on this Island" which I attempted to cast based on vocal quality and skill alone rather than taking physical characteristics into account. I researched the history and implementation of nontraditional casting, both in regards to race and other factors such as gender, socio-economic status, and disability. I also considered the legal and intellectual property challenges that nontraditional casting can pose. I concluded from this research that while nontraditional casting is only one solution to the problem, it still has a great deal of potential to create diversity in theater. For my own show, I held the initial auditions via audio recording, though the callback auditions were held in person so that I and my crew could appraise dance and acting ability. Though there were many challenges with our cast after this initial round of auditions, we were able to solidify our cast and continue through the rehearsal process. All things said, the show was very successful. It is my hope that those who were a part of the show, either as part of the production or the audience, are inspired to challenge the concept of typecasting in contemporary theater.
ContributorsBriggs, Timothy James (Author) / Yatso, Toby (Thesis director) / Dreyfoos, Dale (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor)
Created2014-12
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Description
This thesis explores my experience in teaching a high school music class through composition. I detail pedagogical approaches that helped to shape my lesson planning including constructivism, informal learning, and project based learning. The music education theory is put into action in a real high school setting and I explain

This thesis explores my experience in teaching a high school music class through composition. I detail pedagogical approaches that helped to shape my lesson planning including constructivism, informal learning, and project based learning. The music education theory is put into action in a real high school setting and I explain what happened: what worked, what didn't, and what can we learn from this?
ContributorsWhelihan, Brian Peter (Author) / Tobias, Evan (Thesis director) / Schildkret, David (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor)
Created2014-05
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Description
E-Strings Academy (www.estringsacademy.wordpress.com) is a resource website intended for the beginning violinist, violist, cellist, and bassist. The mission of the website is to extend musical learning opportunities to students outside of the physical string classroom and to engage first-year string students in musical activities at home that supplement the instruction

E-Strings Academy (www.estringsacademy.wordpress.com) is a resource website intended for the beginning violinist, violist, cellist, and bassist. The mission of the website is to extend musical learning opportunities to students outside of the physical string classroom and to engage first-year string students in musical activities at home that supplement the instruction they receive in a school setting. The current website features five different areas for students to explore: lesson videos, tunes, listening activities, games, and resources. In each area, students have the opportunity to learn and reinforce musical concepts and skill sets that they will need in order to be successful in music, both in their first year of playing and beyond. I created E-Strings Academy with the intention that I use it with my own string students in my future teaching career. It is a flexible website that I will continue to revise, adapt, and enhance to best serve the needs of my students and enrich their musical learning outside of the classroom.
ContributorsCook, Christa Marie (Author) / Schmidt, Margaret (Thesis director) / Tobias, Evan (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor)
Created2015-05
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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

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
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Description
Since its discovery in 1524, many people have characterized the vermiform appendix. Charles Darwin considered the human appendix to be a vestige and a useless structure. Others at the time opposed this hypothesis. However, Darwin's hypothesis became prevalent one until recently when there became a renewed interest in the appendix

Since its discovery in 1524, many people have characterized the vermiform appendix. Charles Darwin considered the human appendix to be a vestige and a useless structure. Others at the time opposed this hypothesis. However, Darwin's hypothesis became prevalent one until recently when there became a renewed interest in the appendix because of advancements in microscopes, knowledge of the immune system, and phylogenetics. In this review, I will argue that the vermiform appendix, although still not completely understood, has important functions. First, I will give the anatomy of the appendix. I will discuss the comparative anatomy between different animals and also primates. I will address the effects of appendicitis and appendectomy. I will give background on vestigial structures and will discuss if the appendix is a vestige. Following, I will review the evolution of the appendix. Finally, I will argue that the function of the appendix is as an immune organ, including discussion of gut-associated lymphoid tissue (GALT), development of lymphoid follicles in GALT and their comparison within different organs, Immunoglobulin A (IgA) function in the gut, biofilms as evidence that the appendix is a safe-house for beneficial bacteria, re-inoculation of the bowel, and protection against recurring infection. I will conclude with future studies that should be conducted to further our understanding of the vermiform appendix.
ContributorsPrestwich, Shelby Elizabeth (Author) / Cartwright, Reed (Thesis director) / Lynch, John (Committee member) / Furstenau, Tara (Committee member) / School of Geographical Sciences and Urban Planning (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Theory Jam is a series of online, education videos that teach music theory in a fun, engaging way. Our project is a response to the growing need for successful online education content. It incorporates strategies for creating effective educational video content and engages with contemporary debates in the field of

Theory Jam is a series of online, education videos that teach music theory in a fun, engaging way. Our project is a response to the growing need for successful online education content. It incorporates strategies for creating effective educational video content and engages with contemporary debates in the field of music theory surrounding the purpose of a music theory education.
ContributorsCannatelli, Joshua Bryce (Co-author) / Daval, Charles Joseph (Co-author) / Miller, April (Thesis director) / Scott, Jason (Committee member) / Tobias, Evan (Committee member) / Department of English (Contributor) / School of Film, Dance and Theatre (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
The Cannabis plant has historical roots with human beings. The plant produces compounds called cannabinoids, which are responsible for the physiological affects of Cannabis and make it a research candidate for medicinal use. Analysis of the plant and its components will help build a better database that could be used

The Cannabis plant has historical roots with human beings. The plant produces compounds called cannabinoids, which are responsible for the physiological affects of Cannabis and make it a research candidate for medicinal use. Analysis of the plant and its components will help build a better database that could be used to develop a complete roster of medicinal benefits. Research regarding the cellular protein receptors that bind the cannabinoids may not only help provide reasons explaining why the Cannabis plant could be medicinally relevant, but will also help explain how the receptors originated. The receptors may have been present in organisms before the present day Cannabis plant. So why would there be receptors that bind to cannabinoids? Searching for an endocannabinoid system could help explain the purpose of the cannabinoid receptors and their current structures in humans. Using genetic technologies we are able to take a closer look into the evolutionary history of cannabinoids and the receptors that bind them.
ContributorsSalasnek, Reed Samuel (Author) / Capco, David (Thesis director) / Mangone, Marco (Committee member) / Stump, Edmund (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05