Barrett, The Honors College Thesis/Creative Project Collection
Barrett, The Honors College at Arizona State University proudly showcases the work of undergraduate honors students by sharing this collection exclusively with the ASU community.
Barrett accepts high performing, academically engaged undergraduate students and works with them in collaboration with all of the other academic units at Arizona State University. All Barrett students complete a thesis or creative project which is an opportunity to explore an intellectual interest and produce an original piece of scholarly research. The thesis or creative project is supervised and defended in front of a faculty committee. Students are able to engage with professors who are nationally recognized in their fields and committed to working with honors students. Completing a Barrett thesis or creative project is an opportunity for undergraduate honors students to contribute to the ASU academic community in a meaningful way.
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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
It is unknown which regions of the brain are most or least active for golfers during a peak performance state (Flow State or "The Zone") on the putting green. To address this issue, electroencephalographic (EEG) recordings were taken on 10 elite golfers while they performed a putting drill consisting of hitting nine putts spaced uniformly around a hole each five feet away. Data was collected at three time periods, before, during and after the putt. Galvanic Skin Response (GSR) measurements were also recorded on each subject. Three of the subjects performed a visualization of the same putting drill and their brain waves and GSR were recorded and then compared with their actual performance of the drill. EEG data in the Theta (4 \u2014 7 Hz) bandwidth and Alpha (7 \u2014 13 Hz) bandwidth in 11 different locations across the head were analyzed. Relative power spectrum was used to quantify the data. From the results, it was found that there is a higher magnitude of power in both the theta and alpha bandwidths for a missed putt in comparison to a made putt (p<0.05). It was also found that there is a higher average power in the right hemisphere for made putts. There was not a higher power in the occipital region of the brain nor was there a lower power level in the frontal cortical region during made putts. The hypothesis that there would be a difference between the means of the power level in performance compared to visualization techniques was also supported.
ContributorsCarpenter, Andrea (Co-author) / Hool, Nicholas (Co-author) / Muthuswamy, Jitendran (Thesis director) / Crews, Debbie (Committee member) / Harrington Bioengineering Program (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
Females are highly vulnerable to the effects of methamphetamine, and understanding the mechanisms of this is critical to addressing methamphetamine use as a public health issue. Hormones may play a role in methamphetamine sensitivity; thus, the fluctuation of various endogenous peptides during the postpartum experience is of interest. This honors thesis project explored the relation between anxiety-like behavior, as measured by activity in an open field, and conditioned place preference to methamphetamine in female versus male rats. The behavior of postpartum as well as virgin female rats was compared to that of male rats. There was not a significant difference between males and females in conditioned place preference to methamphetamine, yet females showed higher locomotor activity in response to the drug as well as increased anxiety-like behavior in open field testing as compared to males. Further study is vital to comprehending the complex mechanisms of sex differences in methamphetamine addiction.
ContributorsBaker, Allison Nicole (Author) / Olive, M. Foster (Thesis director) / Presson, Clark (Committee member) / Hansen, Whitney (Committee member) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Two primary contexts for the adaptive evolution of bright coloration are competition for mates (i.e. mate choice) and avoiding predator attacks (i.e. warning coloration). Bright animal coloration can be iridescent, in which the surface appears to change color with changing viewing or illumination angle. Bright animal coloration can also be produced by pigments, which do not appear to change color with changing viewing or illumination angle. The Pipevine Swallowtail, Battus philenor, is unique in having both sexual signals and warning coloration that include iridescent and pigment components, both of which are variable in color. The aim of our study was to examine the role genes play in producing this variation, providing us a sense of potential indirect benefits of female choice. We tested the hypothesis that color variation has a genetic component. We predicted that in a full-sib analysis there should be greater variation in the coloration of the sexual and warning signal among families than within families. We reared B. philenor under standard laboratory conditions and analyzed heritability using a full-sib analysis. We collected reflectance measurements for components of the sexual and warning signal iridescence using a spectrophotometer and used CLR (color analysis software) to extract brightness, hue, and chroma values. We used a multivariate ANOVA (IBM SPSS, v. 21) to analyze the warning signal variation, and a generalized linear mixed model (IBM SPSS, v. 21) to analyze the sexual versus warning signal variation in males. A significance value of 0.05 was used for both analyses. Our results indicated a genetic component to coloration, implicating indirect benefits in B. philenor female mate bias. Further research on bright coloration in B. philenor indicates that there may also be direct benefits of female mate choice.
ContributorsOlzer, Rachel Maureen (Co-author) / Raymundo, Andrew (Co-author) / Pegram, Kimberly (Co-author) / Rutowski, Ronald (Co-author, Thesis director) / Pratt, Stephen (Committee member) / Papaj, Daniel (Committee member) / Barrett, The Honors College (Contributor) / School of Social Transformation (Contributor) / School of Social Sciences (Contributor)
Created2014-12
Description
Environmental and genetic factors contribute to schizophrenia etiology, yet few studies have demonstrated how environmental stimuli impact genes associated with the disorder. Immediate early genes (IEGs) are of great interest to schizophrenia research because they are activated in response to physiological stress from the environment, and subsequently regulate the expression of downstream genes that are essential to neuropsychiatric function. An IEG, early growth response 3 (EGR3) has been identified as a main gene involved in a network of transcription factors implicated in schizophrenia susceptibility. The serotonin 2A receptor (5-HT2AR) seems to play an important role in schizophrenia and the dysfunction of the 5-HT2AR encoding gene, HTR2A, within the prefrontal cortex (PFC) contributes to multiple psychiatric illnesses including schizophrenia. EGR3's role as a transcription factor that is activated by environmental stimuli suggests it may regulate Htr2a transcription in response to physiological stress, thus affecting 5-HT2AR function in the prefrontal cortex (PFC). The aim of this study was to examine the relationship between Egr3 activation and Htr2a expression after an environmental stimulus. Sleep deprivation is an acute physiological stressor that activates Egr3. Therefore to examine the relationship between Egr3 and Htr2a expression after an acute stress, wild type and Egr3 knockout mice that express EGFP under the control of the Htr2a promoter were sleep deprived for 8 hours. We used immunohistochemistry to determine the location and density of Htr2a-EGFP expression after sleep deprivation and found that Htr2a-EGFP expression was not affected by sex or subregions of the PFC. Additionally, Htr2a-EGFP expression was not affected by the loss of Egr3 or sleep deprivation within the PFC. The LPFC subregions, layers V and VI showed significantly more Htr2a-EGFP expression than layers I-III in all animals for both sleep deprivation and control conditions. Possible explanations for the lack of significant effects in this study may be the limited sample size or possible biological abnormalities in the Htr2a-EGFP mice. Nonetheless, we did successfully visualize the anatomical distribution of Htr2a in the prefrontal cortex via immunohistochemical staining. This study and future studies will provide insight into how Egr3 activation affects Htr2a expression in the PFC and how physiological stress from the environment can alter candidate schizophrenia gene function.
ContributorsSabatino, Alissa Marie (Author) / Gallitano, Amelia (Thesis director) / Hruschka, Daniel (Thesis director) / Maple, Amanda (Committee member) / Barrett, The Honors College (Contributor)
Created2014-05
Description
Epilepsy affects numerous people around the world and is characterized by recurring seizures, prompting the ability to predict them so precautionary measures may be employed. One promising algorithm extracts spatiotemporal correlation based features from intracranial electroencephalography signals for use with support vector machines. The robustness of this methodology is tested through a sensitivity analysis. Doing so also provides insight about how to construct more effective feature vectors.
ContributorsMa, Owen (Author) / Bliss, Daniel (Thesis director) / Berisha, Visar (Committee member) / Barrett, The Honors College (Contributor) / Electrical Engineering Program (Contributor)
Created2015-05
Description
Mammals with a habitually orthograde trunk posture possess a more anterior foramen magnum than mammals with non-orthograde trunk postures. Russo & Kirk (2013) also found that bipedal orthograde mammals possess a more anteriorly placed foramen magnum than those that are just habitually orthograde. This finding has allowed us to use foramen magnum position as a predictor of trunk posture in early hominins. This prompts more research of how the other landmarks on the cranial base move in relation to this shift in foramen magnum positioning. I collected landmark data on images of 125 mammalian basicrania spanning 41 species that differed in trunk posture. Using Procrustes and Principal Components Analysis (PCA), I attempted to evaluate the effects of trunk posture on basicranial morphology, primarily focusing on the placement of the carotid and jugular foramina. The results supported Russo and Kirk's finding of a more anterior foramen magnum placement in orthograde mammals; in addition, the results displayed correlations between foramen magnum position and carotid foramen position among primates and diprotodonts.
ContributorsPena, Angela (Author) / Kimbel, William (Thesis director) / Schwartz, Gary T. (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2015-05
Description
Scientists, lawyers, and bioethicists have pondered the impact of scientifically deterministic evidence on a judge or jury when deciding the sentence of a criminal. Though the impact may be one that relieves the amount of personal guilt on the part of the criminal, this evidence may also be the very reason that a judge or jury punishes more strongly, suggesting that this type of evidence may be a double-edged sword. 118 participants were shown three films of fictional sentencing hearings. All three films introduced scientifically deterministic evidence, and participants were asked to recommend a prison sentence. Each hearing portrayed a different criminal with different neurological conditions, a different crime, and a different extent of argumentation during closing arguments about the scientifically deterministic evidence. Though the argumentation from the prosecution and the defense did not affect sentencing, the interaction of type of crime and neurological condition did.
ContributorsMeschkow, Alisha Sadie (Author) / Schweitzer, Nicholas (Thesis director) / Robert, Jason (Committee member) / Patten, K. Jakob (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor)
Created2014-05
Description
An introduction to neuroscientific thought aimed at an audience that is not educated in biology. Meant to be readable and easily understood by anyone with a high school education. The first section is completed in its entirety, with outlines for the proposed final sections to be completed over the next few years.
ContributorsNelson, Nicholas Alan (Author) / Olive, M. Foster (Thesis director) / Brewer, Gene (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor) / School of Life Sciences (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2014-05