Matching Items (51)
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- All Subjects: Evolution
- Creators: School of Life Sciences
- Member of: Barrett, The Honors College Thesis/Creative Project Collection
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
As part of a group project, myself and four teammates created an interactive children's storybook based off of the "Young Lady's Illustrated Primer" in Neal Stephenson's novel The Diamond Age. This electronic book is meant to be read aloud by a caregiver with their child, and is designed for reading over long distances through the use of real-time voice and video calling. While one part of the team focused on building the electronic book itself and writing the program, myself and two others wrote the story and I provided illustrations. Our Primer tells the story of a young princess named Charname (short for character name) who escapes from a tower and goes on a mission to save four companions to help her on her quest. The book is meant for reader-insertion, and teaches children problem-solving, teamwork, and critical thinking skills by presenting challenges for Princess Charname to solve. The Primer borrows techniques from modern video game design, focusing heavily on interactivity and feelings of agency through offering the child choices of how to proceed, similar to choose-your-own-adventure books. If brought to market, the medium lends itself well to expanded quests and storylines for the child to explore as they learn and grow. Additionally, resources are provided for the narrator to help create an engaging experience for the child, based off of research on parent-child cooperative reading and cooperative gameplay. The final version of the Primer included a website to run the program, a book-like computer to access the program online, and three complete story segments for the child and narrator to read together.
ContributorsLax, Amelia Ann Riedel (Author) / Dove-Viebahn, Aviva (Thesis director) / Wetzel, Jon (Committee member) / School of Life Sciences (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
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
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
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
Description
The goal of this study was to understand elementary school children’s perceptions of engineering. A total of 949 elementary school students were surveyed, individually or as a whole group, to examine gender and age differences in achievement-related beliefs (i.e., competency, interest, and importance) pertaining to engineering-related skills and activities. The results of this study found that specific skills and activities showed significant gender and age differences for each of the three measures. Significant findings showed that younger students (kindergarten through second grade) found many of the engineering-related skills and activities more interesting than the older students (third through fifth grade); however, the older students rated more of the skills and activities as being important. Gender differences showed that girls typically rated themselves as being more competent, more interested in, and valuing the skills and activities that pertained more to mindset ideas, such as learning from your mistakes and failures or not giving up, whereas boys rated themselves higher in more of the hands-on activities, such as building with things like legos, blocks, and k’nex.
ContributorsHandlos, Jamie Lynn Harte (Author) / Miller, Cindy (Thesis director) / Reisslein, Martin (Committee member) / School of Life Sciences (Contributor) / Chemical Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
During the formative years, habits, outlooks, and attitudes develop which influence social interaction throughout life. Because empathy is crucial in social interaction, empathy development should be supported. Evidence of empathy is first observed around the age of two (Radke-Yarrow et al., 1983, 1984; Spinrad & Fabes, 2009). The purpose of this thesis is to examine empathy in children from multiple perspectives. The scientific literature reviews the discovery of the mirror neuron system (MNS). A study on nine- and ten-year-old children showed a correlation between MNS activity and empathic concern (Pfeifer et al. 2008). Another study with a mean age of 11 demonstrated that high emotional intelligence (EI) resulted in more nominations for "cooperation" and less for "aggression" (Petrides, Sangareau, Furnham & Frederickson, 2006). The three most common EI tests (MSCEIT, TEIQue, Bar-On) are modeled to measure empathy (Bar-On, 2006; Goleman 1998, 1995; Mayer & Caruso 1997; Petrides & Furnham 2001). Psychologists agree that low measures are linked to narcissistic and aggressive behavior. The Observational Study analyzed both evidence of empathy and a lack of empathy in interactions with three- and four-year-old children. Personal experiences were also shared on how empathy was understood and practiced. Lastly, the children's short story was written to support empathy development through fiction-reading.
ContributorsDominic, Bronson (Author) / Hanish, Laura (Thesis director) / Blasingame, James (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
Self-regulation in the form of coping with emotions is something that most people have effectively adapted to by adulthood. This is an organically learned process that begins in early childhood through play, parenting, education, and peer interactions. This study examines whether six children aged 4-5 (M age= 4.72, SD= 0.372, 50% female, 100% Caucasian) are able to understand basic emotions and how to cope with them through one of two protocols. The conditions were either directive instruction or embodied cognition, and children were evaluated with a pre and post-test measure. Findings did not indicate any significant effect of the conditions on memorizing coping mechanisms, nor did it indicate that there was a significant improvement in emotion understanding following the sessions. These findings were limited by the sample size and participant interest.
ContributorsLittell, Naila Sabre (Co-author) / Frutiger, Kiana (Co-author) / Fey, Richard (Thesis director) / Kupfer, Anne (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12