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- All Subjects: Evolution
- Creators: School of Life Sciences
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 Beauty Within is a ceramics show displaying human body anatomy, which seeks to bridge aspects of my biological sciences major in the School of Life Sciences with aspects of my studio art minor in the Herberger Institute for Design and the Arts. My goal in creating the show was to change the opinion of people on human body organs from unease to admiration by recreating these organs in an artistic light. By stylizing the construction of the pieces and bringing in the contemporary form of art \u2014 makeup art \u2014 I hoped to bring a new light to the pieces and highlight the beauty within the human body. By leaving the pieces partly unfinished I further hoped to draw attention to the natural beauty within the pieces regardless of the makeup that covers them. By holding the show in the human anatomy lab room on campus and having both animal and human organs on display I was able to create that sense of disgust toward the organs in the viewers. The beauty of my created pieces was then directly contrasted with the disgust felt about the real organs by displaying each of my pieces next to a real organ. The reactions of the viewers reflected a change in view from the actual organs to my re-created organs, and therefore the goal of the show was achieved.
ContributorsThomas, Brandon Lee (Author) / Weiser, Kurt (Thesis director) / Chung, Samuel (Committee member) / School of Art (Contributor) / School of Life Sciences (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
‘why we bend' a Bachelor of Fine Arts honors thesis exhibition by Ximenna Hofsetz and Tiernan Warner brings together installation, digital, sculptural, and printed artwork. The main focus concerns memory; and its vague, formless, and hazy nature. The work also examines what would happen if cognitive space could be physically mapped? What would it look like in sculptural form? Memory erodes and distorts with time. We influence our memories as much as they affect us. Thus, just as relationships are ever-changing, and our memories of those we interact with constantly shifting, our relationships with our own memories are malleable and evolve through time. This transient nature of memory is depicted in the various stylistic means of this exhibition by referencing time and space as well as personal memories and ephemera in both concrete and abstract ways. ‘why we bend’ implements a variety of multimedia techniques to examine recollection and its hold on us.
ContributorsHofsetz, Ximenna Cedella (Author) / Gutierrez, Rogelio (Thesis director) / Hood, Mary (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Art (Contributor)
Created2014-12
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
Curative arts and art therapy have been increasingly implicated in promoting health and well-being for patients, but little research has been done for the benefits of drawing therapy for stress management or individuals in a non-diseased state. College students and healthcare professionals are particularly susceptible to high levels of stress, as I experienced firsthand as a medical scribe in the Emergency Room during my undergraduate experience. For this reason, I wanted to focus on using curative arts as a mediator for high-stress situations. My creative project is therefore a portable framework for curative drawing. The framework is designed to help people process complex emotional states in a more effective way using mark-making and color. Specifically, the framework is designed for those who have limited experience with art making but can be used by anyone who feels a need for curative drawing. I used this framework in both individual and group settings, culminating in a final gallery show in which viewers were able to participate in the framework and take home a booklet with the framework printed inside. In conjunction with outside research, the help of my thesis committee, and the students of Drawing and Painting as Seeing and Thinking, the final project can be viewed as one part of the intersection between art and medicine in our ever-changing healthcare environment.
ContributorsCadigan, Megan Sierra (Author) / Button, Melissa (Thesis director) / Belgrave, Melita (Committee member) / School of Art (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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 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
Human nature drives us to focus primarily on the present or near-future, instead of considering what consequences our actions may have many years from now. However, in a new era that is increasingly dominated by humans and their ambitions, this tendency has destructive repercussions on the very environment that once supported and nurtured humankind. Wild animals are highly susceptible to human activities that damage ecosystems, and a loss of animal diversity can have unforeseen consequences on future human populations. In the research, I examine the avoidable reasons for the severe decline in population of four animal species, and through my art, imagine the losses associated with their disappearance. The artwork created evokes an emotional response in the viewer through dramatic, contrasting imagery, making them reassess the relationship between humans, animals and the environment.
ContributorsJudge, Nicole (Author) / Button, Melissa (Thesis director) / Hogden, Heidi (Committee member) / School of Art (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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 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
Description
The evolution of blindness in cave animals has been heavily studied; however, little research has been done on the interaction of migration and drift on the development of blindness in these populations. In this study, a model is used to compare the effect that genetic drift has on the fixation of a blindness allele for varying amounts of migration and selection. For populations where the initial frequency is quite low, genetic drift plays a much larger role in the fixation of blindness than populations where the initial frequency is high. In populations where the initial frequency is high, genetic drift plays almost no role in fixation. Our results suggest that migration plays a greater role in the fate of the blindness allele than selection.
ContributorsMerry, Alexandra Leigh (Author) / Cartwright, Reed (Thesis director) / Rosenberg, Michael (Committee member) / Schwartz, Rachel (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05