Matching Items (54)
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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
Introspective awareness refers to direct access to one’s own internal and subjective thoughts and feelings (Wimmer & Hartl, 1991). Two theories, simulation theory and theory-theory, have been used to understand our access to our mental states. Simulation theory (Harris, 1991) involves imagining yourself in another person’s situation, reading off of your mental state, and attributing that state to the other person. Theory-theory (Gopnik, 1993) involves an interrelated body of knowledge, based on core mental-state constructs, including beliefs and desires, that may be applied to everyone—self and others (Gopnik & Wellman, 1994). Introspection is taken for granted by simulation theory, and explicitly denied by theory-theory. This study is designed to test for evidence of introspection in young children using simple perception and knowledge task. The current evidence is against introspective awareness in children because the data suggest that children cannot report their own false beliefs and they cannot report their on-going thoughts (Flavell, Green & Flavell, 1993; Gopnik & Astington, 1988). The hypothesis in this study states that children will perform better on Self tasks compared to Other tasks, which will be evidence for introspection. The Other-Perception tasks require children to calculate the other’s line of sight and determine if there is something obscuring his or her vision. The Other-Knowledge tasks require children to reason that the other’s previous looking inside a box means that he or she will know what is inside the box when it is closed. The corresponding Self tasks could be answered either by using the same reasoning for the self or by introspection to determine what it is they see and do not see, and know and do not know. Children performing better on Self tasks compared to Other tasks will be an indication of introspection. Tests included Yes/No and Forced Choice questions, which was initially to ensure that the results will not be caused by a feature of a single method of questioning. I realized belatedly, however, that Forced Choice was not a valid measure of introspection as children could introspect in both the Self and Other conditions. I also expect to replicate previous findings that reasoning about Perception is easier for children than reasoning about Knowledge.
ContributorsAamed, Mati (Author) / Fabricius, William (Thesis director) / Glenberg, Arthur (Committee member) / Kupfer, Anne (Committee member) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor) / T. Denny Sanford School of Social and Family Dynamics (Contributor)
Created2013-12
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
For many years now, early word learning in children has been an important subject among many researchers. There are many ways in which children learn word-object pairings including using co-occurrences, forwards integration, and backwards integration. This study primarily focuses on backwards integration. Backwards integration entails using learned information to be able to recall a word-object pairing from a previous time. In this thesis, three different studies were conducted with children aged 3-7 years old. In the general task, children were presented with a computerized word-learning task in which they could track word-referent pairings using co-occurrence statistics, forward integration, and backward integration. The goal of Study 1 and Study 2 was to determine the best task design to study backwards integration. The goal of the final study, Study 3, was to provide preliminary data on backwards integration. The overall results indicate that a between subjects design is the most beneficial way to test backwards integration because as a group, children were learning when compared to chance. In addition, the results from Study 3 showed that children were not learning in the task. In general, this suggests that this task may have been very difficult for children to complete. One limitation of Study 3
was that there was a small sample size of only 29 children. In order to account for this, the sample sizes in Study 2 and Study 3 were combined. This combined data did show that children succeeded at the backwards integration condition. It is noteworthy to mention that backwards integration was above chance in Study 2 and in the Study 2 and 3 combination. Therefore, the overall results suggest that children may possibly be able to backwards integrate; however, no evidence of learning in any of the other conditions were present.
was that there was a small sample size of only 29 children. In order to account for this, the sample sizes in Study 2 and Study 3 were combined. This combined data did show that children succeeded at the backwards integration condition. It is noteworthy to mention that backwards integration was above chance in Study 2 and in the Study 2 and 3 combination. Therefore, the overall results suggest that children may possibly be able to backwards integrate; however, no evidence of learning in any of the other conditions were present.
ContributorsLalani, Hanna Alyssa (Author) / Benitez, Viridiana (Thesis director) / Kupfer, Anne (Committee member) / Fabricius, William (Committee member) / Department of Psychology (Contributor) / Department of Management and Entrepreneurship (Contributor) / Sanford School of Social and Family Dynamics (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05