Matching Items (43)
Filtering by
- All Subjects: Evolution
- Creators: School of Life Sciences
- Member of: Theses and Dissertations
- Resource Type: Text
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
Over the past three decades, medical anthropology research, published within both public health and anthropological journals, demonstrates both the prevalence of traditional folk medicine in Latino populations in the United States and the potential difficulty of negotiating these beliefs and practices with clinical, western biomedicine. I bring attention to what might be a narrative of divergent values that occurs in Latino communities in the United States. A well-documented source (Pachter, 1994) of this clash is the culturally pervasive use of folk medicine in Latino layperson populations seeking biomedical care in the Unites States (U.S.). Numerous studies (Padilla, 2001; Koss 1972) suggest that a significant portion of Latinos in the continental United States call upon folk knowledge to diagnose, reinterpret, and treat illness. The Puerto Rican population seems to be no exception, though few studies are specific to native-born Puerto Ricans living in Puerto Rico, where the issue of access to quality public health care becomes increasingly problematic. In this honors undergraduate thesis project, I conduct a review of the literature that bridges anthropology and public health research and proceed to describe a study I conducted on Culebra Island, Puerto Rico in May of 2015. The study aims to determine whether patient satisfaction can be linked to being treated by a physician hailing from a similar cultural background, or if an irredeemable disparity between patient and provider present a roadblock to health outcomes. I found that the Puerto Rican physicians are receptive to folk illness (symptoms) and consider folk therapy as part of the treatment regimen. The physicians make patients feel understood, which might improve treatment adherence and thus health outcomes. Still, respondents demonstrated that there is high patient trust in the biomedical model by emphasizing the use of conventional medications in tandem with the folk therapy. Nevertheless, the health care provider's disposition in regards to folk knowledge and modalities are important but does not present a roadblock to optimal care and health outcomes as much as access, available services or clinic resources.
ContributorsVanasse-Torres, Elena Georgina (Author) / Maupin, Jonathan (Thesis director) / Maienschein, Jane (Thesis director) / MartÃÂnez, AirÃÂn (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Physician-assisted suicide occurs when a physician facilitates a patient's death by prescribing a lethal medication that they understand will be used for the purpose of ending the patient's life. It is a highly contentious subject and, with the recent addition of California to the list of states that allow physician-assisted suicide, is an increasingly relevant subject. Physician-assisted suicide is rarely framed as a healthcare experience, despite being a choice in the process of end-of-life care. The research seeks to bring together the debates about physician-assisted suicide with conversations about health care experiences. The experiences and perspectives of young people are particularly valuable to evaluate now, as their voices will soon be the leaders in the debate over physician-assisted suicide. Within this research, there is an underlying theme of independence of individuals that is present through both the literature review and the body of data collected and analyzed. The study found that there was no significant relationship between the quality of a person's healthcare and their perspectives about physician-assisted suicide.
ContributorsMoeur, Katherine Elizabeth (Author) / Brian, Jennifer (Thesis director) / Graff, Sarah (Committee member) / Stevenson, Christine (Committee member) / School of Life Sciences (Contributor) / School of Human Evolution and Social Change (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
In this study, we propose and then assess the efficacy of a new approach to static suspension to correct for facial paralysis. Our method involves placing barbed sutures through the superficial muscular aponeurotic system (SMAS) and anchoring them in the temporal fascia parallel to the underlying facial muscles. We first analyzed the ability of this procedure to improve facial symmetry by comparing the degree of asymmetry between the paralyzed and unaffected sides of a patient's face (N=10) prior to and following surgery. Then, to determine if symmetry is improved as a result of placing the sutures parallel to the direction of facial muscle forces, we measured the vectors of levator labii superioris and zygomaticus major in cadaver hemifaces (N=3) and compared them to the angles of the vectors of correction from the patient sample to angles of muscle vectors in three facial hemispheres from cadaver controls. Results indicate that: (1) facial symmetry was significantly improved in these patients and (2) this improvement. We conclude that, compared to existing protocols, our novel surgical method is a better means of static suspension for reconstruction following onset of facial paralysis as it is simple to perform, easy to replicate, able to be post-operatively adjusted in-office, has a good long-term prognosis, and, as we have demonstrated, effectively corrects the appearance of asymmetry by working with the underlying facial anatomy.
ContributorsLeach, Garrison Alecsander (Co-author) / Joganic, Jessica (Co-author) / Hooft, Nicole (Co-author) / Joganic, Edward (Co-author, Committee member) / Foy, Joseph (Thesis director) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Paleodietary analysis through the interpretation of stable isotopic analyses can be used to determine the approximate diet consumed at archaeological sites. The following question was investigated through the course of this research: What are the differences between the Middle Horizon capital of Tiwanaku and the associated colony of Chen Chen; and what do these differences, including those associated with paleodiet, suggest about interactions between the two sites? The main hypothesis suggested a similar dietary analysis between the two sites with two possible explanations. First, it is possible that similarities between the sites were due to the exchange and consumption of goods at both locations, perhaps through trade. Secondly, it is possible that the similarities were due to the acquisition of similar goods through local sourcing or limited trade. To assess this, an analysis was conducted based on δ13Cdiet (VPDB) values in the comparison of the city center Tiwanaku and the agricultural site of Chen Chen. Archaeological bone samples were processed from a diverse group of individuals at Chen Chen and combined with published values by Tomczak (2001), then compared against δ13C from Tiwanaku, published by Berryman (2010). After conversion to δ13Cdiet (VPDB) as described by Kellner and Schoeninger (2007), it was determined that there was no statistically significant difference between the δ13Cdiet (VPDB) values from either site, suggesting a similar ratio of goods consumed. These values were then compared to baseline values from the region to determine an approximate ratio of C3 to C4 flora or dependent fauna consumed. These data most likely support the second explanation of the main hypothesis, that both sites had access to similar goods through local sourcing or limited trade as an explanation for their similarity. However, because a similar ratio of foods consumed was determined in this analysis, it is still possible that trade occurred in both directions between Tiwanaku and Chen Chen. Additional isotopic analyses would be required to support the first claim, which can be addressed in future research projects.
ContributorsDouglas, Brynn Babette (Author) / Knudson, Kelly (Thesis director) / Spielmann, Katherine (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (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
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 NCAA recently declared sickle cell trait (SCT) to be a risk factor for sudden illness and death among student athletes. Fetal hemoglobin (HbF) concentration in adults is negatively correlated with disease severity in sickle cell anemia, although its effect on SCT is not fully understood and the concentration is found to have high variability across populations. Two single nucleotide polymorphisms (SNPs) at the human beta globin gene cluster, rs7482144 and rs10128556, contribute to the heritable variation in HbF levels and are associated with increased HbF concentrations in adults. A sample population of NCAA football student athletes was genotyped for these two polymorphisms, and their allele frequencies were compared to those of other populations. The minor allele of both polymorphisms had allele frequencies of 0.091 in the sample population, which compared closely with other populations of recent African heritage but was significantly different from European populations. The results of this study will be included in a larger study to predict whether these among other polymorphisms can be used as markers to predict susceptibility to heat-related emergencies in NCAA student athletes with SCT, although the small sample size will delay this process until participation in the study increases. Since both rs7482144 and rs10128556 exhibit high levels of linkage disequilibrium, and as their contributions to the heritable variability of HbF concentrations tend to differ greatly between populations of different ancestry, further investigations should be aimed at distinguishing between the effects of each SNP in African American, European, and other populations represented in NCAA football before conclusions can be drawn as to their practical use as genetic markers of heat susceptibility in student athletes with SCT.
ContributorsGrieger, Ryan Wayne (Author) / Stone, Anne C. (Thesis director) / Rosenberg, Michael (Committee member) / Madrigal, Lorena (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
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