Theses and Dissertations from UMD
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New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a give thesis/dissertation in DRUM
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Item Characterizing the hypothalamic-pituitary-gonadal axis in turkeys genetically selected for increased egg production(2020) Galleher, Catherine Elizabeth; Porter, Tom E; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Within the United States, the turkey industry has historically focused on increased meat production. Studies have shown that there is a negative correlation between meat and egg production. Previous research in our laboratory compared high egg producing hens (HEPH) to low egg producing hens (LEPH). It was found that HEPH express increased levels of mRNA for genes associated with stimulating the hypothalamic-pituitary-gonadal (HPG) axis. We also demonstrated that the hypothalamic-pituitary-thyroid (HPT) axis exerts some effect on egg production. In order to increase our understanding of differences in egg production, we focused on a genetically selected line with increased egg production (E line) and a random bred control line (RBC1). Related to the HPG axis, differences were found related to steroidogenesis and feedback mechanisms. Within the HPT axis, the RBC1 line tended to have increased mRNA levels of genes associated with stimulation of the axis compared to E line.Item REDUCED CAMPYLOBACTER INFECTION AND ENHANCED PERFORMANCE IN POULTRY WITH BIOACTIVE PHENOLICS THROUGH EPIGENETIC MODULATION OF THE GUT MICROBIOME(2017) Salaheen, Serajus; Biswas, Debabrata; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Campylobacter jejuni, a major enteric pathogen and a natural resident in the poultry gut, causes gastrointestinal illness followed by severe post-infection complications, including Guillain-Barré syndrome, reactive arthritis, myocarditis, and ulcerative colitis in humans. Risk assessment studies have projected a 30-fold reduction in human campylobacteriosis cases with only a 100-fold reduction in the number of C. jejuni colonizing the poultry gut. Current commercial poultry production practices involve use of antibiotic growth promoters (AGP); modulation of gut microbiota with AGPs for food safety and enhanced performance in poultry can be justified until acquisition of antibiotic resistance in zoonoses through inter-bacterial transfer of antibiotic resistance genes (ARGs) in a complex microbial community is considered. As an alternative, natural phenolics extracted from by-products of berry juice industry, with antimicrobial, anti-inflammatory, anticarcinogenic, antioxidant and vasodilatory activities, demonstrate promising prospects. In this study, we adopted mass-spectrometry, microbiological, phylogenetic, and metagenomic approaches to evaluate bioactive phenolic extracts (BPE) from blueberry (Vaccinium corymbosum) and blackberry (Rubus fruticosus) pomaces as AGP alternative. We detected that major phenolics in BPE included, but were not limited to, apigenin, catechol, chlorogenic acid, cinnamic acid, coumarin, ellagic acid, eugenols, flavan, gallic acid, gingerol, glucosides, glucuronides, myricetin, phenols, quercetin, quinones, rhamnosides, stilbenol, tannins, triamcinolone, and xanthine. BPE reduced C. jejuni growth and motility in vitro, resulting in lower adherence and invasiveness to chicken fibroblast cells. Anti-inflammatory effects of BPE significantly reduced the expression of pro-inflammatory cytokine genes in chick macrophage cell line ex vivo. Furthermore, BPE reduced the colonization of C. jejuni in broiler cecum by 1 to 5 logs while increasing broiler weight by 6% compared to 9.5% with commercial AGPs. Metagenomic analysis of broiler gut indicated that BPE caused an AGP-like pattern in bacterial communities with a comparative increase of Firmicutes and a concomitant reduction of Bacteroidetes in broiler ceca. AGP supplementation clearly caused phage induction and a richer resistome profile in the cecal microbiome compared to BPE. Functional characterization of cecal microbiomes revealed a significant variation in the abundance of genes involved in energy and carbohydrate metabolism. Our findings established a baseline upon which mechanisms of plant based antimicrobial performance-enhancers in regulation of animal growth can be investigated.Item Echolocation, high frequency hearing, and gene expression in the inner ear of bats(2017) Mao, Beatrice; Wilkinson, Gerald S; Moss, Cynthia F; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Bats are the only mammals capable of true flight, and are the second-most speciose mammalian radiation, represented by over 1200 extant species. Key to their evolutionary success was echolocation, which is a complex trait requiring specializations for vocalization, hearing, and echo processing. Because they rely on detecting and analyzing echoes that may return greatly attenuated relative to their outgoing calls, interference from non-target ‘clutter’ echoes poses a challenge for echolocating bats. Here, I demonstrate that the echolocating bat Eptesicus fuscus alters its echolocation behavior to ameliorate the impact of clutter echoes when tracking a moving target, and that the magnitude of its behavioral adjustments depended on the distance and angular offset of two symmetrically placed ‘distracter’ objects. Furthermore, I found that individual bats make different adjustments to their calls, call timing, or head movements, suggesting that multiple strategies for echolocating in clutter may exist. In my second chapter, I examined the expression patterns of hearing-related genes in juvenile bats. Biomedical research establishing the functional roles of hearing genes rarely examines gene expression beyond the early post-natal stage, even though high frequency hearing does not mature until late in development. I show that several key hearing genes implicated in human deafness are upregulated in juvenile bats relative to adults, or exhibit sustained upregulation through the developmental period corresponding to the maturation of echolocation behavior. In my third chapter, I review the evolution of high frequency hearing in mammals, focusing on echolocating bats and whales, which have independently evolved this complex trait. I provide an overview of recent studies that have reported molecular convergence in hearing genes among distantly related echolocators, and assert that the contribution of gene expression to hearing deserves further investigation. Finally, I argue that echolocators provide a unique opportunity to investigate the basis of high frequency amplification, and may possess mechanisms of hearing protection which enable them to prolong the use of echolocation throughout their long lives.Item Epiviz: Integrative Visual Analysis Software for Genomics(2015) Chelaru, Florin; Corrada Bravo, Hector; Computer Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling of a small number of moderately sized datasets. Workflows that involve the integration and exploration of multiple heterogeneous data sources, small and large, public and user specific have been poorly addressed by these tools. Commonly, the data visualized in these tools is the output of analyses performed in powerful computing environments like R/Bioconductor or Python. Two essential aspects of data analysis are usually treated as distinct, in spite of being part of the same exploratory process: algorithmic analysis and interactive visualization. In current technologies these are not integrated within one tool, but rather, one precedes the other. Recent technological advances in web-based data visualization have made it possible for interactive visualization tools to tightly integrate with powerful algorithmic tools, without being restricted to one such tool in particular. We introduce Epiviz (http://epiviz.cbcb.umd.edu), an integrative visualization tool that bridges the gap between the two types of tools, simplifying genomic data analysis workflows. Epiviz is the first genomics interactive visualization tool to provide tight-knit integration with computational and statistical modeling and data analysis. We discuss three ways in which Epiviz advances the field of genomic data analysis: 1) it brings code to interactive visualizations at various different levels; 2) takes the first steps in the direction of collaborative data analysis by incorporating user plugins from source control providers, as well as by allowing analysis states to be shared among the scientific community; 3) combines established analysis features that have never before been available simultaneously in a visualization tool for genomics. Epiviz can be used in multiple branches of genomics data analysis for various types of datasets, of which we detail two: functional genomics data, aligned to a continuous coordinate such as the genome, and metagenomics, organized according to volatile hierarchical coordinate spaces. We also present security implications of the current design, performance benchmarks, a series of limitations and future research steps.Item RIBOSOME IN THE BALANCE: STRUCTURAL EQUILIBRIUM ENSURES TRANSLATIONAL FIDELITY AND PROPER GENE EXPRESSION(2014) Musalgaonkar, Sharmishtha; Dinman, Jonathan D; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)At equilibrium, empty ribosomes freely transit between the rotated and un-rotated states. In translation elongation, the binding of two translation elongation factors to the same general region of the ribosome stabilizes them in one of the two extremes of intersubunit rotation; rotated or unrotated. These stabilized states are resolved by expenditure energy in the form of GTP hydrolysis. Here, mutants of the early assembling integral ribosomal protein uL2 (universal L2) are used to test the generality of this hypothesis. A prior study employing mutants of a late assembling peripheral ribosomal protein suggested that ribosome rotational status determines its affinity for elongation factors, and hence translational fidelity and gene expression. rRNA structure probing analyses reveal that mutations in the uL2 B7b bridge region shift the equilibrium towards the rotated state, propagating rRNA structural changes to all of the functional centers of ribosome. Shift in structural equilibrium affects the biochemical properties of ribosomes: rotated ribosomes favor binding of the eEF2 translocase and disfavor that of the elongation ternary complex. This manifests as specific translational fidelity defects, impacting the expression of genes involved in telomere maintenance. A model is presented here describing how cyclic intersubunit rotation ensures the unidirectionality of translational elongation, and how perturbation of rotational equilibrium affects specific aspects of translational fidelity and cellular gene expression.Item DIFFERENTIAL ABILITIES OF THE CHICKEN PIT1 ISOFORMS TO REGULATE THE CHICKEN GROWTH HORMONE PROMOTER(2011) Mukherjee, Malini; Porter, Tom E; Molecular and Cell Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Pit1, a pituitary-specific transcription factor, regulates differentiation of cells of the PIT1 lineage in the anterior pituitary. PIT1 also regulates the synthesis of peptide hormones from these cell types, including growth hormone (GH). A founding member of the POU-homeodomain family of transcription factors, PIT1 is characterized by a serine-threonine rich N-terminal transactivation domain and a C-terminal POU-domain. Alternative forms of PIT1, differing from each other in the N-terminal domain have been reported in several species, but the functional implication of having multiple isoforms is not known. Several Pit1 isoform mRNAs exist in chickens which have not been characterized. The main aim of this study was to determine which, if any, of the chicken PIT1 isoforms regulated the chicken Gh (cGh) promoter. PIT1β2, a novel isoform of chicken PIT1 was discovered, and known and novel isoforms (PIT1α, PIT1β1, PIT1β2 and PIT1γ) were characterized. A luciferase reporter construct containing 1775bp of the cGh promoter driving expression of firefly luciferase was used to determine the ability of the isoforms to regulate the target gene promoter activity in chicken LMH cells. We showed that three of the isoforms, PIT1α, PIT1β1 and PIT1β2, expressed from recombinant plasmids, regulated the cGh promoter, while PIT1γ did not. All the isoforms localized to the nucleus in both non-pituitary and pituitary cells. Results from gel-shift assays show that PIT1γ did not bind the proximal PIT1-binding site of the cGh promoter as well as the other isoforms, suggesting a possible mechanism behind the inactivity. Our result did not suggest a negative regulatory role for this isoform. In contrast, we found a functional advantage for having multiple isoforms. PIT1β1, the isoform that activated the promoter most strongly, when co-transfected with other activating isoforms, such as PIT1α and PIT1β2, induced significantly higher level of activation than one isoform alone. Whether this increased activation required, or was facilitated by, heterodimerization of two isoforms is not known. Nevertheless, identification of isoforms with specific functions will facilitate identification of their respective interacting partners, which are essential for GH gene expression.Item FROM GENES TO BEHAVIOR: VARIATION IN THE VISUAL SYSTEMS OF LAKE MALAWI CICHLID FISHES(2011) Smith, Adam Ray; Carleton, Karen L; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Visual systems are ideal models for the study of sensory evolution. The cichlids of Lake Malawi possess an elaborated complex of genes (opsins) that encode chromatic visual pigments, which allows us to study the evolution and diversification of chromatic vision in great detail. In this dissertation, we investigated the molecular and behavioral properties of cichlid visual systems in order to more thoroughly understand the diversification of visual systems and the behavioral consequences of these changes. The work is organized into three research projects, with the following results: (1) Opsin gene sequence variation, with corresponding functional sensitivity changes, were found for the SWS1 (ultraviolet-sensitive), SWS2B (violet-sensitive), RH2Aβ (green-sensitive), and LWS (red-sensitive) opsin genes. Of the two genera profiled, each had two variable genes, suggesting that diversifying selection acts on different opsins in each genus. Furthermore, our data suggest that the variation in the SWS1 gene has arisen recently in Lake Malawi and is under rapid selection. (2) Intraspecific cone opsin gene expression variation was found in wild populations of multiple species. Expression variation was found primarily for the LWS and SWS1 genes, while the other genes were relatively consistent within species. This finding suggests that expression can be modulated by adding genes to what may otherwise be considered a species-specific expression pattern. Quantitative models suggested that this expression variation was not the result of environmental constraint. (3) Fish raised in different ambient developmental light environments had different cone opsin gene expression, primarily in the LWS opsin gene. These expression differences caused an increase in behavioral sensitivity in the optomotor response. Furthermore, analyses indicated that the OMR response is determined solely by the LWS cone pigment, rather than a complement of different cone types. Taken together, these findings shed new light on how visual systems diversify over short evolutionary time-scales, and the possible linkage of early determinants of visual sensitivities (opsin genes) and processes that directly influence speciation (behavior).Item PHYLOGENETIC RELATIONSHIP AMONG POLYMORPHIC OLIGOHYMENOPHOREAN CILIATES, WITH GENE EXPRESSION IN LIFE-HISTORY STAGES OF MIAMIENSIS AVIDUS (CILIOPHORA, OLIGOHYMENOPHOREA)(2007-11-29) Gebler, Glenn Frederick; Small, Eugene B.; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The Class Oligohymenophorea is a monophyletic group possessing polymorphic taxa. Thus far, relationships within subclasses of oligohymenophorean ciliates and between polymorphic taxa within families are not well resolved. Here, nuclear small subunit rRNA (SSU rRNA) gene sequences from 63 representative taxa, including several polymorphic species, were used to construct phylogenies and test monophyly of the subclass Scuticociliatia and of the polymorphic taxa within the Oligohymenophorea. In addition, suppression subtraction hybridization (SSH) was used to test the hypothesis that genes are differentially expressed during microstome-to-macrostome and tomite-to-microstome transformation in the polymorphic scuticociliate Miamiensis avidus. Phylogenetic analyses confirmed monophyly of the subclasses Peritrichia and Hymenostomatia. The monophyletic scuticociliates encompassed most, but not all, taxa included in this study. The conditional acceptance of the hypothesis supporting monophyly of the Scuticociliatia was due to the ambiguous placement of three taxa, the apostome Anoplophrya marylandensis, the scuticociliate Dexitrichides pangi, and the peniculine Urocentrum turbo. The polymorphic trait most likely arose on at least four, and perhaps on as many as six, separate occasions within the oligohymenophorean ciliates. Several genes previously implicated in morphogenetic processes in eukaryotes were upregulated during microstome-to-macrostome transformation in M. avidus. Those genes were, elongation factor-1 alpha (Ef-1α), Constans, Constans-like TOC1 (CCT) transcription factor, a disulfide isomerase, heat shock protein 70, step II splicing factor (Slu7), U1 zinc finger protein, and WD40-16 repeat protein. A similar analysis for M. avidus undergoing tomite-to-microstome transformation identified genes previously linked to transformation processes in other protists: two cysteine protease genes lacking formal description (papain-family and XCP1 cysteine protease), two described cysteine protease genes, cathepsin B and cathepsin L, and one cysteine protease inhibitor (cystatin-1) gene. The roles of candidate genes for regulation of M. avidus life-history stages (Ef-1α for microstome-to-macrostome transformation; cathepsin B and cathepsin L for tomite-to-microstome transformation) were examined using pharmacological inhibition experiments. Drug treatments significantly reduced transformation of M. avidus microstomes into macrostomes within 6 h and prevented tomite-to-microstome transformation after 2.5 h. Results indicated that genes specifically linked to oral transformation in M. avidus are differentially expressed during microstome-macrostome and tomite-microstome transformation. Thus, this study used molecular techniques to understand the evolutionary history and development of polymorphism within the Oligohymenophorean ciliates.