Alumni Dissertations

 

Alumni Dissertations

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  • Adaptive Plasticity in the Human Saccade System

    Author:
    James Herman
    Year of Dissertation:
    2012
    Program:
    Biology
    Advisor:
    Jonathan Levitt
    Abstract:

    The rapid point-to-point movements of the eyes called saccades are some of the most commonly made by humans, yet differ from nearly every other type of motor output in that they are completed too quickly to be adjusted during their execution by visual feedback. Yet, saccadic accuracy remains quite high over a lifetime despite inevitable changes to the physical structures controlling the eyes, indicating that the oculomotor system actively monitors and adjusts motor commands to achieve this consistent behavioral production. Indeed, it seems that beyond the ability to compensate for slow, age-related bodily changes, saccades can be modified following traumatic injury or pathology that affects their production, or in response to more short-term systematic alterations to post-saccadic visual feedback in a lab setting. It is, in fact, thought that all of these forms of plasticity rely on the visual detection of accuracy errors by a unified set of mechanisms that support the process known as saccade adaptation. A great deal has been learned about saccade adaptation, as it has been extensively studied as a phenomenon in its own right, as well as being used to explore the process of motor learning in general. However, many fundamental questions about saccade adaptation remain unanswered, often related to the way that saccade adaptation might operate in the natural environment with substantially more complex visual stimuli than are generally used in the lab. Here, we addressed these questions with (in some cases original) variants and more conventional examples of the frequently used intrasaccadic target step (ISS) paradigm (in which an experimenter causes saccadic error by shifting a target during the movement). By exploring the responses to whole-field-ISSs, we have inferred that saccade adaptation might be supported by a trans-saccadic integration mechanism, and may be sensitive to intrasaccadic motion signals. Challenging the oculomotor system by confronting it with multiple post-saccadic targets has revealed that saccade adaptation can occur in a target-identity specific manner, so that even if post-saccadic error varies from trial-to-trial, adaptation seems to reflect the average behavior of the target. At a more basic level, we systematically varied ISSs to determine the lower limits of the oculomotor system's sensitivity to intrasaccadic displacement during adaptation. Also at a more basic level, we looked at the effects of rendering post-saccadic feedback more intermittent during adaptation, finding it to have little effect on the magnitude or rate of adaptive dynamics, similar to other forms of motor learning but somewhat dissimilar from operant conditioning. These experiments also furnished a useful setting to develop and test a novel model of saccade adaptation which more explicitly relies on post-saccadic sensory prediction than previous models, but that is nonetheless in keeping with the ethos of modern motor learning theory. Finally, we found that the establishment and maintenance of a context for saccadic performance by adaptation could be achieved by consistently pairing a target's visual-identity with a specific ISS, extending what had been previously recognized as constituting a cue for contextual motor learning. In general, our results suggest that saccade adaptation is a highly flexible mechanism that not only supports the maintenance of accuracy, but also makes use of a wide range of brain functions to deftly tailor saccadic behavior contingent on task demands.

  • Systematics of Lecythidoideae (Lecythidaceae) with emphasis on Bertholletia, Corythophora, Eschweilera, and Lecythis

    Author:
    Ya-Yi Huang
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Scott Mori
    Abstract:

    Phylogenetic analyses based on morphological and DNA sequence data were generated to test the monophyly of Eschweilera and Lecythis and to investigate the relationships of these two genera and their close relatives (Bertholletia and Corythophora). The final results were applied to questions of taxonomic rearrangements and character evolution in traits related to pollination. A cladistic analysis based on morphology indicates that Bertholletia, Corythophora, Eschweilera, and Lecythis form a clade (the Bertholletia clade), but the resolution within the clade is too poor to elucidate the phylogenetic relationships among the genera. Nonetheless, the data support the monophyly of Corythophora. Eschweilera is divided into two clades: Eschweilera section Tetrapetala and Eschweilera s.s. Whether or not the two clades form a clade remains as unresolved. Lecythis is not resolved as monophyletic, but each of the Sections Corrugata, Pisonis, and Poiteaui is monophyletic. A combined analysis based on morphology and nuclear ITS and plastid ndhF, trnL-F, and trnH-psbA sequence data was conducted to improve the resolution of the phylogenetic tree. The results support the generic circumscriptions of Bertholletia and Corythophora based on morphology, but suggest the revision of Eschweilera and Lecythis. Eschweilera is paraphyletic and divided into three clades: the Eschweilera section Tetrapetala clade, the Eschweilera andina clade, and the core Eschweilera clade. Lecythis is polyphyletic and consists of five clades: the Lecythis s.s. clade, the Pachylecythis clade, the Lecythis chartacea clade, the Holopyxidium clade, and the Section Corrugata clade. Based on the results of these analyses, Section Tetrapetala clade merits recognition as an independent genus and should be segregated from Eschweilera. On the other hand, the five clades of Lecythis are distinct from each other and should be recognized as five separate genera. Androecial evolution inferred from the resulting phylogeny demonstrates that features such as floral zygomorphy, closed androecia, coiled ligules, and the production of nectar are homoplasious. Evolution of these characters most likely is because of the adaptation in response to pollinator shift and does not simply represent a process of morphological transformation from a simpler to a more complicated structure as previously suggested.

  • The Sustainable Management and Conservation Santalum yasi (Sandalwood) in Fiji and Tonga: A Combined Ecological and Genetic Approach

    Author:
    Ryan Huish
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Michael Balick
    Abstract:

    Valued internationally for the aromatic oil found within its heartwood, Sandalwood (Santalum, Santalaceae) is one of the most heavily exploited groups of plants across its range. While historically, most oil has been harvested from Santalum album in Southeast Asia and India, the decrease of S. album sources has caused a widening gap between supply and demand, which creates profitable market opportunities and increasing harvest pressure for alternative sandalwood oil sources. Santalum yasi, a quality alternative, has been harvested extensively in Fiji and Tonga, yet is vastly under-studied. The absence of basic data on population dynamics and genetic variation for remnant populations remains a major constraint to the sustainable management of this culturally and economically valued resource. This dissertation focuses on the ecological and genetic data and analyses that can aid in developing sustainable management strategies. Population size-class structure data was collected using transects in the three densest natural populations of Santalum yasi. Population dynamics, current species distribution, and ecological threats were investigated to find that the few remaining wild stands display discontinuous size class structures, are under regenerative stress and that the natural distribution has diminished significantly, even to local extinction in some areas. Using a nuclear microsatellite analysis, genetic variability within and between populations was investigated. Results suggest that there is no significant genetic variation between populations, but that most of the genetic variation lies within populations. This genetic distribution suggests that there is a significant level of gene flow between and among populations, most likely through human induced dispersal, showing a more panmictic trend than previously supposed. This may provide molecular evidence confirming the Western documentation and traditional oral history of extensive interaction between Fiji and Tonga and their trade of plants and culture. Based on these dwindling levels of yasi population size and unstructured genetic variation in Fiji and Tonga, further enumerations and resource surveys are not practical to conduct at this time. Rather, forestry and governmental efforts should be focused on promotion of local involvement in assisted natural regeneration of wild stands and preservation of genetic variation through in situ, community-mediated conservation.

  • The Sustainable Management and Conservation Santalum yasi (Sandalwood) in Fiji and Tonga: A Combined Ecological and Genetic Approach

    Author:
    Ryan Huish
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Michael Balick
    Abstract:

    Valued internationally for the aromatic oil found within its heartwood, Sandalwood (Santalum, Santalaceae) is one of the most heavily exploited groups of plants across its range. While historically, most oil has been harvested from Santalum album in Southeast Asia and India, the decrease of S. album sources has caused a widening gap between supply and demand, which creates profitable market opportunities and increasing harvest pressure for alternative sandalwood oil sources. Santalum yasi, a quality alternative, has been harvested extensively in Fiji and Tonga, yet is vastly under-studied. The absence of basic data on population dynamics and genetic variation for remnant populations remains a major constraint to the sustainable management of this culturally and economically valued resource. This dissertation focuses on the ecological and genetic data and analyses that can aid in developing sustainable management strategies. Population size-class structure data was collected using transects in the three densest natural populations of Santalum yasi. Population dynamics, current species distribution, and ecological threats were investigated to find that the few remaining wild stands display discontinuous size class structures, are under regenerative stress and that the natural distribution has diminished significantly, even to local extinction in some areas. Using a nuclear microsatellite analysis, genetic variability within and between populations was investigated. Results suggest that there is no significant genetic variation between populations, but that most of the genetic variation lies within populations. This genetic distribution suggests that there is a significant level of gene flow between and among populations, most likely through human induced dispersal, showing a more panmictic trend than previously supposed. This may provide molecular evidence confirming the Western documentation and traditional oral history of extensive interaction between Fiji and Tonga and their trade of plants and culture. Based on these dwindling levels of yasi population size and unstructured genetic variation in Fiji and Tonga, further enumerations and resource surveys are not practical to conduct at this time. Rather, forestry and governmental efforts should be focused on promotion of local involvement in assisted natural regeneration of wild stands and preservation of genetic variation through in situ, community-mediated conservation.

  • THE ROLE OF Na+/H+ EXCHANGER-1 (NHE1) IN MAMMARY BRANCHING MORPHOGENESIS AND MAINTENANCE OF TISSUE ARCHITECTURE

    Author:
    Edmund Jenkins
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Jimmie Fata
    Abstract:

    Branching morphogenesis in vivo is a highly ordered process that necessitates spatially and temporally choreographed cues by growth factors and hormones, as well as mechanical and signal feedback from the extracellular matrix. Successful completion of this developmental process results in the architectural, and thereby the functional, basis for the lung, collecting ducts of the kidney, salivary, and mammary glands. The quest to understand the basic biological mechanisms underlying this developmental morphogenesis has lead to many seminal findings in the field of epithelial tube generation, as well as provided valuable insight into the pathogenesis of cancer. The primary focus of this thesis was elucidating the role of the Na+/H+ exchanger type 1 (NHE1) in branching morphogenesis of the mouse mammary gland. To accomplish this goal, we used three-dimensional (3D) primary tissue culture of mammary gland pieces (organoids) in a four day organotypic assay of growth factor induced branching morphogenesis. NHE1 is a ubiquitously expressed master regulator of intracellular pH (pHi). We found that blocking the function of this exchanger in the presence of growth factor stimulation led to altered kinase signaling, inhibition of growth factor induced alkalization, sustained proliferation after four days, ectopic expression of keratin 6 (K6), and a dramatic failure to undergo branching morphogenesis. These findings led us to question the role of NHE1 in the maintenance of branched mammary tissue architecture. We, therefore, inhibited NHE1 function on fully branched structures in our assay and found that NHE1 inhibition led to rapid loss (within 24 hours) of branched architecture by a process of branch fusion, with complete loss of the branched morphology after four days. This was not accompanied by cell death or altered proliferation, however, we did record altered intracellular pH (pHi) in the end buds of branched structures that had NHE1 inhibited. NHE1 localization, F-actin organization, and myoepthelial cell location were altered in structures that had undergone a loss of architecture, indicating a loss of tissue organization. Finally, we found that NHE1 inhibition resulted in a decrease in mammary Ecadherin. Having found that NHE1 function is vital for both branching morphogenesis and the maintenance of branched architecture, we considered the role that NHE1 could be playing in the pathology of breast cancer. Both intracellular and extracellular pH is deregulated in cancer. This could be attributed to over activity of NHE1. Additionally, NHE1 is over expressed in many cancers. We used the ER+ breast cancer cell line MCF7 to investigate the therapeutic potential of chemotherapy augmentation by NHE1 inhibition. We found that Cycylophosphamide, a DNA alkylating chemotherapeutic agent known to be more effective in an acidic environment, was roughly 5 times more effective when used along with NHE1 inhibition. These findings indicate that NHE1 is a critical regulator of branching morphogenesis and tissue stability, as well as suggests a potential therapeutic target for the treatment of breast cancer.

  • Origin and development of hematopoietic tumors in sumoylation mutants of Drosophila melanogaster

    Author:
    Marta Kalamarz
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Shubha Govind
    Abstract:

    The larval hematopoietic system of Drosophila melanogaster consists of freely circulating cells, the sessile population, and the hematopoietic organ called the lymph gland. Most hemocytes function as macrophages and play a significant role in innate immunity. Hemocytes also remodel tissues, aiding in development of the organism. Constitutive activation of immune signaling pathways, as well as various mutations in genes which are not linked to immune pathways, result in the overabundance of circulating hemocytes and tumor formation. Many aspects of tumor development, such as the identity of the affected hematopoietic population and mechanisms of tumor growth are either not characterized or not well understood. The overall goal of this project was to understand the origin and development of hematopoietic tumor formation in Ubc9 mutants. Ubc9 is an E2 enzyme, which conjugates SUMO (small ubiquitin-like modifier) to a range of target proteins. Sumoylation targets vary in function from structural components to enzymes and transcription factors. Thus, sumoylation affects multiple cellular functions via modification of protein localization, stability or activity. Loss-of-function Ubc9 mutants of Drosophila exhibit severe defects in hematopoietic and immune tissues, including hemocyte overproliferation and tumor formation during larval stages. In this dissertation, we report that the hemolymph of Ubc9 mutants contains hematopoietic cells and structures that range from aggregates (composed of only few cells) to small and large tumors. The largest tumors are less than 1 mm3 in volume. Most cells and aggregates exhibit high ration of mitotic cells, but only a few of the largest tumors in the hemolymph contain actively dividing cells. Based on staining patterns and genetic rescue experiments, we propose that the large tumors are derived specifically from overgrown posterior lobes of the hematopoietic organ. The origin of smaller tumors and aggregates is less clear. Our data suggest that these structures likely derive from circulating hemocytes and fragments of dispersed anterior lobes. Microtumors in Ubc9 mutants arise from the highly-mitotic mutant stem/progenitor cells of the lymph gland. Loss of sumoylation cascade enzymes E1 (Aos1/Uba2), E2 (Ubc9), or E3 (PIAS) leads to loss of proliferative quiescence in hematopoietic precursors localized within the lymph gland. Proliferative quiescence of these precursors is at least in part mediated by the activity of the cyclin-dependent kinase inhibitor Dacapo/p21. Expression of Dacapo homolog, human p21, in the Ubc9 progenitor cells relieves tumor formation. These studies suggest that sumoylation provides a cell-intrinsic mechanism to preserve stem/progenitor cell states for stress response, immunity and development of the fly.

  • Effects of endophyte infection, environmental stress and competition on Lolium perenne populations from the Mediterranean region

    Author:
    Kristin Kane
    Year of Dissertation:
    2012
    Program:
    Biology
    Advisor:
    Gregory Cheplick
    Abstract:

    No

  • The role of ubiquitin-mediated proteolysis in Drosophila glia development

    Author:
    Margarita Kaplow
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Tadmiri Venkatesh
    Abstract:

    Biological processes are dynamic, requiring both simple and complex mechanisms that enable cells to adapt with the ever-changing environment. Ubiquitination is one of many posttranslational modifications that result in a change in cellular activity. Mono-ubiquitination, the addition of a single ubiquitin moeity leads to endocytosis and membrane trafficking, while the addition of a multiple ubiquitin chains primarily results in protein degradation. Rap/Fzr acts as an activator of the E3 ubiquitin ligase, Anaphase Promoting Complex (APC) which has been studied for its role in the timely degradation of cell cycle regulators. My thesis work focuses on novel roles Rap/Fzr during nervous system development and specifically investigates its role during glia development. My results show that Rap/Fzr regulates glia development through its interaction with Loco, an RGS protein and Nonstop, a ubiquitin specific protease. Bioinformatic analysis revealed that both Loco and Nonstop contain Destruction box (D-box) motifs and KEN box motifs, which are amino acid sequences used by Rap/Fzr for substrate recognition. My thesis work shows that Rap/Fzr targets Loco for ubiquitination, and subsequent degradation and thus, inhibits the formation of glia from dividing neuroblasts. Furthermore, Rap/Fzr together with Nonstop, regulates the migration and the endoreplication of glia cells.

  • Effects of bisphenol-A on oxidative stress, mitochondrial dysfunction and behavior: lymphoblasts and Drosophila melanogaster studies - Potential implications in autism

    Author:
    Kulbir Kaur
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Abha Chauhan
    Abstract:

    Autism is a behaviorally defined neurodevelopmental disorder characterized by impairments in three main areas of social interaction, communication, and repetitive, restricted interests and behaviors. There has been an increase in the prevalence of autism with recent estimation of 1 in every 50 children diagnosed with autism. Though there is no single identifiable cause for autism, several studies have shown an increase in oxidative stress and decrease in antioxidants in autism. The role of environmental factors has also been implicated in autism. Bisphenol A (BPA) is a widely used chemical in the manufacturing of plastics, and its exposure has raised concerns in a variety of conditions. The present study with lymphoblastoid cells and Drosophila melanogaster identifies BPA as an environmental risk factor for the increased oxidative stress, mitochondrial dysfunction and behavioral impairments in lymphoblasts and Drosophila melanogaster. When lymphoblastoid cells were exposed to BPA, there was an increase in lipid peroxidation and free radicals (reactive oxygen species) and decrease in mitochondrial membrane potential generation suggesting BPA induced oxidative stress and mitochondrial dysfunction. The study also illustrates an increase in the mitochondrial DNA (mtDNA) copy number in the lymphoblasts in response to the BPA exposure. In neurodevelopmental disorders such as autism, behavior is an important component of the condition. We therefore attempted to detect behavioral modifications in Drosophila melanogaster following exposure to BPA. In this study, we used an open field assay to help identify disturbances in locomotion along with repetitive behavior in BPA-exposed flies. We also observed an abnormal social interaction between the BPA-exposed flies in a social setting. Along with the behavioral modifications, there was also an increase in the lipid peroxidation in the brains of the BPA-exposed flies. Furthermore there was also a delay in the development of the Drosophila embryos, although we did not detect any gross morphological changes in the peripheral nervous system of the embryos following BPA exposure. We have therefore demonstrated that Drosophila may be used as an animal model for complex neurodevelopmetal disorders, which have a poorly understood etiology.

  • Effects of The Enzyme Inhibitor Prohexadione-calcium on Hops Determined by LC-TOF-MS

    Author:
    Adam Kavalier
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Edward Kennelly
    Abstract:

    Humulus lupulus L. (hops) is an agricultural crop valued for its inflorescences, commonly known as hop cones, which produce a diverse collection of secondary metabolites. Hop cones are most valued for their terpenophenolic contents, which are essential to beer production, and the subject of biomedical research. We studied two hop cultivars, Willamette and Zeus, over five stages of development, which were characterized by detailed flower morphology, gross cone measurements, and phytochemical quantitation. By combining morphological observations with phytochemical quantitation we produced an index to inform our developmentally dependent experiments. In order to understand these developmental processes and in an attempt to induce agronomically positive effects, we perturbed hop morphological and phytochemical development using enzyme inhibition. Prohexadione-calcium (Pro-Ca) is a known inhibitor of 2-oxoglutaric acid dependent dioxygenases present in the flavonoid, gibberellic acid, and ethylene biosynthetic pathways. We treated hops with Pro-Ca at each of the five time-points over two seasons; these time-points were later characterized as five developmental stages. Pro-Ca treatment induced significant increases in terpenophenolic content by 9.1-87.3%; however some treatments also induced significant decreases. Increases in cone biomass production by 1.5-19.6% were also measured in response to treatment in both seasons. Induced changes in cone biomass production and terpenophenolic accumulation were most dependent on cultivar and the developmental stage at which plants were treated. In a second series of experiments we conducted a targeted analysis of phenolic acids, flavonoids, and terpenophenolics over 22 days following a single Pro-Ca treatment conducted during early flowering. Terpenophenolics significantly increased following treatment, and coincided with changes in the flavonoid biosynthetic pathway including accumulation of metabolic precursors upstream from flavanone-3-hydroxylase, and decreases in flavonoid products downstream from flavanone-3-hydroxylase. In addition to changes in known compounds, marker analysis revealed the presence of two markers in treated samples not previously reported from hops. One of these markers has been tentatively identified as the antimicrobial compound luteoliflavan. This research provides insight into the relationship between secondary metabolic pathways in hops and indicates targets for future research into perturbation of metabolic pathways to increase medicinal and flavor compounds in hops.