Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
Displaying 11 - 20 of 36
Description
The oceans play an essential role in global biogeochemical cycles and in regulating climate. The biological carbon pump, the photosynthetic fixation of carbon dioxide by phytoplankton and subsequent sequestration of organic carbon into deep water, combined with the physical carbon pump, make the oceans the only long-term net sink for anthropogenic carbon dioxide. A full understanding of the workings of the biological carbon pump requires a knowledge of the role of different taxonomic groups of phytoplankton (protists and cyanobacteria) to organic carbon export. However, this has been difficult due to the degraded nature of particles sinking into particle traps, the main tools employed by oceanographers to collect sinking particulate matter in the ocean. In this study DNA-based molecular methods, including denaturing gradient gel electrophoresis, cloning and sequencing, and taxon-specific quantitative PCR, allowed for the first time for the identification of which protists and cyanobacteria contributed to the material collected by the traps in relation to their presence in the euphotic zone. I conducted this study at two time-series stations in the subtropical North Atlantic Ocean, one north of the Canary Islands, and one located south of Bermuda. The Bermuda study allowed me to investigate seasonal and interannual changes in the contribution of the plankton community to particle flux. I could also show that small unarmored taxa, including representatives of prasinophytes and cyanobacteria, constituted a significant fraction of sequences recovered from sediment trap material. Prasinophyte sequences alone could account for up to 13% of the clone library sequences of trap material during bloom periods. These observations contradict a long-standing paradigm in biological oceanography that only large taxa with mineral shells are capable of sinking while smaller, unarmored cells are recycled in the euphotic zone through the microbial loop. Climate change and a subsequent warming of the surface ocean may lead to a shift in the protist community toward smaller cell size in the future, but in light of these findings these changes may not necessarily lead to a reduction in the strength of the biological carbon pump.
ContributorsAmacher, Jessica (Author) / Neuer, Susanne (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Lomas, Michael (Committee member) / Wojciechowski, Martin (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011
Description
Intrinsic antibiotic resistance is of growing concern in modern medical treatment. The primary action of multidrug resistant strains is through over-expression of active transporters which recognize a broad range of antibiotics. In Escherichia coli, the TolC-AcrAB complex has become a model system to understand antibiotic efflux. While the structures of these three proteins (and many of their homologs) are known, the exact mechanisms of interaction are still poorly understood. By mutational analysis of the TolC turn 1 residues, a drug hypersensitive mutant has been identified which is defective in functional interactions with AcrA and AcrB. Antibiotic resistant revertants carry alterations in both TolC and AcrA act by stabilizing functional complex assembly and opening of the TolC aperture, as monitored by stability of a labile TolC mutant and sensitivity to vancomycin, respectively. Alterations in the AcrB periplasmic hairpin loops lead to a similar antibiotic hypersensitivity phenotype and destabilized complex assembly. Likewise, alterations in TolC which constitutively open the aperture suppress this antibiotic sensitivity. Suppressor alterations in AcrA and AcrB partially restore antibiotic resistance by mediating stability of the complex. The AcrA suppressor alterations isolated in these studies map to the three crystallized domains and it is concluded they alter the AcrA conformation such that it is permanently fixed in an active state, which wild type only transiently goes through when activated by AcrB. Through this genetic evidence, a direct interaction between TolC and AcrB which is stabilized by AcrA has been proposed. In addition to stabilizing the interactions between TolC and AcrB, AcrA is also responsible for triggering opening of the TolC aperture by mediating energy flow from AcrB to TolC. By permanently altering the conformation of AcrA, suppressor mutants allow defective TolC or AcrB mutants to regain functional interactions lost by the initial mutations. The data provide the genetic proof for direct interaction between AcrB and that AcrA mediated opening of TolC requires AcrB as a scaffold.
ContributorsWeeks, Jon William (Author) / Misra, Rajeev (Thesis advisor) / Stout, Valerie (Committee member) / Shi, Yixin (Committee member) / Clark-Curtiss, Josephine (Committee member) / Arizona State University (Publisher)
Created2012
Description
Plants are a promising upcoming platform for production of vaccine components and other desirable pharmaceutical proteins that can only, at present, be made in living systems. The unique soil microbe Agrobacterium tumefaciens can transfer DNA to plants very efficiently, essentially turning plants into factories capable of producing virtually any gene. While genetically modified bacteria have historically been used for producing useful biopharmaceuticals like human insulin, plants can assemble much more complicated proteins, like human antibodies, that bacterial systems cannot. As plants do not harbor human pathogens, they are also safer alternatives than animal cell cultures. Additionally, plants can be grown very cheaply, in massive quantities.
In my research, I have studied the genetic mechanisms that underlie gene expression, in order to improve plant-based biopharmaceutical production. To do this, inspiration was drawn from naturally-occurring gene regulatory mechanisms, especially those from plant viruses, which have evolved mechanisms to co-opt the plant cellular machinery to produce high levels of viral proteins. By testing, modifying, and combining genetic elements from diverse sources, an optimized expression system has been developed that allows very rapid production of vaccine components, monoclonal antibodies, and other biopharmaceuticals. To improve target gene expression while maintaining the health and function of the plants, I identified, studied, and modified 5’ untranslated regions, combined gene terminators, and a nuclear matrix attachment region. The replication mechanisms of a plant geminivirus were also studied, which lead to additional strategies to produce more toxic biopharmaceutical proteins. Finally, the mechanisms employed by a geminivirus to spread between cells were investigated. It was demonstrated that these movement mechanisms can be functionally transplanted into a separate genus of geminivirus, allowing modified virus-based gene expression vectors to be spread between neighboring plant cells. Additionally, my work helps shed light on the basic genetic mechanisms employed by all living organisms to control gene expression.
In my research, I have studied the genetic mechanisms that underlie gene expression, in order to improve plant-based biopharmaceutical production. To do this, inspiration was drawn from naturally-occurring gene regulatory mechanisms, especially those from plant viruses, which have evolved mechanisms to co-opt the plant cellular machinery to produce high levels of viral proteins. By testing, modifying, and combining genetic elements from diverse sources, an optimized expression system has been developed that allows very rapid production of vaccine components, monoclonal antibodies, and other biopharmaceuticals. To improve target gene expression while maintaining the health and function of the plants, I identified, studied, and modified 5’ untranslated regions, combined gene terminators, and a nuclear matrix attachment region. The replication mechanisms of a plant geminivirus were also studied, which lead to additional strategies to produce more toxic biopharmaceutical proteins. Finally, the mechanisms employed by a geminivirus to spread between cells were investigated. It was demonstrated that these movement mechanisms can be functionally transplanted into a separate genus of geminivirus, allowing modified virus-based gene expression vectors to be spread between neighboring plant cells. Additionally, my work helps shed light on the basic genetic mechanisms employed by all living organisms to control gene expression.
ContributorsDiamos, Andy (Author) / Mason, Hugh S (Thesis advisor) / Mor, Tsafrir (Committee member) / Hogue, Brenda (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2017
Description
Guided by Tinto’s Theory of College Student Departure, I conducted a set of five studies to identify factors that influence students’ social integration in college science active learning classes. These studies were conducted in large-enrollment college science courses and some were specifically conducted in undergraduate active learning biology courses. Using qualitative and quantitative methodologies, I identified how students’ identities, such as their gender and LGBTQIA identity, and students’ perceptions of their own intelligence influence their experience in active learning science classes and consequently their social integration in college. I also determined factors of active learning classrooms and instructor behaviors that can affect whether students experience positive or negative social integration in the context of active learning. I found that students’ hidden identities, such as the LGBTQIA identity, are more relevant in active learning classes where students work together and that the increased relevance of one’s identity can have a positive and negative impact on their social integration. I also found that students’ identities can predict their academic self-concept, or their perception of their intelligence as it compares to others’ intelligence in biology, which in turn predicts their participation in small group-discussion. While many students express a fear of negative evaluation, or dread being evaluated negatively by others when speaking out in active learning classes, I identified that how instructors structure group work can cause students to feel more or less integrated into the college science classroom. Lastly, I identified tools that instructors can use, such as name tents and humor, which can positive affect students’ social integration into the college science classroom. In sum, I highlight inequities in students’ experiences in active learning science classrooms and the mechanisms that underlie some of these inequities. I hope this work can be used to create more inclusive undergraduate active learning science courses.
ContributorsCooper, Katelyn M (Author) / Brownell, Sara E (Thesis advisor) / Stout, Valerie (Committee member) / Collins, James (Committee member) / Orchinik, Miles (Committee member) / Zheng, Yi (Committee member) / Arizona State University (Publisher)
Created2018
Description
Biomarkers find a wide variety of applications in oncology from risk assessment to diagnosis and predicting and monitoring recurrence and response to therapy. Developing clinically useful biomarkers for cancer is faced with several challenges, including cancer heterogeneity and factors related to assay development and biomarker performance. Circulating biomarkers offer a rapid, cost-effective, and minimally-invasive window to disease and are ideal for population-based screening. Circulating immune biomarkers are stable, measurable, and can betray the underlying antigen when present below detection levels or even no longer present. This dissertation aims to investigate potential circulating immune biomarkers with applications in cancer detection and novel therapies. Over 600,000 cancers each year are attributed to the human papillomavirus (HPV), including cervical, anogenital and oropharyngeal cancers. A key challenge in understanding HPV immunobiology and developing immune biomarkers is the diversity of HPV types and the need for multiplexed display of HPV antigens. In Project 1, nucleic acid programmable protein arrays displaying the proteomes of 12 HPV types were developed and used for serum immunoprofiling of women with cervical lesions or invasive cervical cancer. These arrays provide a valuable high-throughput tool for measuring the breadth, specificity, heterogeneity, and cross-reactivity of the serologic response to HPV. Project 2 investigates potential biomarkers of immunity to the bacterial CRISPR/Cas9 system that is currently in clinical trials for cancer. Pre-existing B cell and T cell immune responses to Cas9 were detected in humans and Cas9 was modified to eliminate immunodominant epitopes while preserving its function and specificity. This dissertation broadens our understanding of the immunobiology of cervical cancer and provides insights into the immune profiles that could serve as biomarkers of various applications in cancer.
ContributorsEwaisha, Radwa Mohamed Emadeldin Mahmoud (Author) / Anderson, Karen S (Thesis advisor) / LaBaer, Joshua (Committee member) / Lake, Douglas F (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2018
Description
ABSTRACT
Environmental and genetic factors influence schizophrenia risk. Individuals who have direct family members with schizophrenia have a much higher incidence. Also, acute stress or life crisis may precede the onset of the disease. This study aims to understand the effects of environment on genes related to schizophrenia risk. It investigates the impact of sleep deprivation as an acute environmental stressor on the expression of Htr2a in mice, a gene that codes for the serotonin 2A receptor (5-HT2AR). HTR2A is associated with schizophrenia risk through genetic association studies and expression is decreased in post-mortem studies of patients with the disease. Furthermore, sleep deprivation as a stressor in human trials has been shown to increase the binding capacity of 5-HT2AR. We hypothesize that sleep deprivation will increase the number of cells expressing Htr2a in the mouse anterior prefrontal cortex when compared to controls. Sleep deprived that mice express EGFP under control of the Htr2a promoter displayed anteroposterior gradients of expression across sagittal sections, with concentrations seen most densely within the prefrontal cortex as well as the anterior pretectal nucleus, thalamic nucleus, as well as the cingulate gyrus. Htr2a-EGFP expression was most densely visualized in cortical layer V and VI pyramidal neurons within the lateral prefrontal cortex of coronal sections. Furthermore, the medial prefrontal cortex contained significantly cells expressing Htr2a¬-EGFP than the lateral prefrontal cortex. Ultimately, the hypothesis was not supported and sleep deprivation did not result in more ¬Htr2a-EGFP expressing cells compared to basal levels. However, expressing cells appeared visibly brighter in sleep-deprived animals when compared to controls, indicating that the amount of intracellular Htr2a-GFP expression may be higher. This study provides strong visual representations of expression gradients following sleep deprivation as an acute stressor and paves the way for future studies regarding 5H-T2AR’s role in schizophrenia.
Environmental and genetic factors influence schizophrenia risk. Individuals who have direct family members with schizophrenia have a much higher incidence. Also, acute stress or life crisis may precede the onset of the disease. This study aims to understand the effects of environment on genes related to schizophrenia risk. It investigates the impact of sleep deprivation as an acute environmental stressor on the expression of Htr2a in mice, a gene that codes for the serotonin 2A receptor (5-HT2AR). HTR2A is associated with schizophrenia risk through genetic association studies and expression is decreased in post-mortem studies of patients with the disease. Furthermore, sleep deprivation as a stressor in human trials has been shown to increase the binding capacity of 5-HT2AR. We hypothesize that sleep deprivation will increase the number of cells expressing Htr2a in the mouse anterior prefrontal cortex when compared to controls. Sleep deprived that mice express EGFP under control of the Htr2a promoter displayed anteroposterior gradients of expression across sagittal sections, with concentrations seen most densely within the prefrontal cortex as well as the anterior pretectal nucleus, thalamic nucleus, as well as the cingulate gyrus. Htr2a-EGFP expression was most densely visualized in cortical layer V and VI pyramidal neurons within the lateral prefrontal cortex of coronal sections. Furthermore, the medial prefrontal cortex contained significantly cells expressing Htr2a¬-EGFP than the lateral prefrontal cortex. Ultimately, the hypothesis was not supported and sleep deprivation did not result in more ¬Htr2a-EGFP expressing cells compared to basal levels. However, expressing cells appeared visibly brighter in sleep-deprived animals when compared to controls, indicating that the amount of intracellular Htr2a-GFP expression may be higher. This study provides strong visual representations of expression gradients following sleep deprivation as an acute stressor and paves the way for future studies regarding 5H-T2AR’s role in schizophrenia.
ContributorsSchmitz, Kirk Andrew (Author) / Gallitano, Amelia (Thesis director) / Stout, Valerie (Committee member) / Maple, Amanda (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
ABSTRACT Telomeres are vital in protecting chromosome ends to prevent telomere shortening. Telomerase is a ribonucleoprotein responsible for adding telomere repeats and maintaining telomere length. Telomerase holoenzyme consists of 2 major subcomponents: telomerase reverse transcriptase (TERT) and telomerase RNA (TR). The catalytic subunit is TERT and the subunit that adds deoxyribonucleotide to the ends of chromosome is TR. TR contains an alignment portion and a template portion. Japanese Medaka (Oryzias latipes) has 4 nucleotide bases in its alignment region, which is similar to the 5-nucleotide bases in the human telomerase RNA alignment region. Because of the similar alignment region length, Japanese Medaka with 24 chromosomes was chosen to be used in this study. The question in this research was whether we could overcome heterogeneity. It was expected that when breeding short mean telomere length fish with another short mean telomere length fish, the new generation would have homogeneity. If short average telomere length fish and long average telomere length fish were to breed, the next generation fish would have heterogeneity in their average telomere length. In order to make a strong result statement further research needs to be done. The results from this study have somewhat supported the hypothesis, but will need additional information for a stronger validation. There were two inbreedings of short mean telomere length fish with another short telomere length; however, only one of the inbreeding pairs produced a fish with homogeneity (and supported the hypothesis). The other inbreeding pair depicted a large smear, a sign of heterogeneity. This may be due to a mutation in the subtelomeric portion. The method used to measure average telomere length was the terminal restriction fragment assay. Future research will involve using a different technique, quantitative fluorescence in sifu hybridizatrort to measure a more accurate telomere length of each chromosome.
ContributorsYee, Stephanie (Author) / Chen, Julian (Thesis director) / Stout, Valerie (Committee member) / Qi, Xiaodong (Committee member) / Barrett, The Honors College (Contributor)
Created2012-05
Description
Methane (CH4) is very important in the environment as it is a greenhouse gas and important for the degradation of organic matter. During the last 200 years the atmospheric concentration of CH4 has tripled. Methanogens are methane-producing microbes from the Archaea domain that complete the final step in breaking down organic matter to generate methane through a process called methanogenesis. They contribute to about 74% of the CH4 present on the Earth's atmosphere, producing 1 billion tons of methane annually. The purpose of this work is to generate a preliminary metabolic reconstruction model of two methanogens: Methanoregula boonei 6A8 and Methanosphaerula palustris E1-9c. M. boonei and M. palustris are part of the Methanomicrobiales order and perform hydrogenotrophic methanogenesis, which means that they reduce CO2 to CH4 by using H2 as their major electron donor. Metabolic models are frameworks for understanding a cell as a system and they provide the means to assess the changes in gene regulation in response in various environmental and physiological constraints. The Pathway-Tools software v16 was used to generate these draft models. The models were manually curated using literature searches, the KEGG database and homology methods with the Methanosarcina acetivorans strain, the closest methanogen strain with a nearly complete metabolic reconstruction. These preliminary models attempt to complete the pathways required for amino acid biosynthesis, methanogenesis, and major cofactors related to methanogenesis. The M. boonei reconstruction currently includes 99 pathways and has 82% of its reactions completed, while the M. palustris reconstruction includes 102 pathways and has 89% of its reactions completed.
ContributorsMahendra, Divya (Author) / Cadillo-Quiroz, Hinsby (Thesis director) / Wang, Xuan (Committee member) / Stout, Valerie (Committee member) / Barrett, The Honors College (Contributor) / Computing and Informatics Program (Contributor) / School of Life Sciences (Contributor) / Biomedical Informatics Program (Contributor)
Created2014-05
Description
Course-Based Undergraduate Research Experiences, or CUREs have become an increasingly popular way to integrate research opportunities into the undergraduate biology curriculum. Unlike traditional cookbook labs which provide students with a set experimental design and known outcome, CUREs offer students the opportunity to participate in novel and interesting research that is of interest to the greater biology community. While CUREs have been championed as a way to provide more students with the opportunity to experience, it is unclear whether students benefit differently from participating in different CURE with different structural elements. In this study we focused in on one proposed element of a CURE, collaboration, to determine whether student's perception of this concept change over the course of a CURE and whether it differs among students enrolled in different CUREs. We analyzed pre and post open-ended surveys asking the question "Why might collaboration be important in science?" in two CUREs with different structures of collaboration. We also compared CURE student responses to the responses of senior honors thesis students who had been conducting authentic research. Five themes emerged in response to students' conceptions of collaboration. Comparing two CURE courses, we found that students' conceptions of collaboration were varied within each individual CURE, as well as what students were leaving with compared to the other CURE course. Looking at how student responses compared between 5 different themes, including "Different Perspectives", "Validate/Verify Results", "Compare Results", "Requires Different Expertise", and "Compare results", students appeared to be thinking about collaboration in distinct different ways by lack of continuity in the amount of students discussing each of these among the classes. In addition, we found that student responses in each of the CURE courses were not significantly different for any of the themes except "Different Expertise" compared to the graduating seniors. However, due to the small (n) that the graduating seniors group had, 22, compared to each of the CURE classes composing of 155 and 98 students, this comparison must be taken in a preliminary manner. Overall, students thought differently about collaboration between different CUREs. Still, a gap filling what it means to "collaborate", and whether the structures of CUREs are effective to portray collaboration are still necessary to fully elaborate on this paper's findings.
ContributorsWassef, Cyril Alexander (Author) / Brownell, Sara (Thesis director) / Stout, Valerie (Committee member) / Cooper, Katelyn (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Learning student names has been promoted as an inclusive classroom practice, but it is unknown whether students value having their names known by an instructor. We explored this question in the context of a high-enrollment active-learning undergraduate biology course. Using surveys and semistructured interviews, we investigated whether students perceived that instructors know their names, the importance of instructors knowing their names, and how instructors learned their names. We found that, while only 20% of students perceived their names were known in previous high-enrollment biology classes, 78% of students perceived that an instructor of this course knew their names. However, instructors only knew 53% of names, indicating that instructors do not have to know student names in order for students to perceive that their names are known. Using grounded theory, we identified nine reasons why students feel that having their names known is important. When we asked students how they perceived instructors learned their names, the most common response was instructor use of name tents during in-class discussion. These findings suggest that students can benefit from perceiving that instructors know their names and name tents could be a relatively easy way for students to think that instructors know their names. Academic self-concept is one's perception of his or her ability in an academic domain compared to other students. As college biology classrooms transition from lecturing to active learning, students interact more with each other and are likely comparing themselves more to students in the class. Student characteristics, such as gender and race/ethnicity, can impact the level of academic self-concept, however this has been unexplored in the context of undergraduate biology. In this study, we explored whether student characteristics can affect academic self-concept in the context of a college physiology course. Using a survey, students self-reported how smart they perceived themselves in the context of physiology compared to the whole class and compared to the student they worked most closely with in class. Using logistic regression, we found that males and native English speakers had significantly higher academic self-concept compared to the whole class compared with females and non-native English speakers, respectively. We also found that males and non-transfer students had significantly higher academic self-concept compared to the student they worked most closely with in class compared with females and transfer students, respectively. Using grounded theory, we identified ten distinct factors that influenced how students determined whether they are more or less smart than their groupmate. Finally, we found that students were more likely to report participating less than their groupmate if they had a lower academic self-concept. These findings suggest that student characteristics can influence students' academic self-concept, which in turn may influence their participation in small group discussion.
ContributorsKrieg, Anna Florence (Author) / Brownell, Sara (Thesis director) / Stout, Valerie (Committee member) / Cooper, Katelyn (Committee member) / School of Life Sciences (Contributor) / School of Politics and Global Studies (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05