Microbiology Commons^™

Cis-Regulatory Sequence And Co-Regulatory Transcription Factor Functions In Erα-Mediated Transcriptional Repression, Richard Leroy Smith

Theses and Dissertations

Estrogens exert numerous actions throughout the human body, targeting healthy tissue while also enhancing the proliferative capacity of breast cancers. Estrogen signaling is mediated by the estrogen receptor (ER), which binds DNA and ultimately affects the expression of adjacent genes. Current understanding of ER-mediated transcriptional regulation is mostly limited to genes whose transcript levels increase following estrogen exposure, though recent studies demonstrate that direct down-regulation of estrogen-responsive genes is also a significant feature of ER action. We hypothesized that differences in cis-regulatory DNA was a factor in determining target gene expression and performed computational and experimental studies to test this …

A Population Genetic Study Of Middle Eastern Populations Using Dys 458 Microvariants And Cohen Modal Haplotypes, Enass Nabeel Tinah

Theses and Dissertations

A comprehensive population study in the Middle East was conducted using different genetic markers in order to establish a wider genetic profile of the Middle Eastern populations. The main goal of this study was to analyze DNA from samples collected from different locations, and produce genetic motifs and patterns that could be used to identify and distinguish the target populations. This information will allow us to analyze the ancestry of these populations, their interactions through time and space, and the effects these interactions have on the populations' structure. We have collected around 1300 individual samples from different populations in the …

Evolution Of Picornaviruses: Impacts Of Recombination And Selection, Nicole Noel Lewis-Rogers

Theses and Dissertations

Picornaviruses are responsible for some of the most common and debilitating diseases affecting humans and animals worldwide. The objectives of this dissertation research were (1) estimate phylogenetic relationships among 11 picornavirus genera and within three species: foot-and-mouth disease virus (FMDV: Aphthovirus) which afflicts cloven-hoofed animals and human rhinovirus A and B (HRV: Enterovirus) which cause the common cold; (2) better understand the impact recombination has on genomic organization and evolution; (3) characterize where positive and purifying selection has occurred in proteins and how selection has influenced phenotype. The dissertation includes four studies. The first chapter provides an overview of the …

Specific Compartmentalization Of Iga Ascs In Mouse Salivary Glands Via Differential Expression Of Chemokines And Chemokine Receptors, Yuet Ching Law

Theses and Dissertations

The mucosal system, which forms a barrier between internal organ systems and the external environment, is frequently exposed to pathogenic microorganisms. Immunoglobulin A (IgA) antibody secreting cells (ASCs) localize in the lamina propria, and produce IgA antibodies which help protect mucosal tissues. The concept of a common mucosal immune system in which IgA ASCs have the ability to populate any mucosal site has been proposed (1, 2). However, recent research has suggested that IgA ASCs primed in different mucosal sites might possess different sets of chemokine receptors, and therefore migrate specifically to particular mucosal locations (3). In this study, the …

The Antioxidant Defense Network: Synergistic Combinations To Prevent Oxidative Damage, Amy Marie Clement

Theses and Dissertations

One of the matchless ironies of the human body is its requirement for the highly reactive oxygen molecule, which has been clearly implicated in many diseases and the aging processes. Oxidants produced by metabolic processes damage cells by starting chemical chain reactions including oxidation of DNA and proteins as well as lipid peroxidation. Damage to DNA can cause mutations and lead to cancer if not reversed by DNA repair mechanisms. Damage to proteins causes enzyme inhibition, denaturation and protein degradation. Lipid peroxidation can cause cell lysis as well as creating mutagenic and carcinogenic by-products. The human body contains antioxidants and …

Decline In A Dominant Invertebrate Species Contributes To Altered Carbon Cycling In A Low-Diversity Soil Ecosystem, Byron J. Adams, J. E. Barrett, Ross A. Virginia, Diana H. Wall

Faculty Publications

Low-diversity ecosystems cover large portions of the Earth's land surface, yet studies of climate change on ecosystem functioning typically focus on temperate ecosystems, where diversity is high and the effects of individual species on ecosystem functioning are difficult to determine. We show that a climate-induced decline of an invertebrate species in a low-diversity ecosystem could contribute to significant changes in carbon © cycling. Recent climate variability in the McMurdo Dry Valleys of Antarctica is associated with changes in hydrology, biological productivity, and community composition of terrestrial and aquatic ecosystems. One of the greatest changes documented in the dry valleys is …

Comparative Phylogeography Of Codistributed Species Of Chilean Liolaemus (Squamata: Tropiduridae) From The Central-Southern Andean Range, Byron J. Adams, Pedro F. Victoriano, Juan Carlos Ortiz, Edgar Benavides, Jack W. Sites

Faculty Publications

In this study, we used a recently developed supertrees method to test for shared phylogeographical signal in partially overlapping geographical ranges of lizards of the genus Liolaemus from the Andean Range in south-central Chile. We reconstruct mtDNA gene trees for three partially codistributed species (Liolaemus tenuis, L. lemniscatus and L. pictus), and our sampling effort is sufficient to allow statistical tests of shared signal between the combinations L. tenuis-L. pictus, and L. tenuis-L. lemniscatus. For both combinations, standardized maximum agreement subtrees scores showed statistically significant signal for shared pattern in regions of overlap, as evaluated by randomization tests (P < 0.001 and < 0.05, respectively). The matrix representation with parsimony tree obtained from the combination of the three different gene trees revealed concordant phylogeographical associations of all species, and was consistent with the geographical association of intraspecific haploclades with three Chilean bioclimatic zones. A multidimensional scaling analysis of several climate variables showed highly significant differences among these zones, which further suggests that they may have contributed to similar patterns of intraspecific divergence across all three species. In the mesomorphic zone in Central Chile, the species L. tenuis and L. lemniscatus may have codiverged in response to shared orogenic vicariant events, which likely predominated over climatic events associated with cycles of glacial advance and retreat. In the hygromorphic zone in southern Chile, however, glacial cycles likely predominated in structuring the phylogeographical histories of L. tenuis and L. pictus, although important ecological differences between these two caution against broad generalizations at this point.

The Effect Of Febrile Temperature On Plasmodium Falciparum, Heidi Sue Porter

Theses and Dissertations

Previously it has been shown that cultures of Plasmodium falciparum died following exposure to a febrile temperature of 40°C, as demonstrated by a decrease in parasitemia of the following generation. In the current study, the effect of 40°C treatment on culture media, erythrocytes, and parasite glucose consumption, were ruled out as possible influences on parasite death, demonstrating that 40°C impacted the parasites directly. Metabolic profiling of DNA synthesis, protein synthesis, and glucose utilization during exposure to 40°C clearly indicated that febrile temperatures had direct effect on major metabolic pathways and parasite development, beginning 20-24 hr after erythrocyte invasion. The ring …

Differential Resource Allocation In Deer Mice Exposed To Sin Nombre Virus, Eric Wilson, Erin M. Lehmer, Christine A. Clay, Stephen St. Jeor, Denise M. Dearing

Faculty Publications

The resource allocation hypothesis predicts that reproductive activity suppresses immunocompetence; however, this has never been tested in an endemic disease system with free-ranging mammals. We tested the resource allocation hypothesis in wild deer mice (Peromyscus maniculatus) with natural exposure to Sin Nombre Virus (SNV). Immunocompetence was estimated from the extent of swelling elicited after deer mice were injected with phytohemagglutinin (PHA); swelling is positively correlated with immunocompetence. After livetrapping deer mice, we determined their reproductive state and SNV infection status. Males were more likely to be seropositive for SNV than females (37% vs. 25%) and exhibited 10% less swelling after …

Differential Response Of Various Spore Species To Sporicidal Disinfectants, Michael David Pratt

Theses and Dissertations

In the fall of 2001, letters laced with anthrax spores were delivered to various news organizations in New York and Florida, as well as to two Senators in Washington, D.C. Over 22 anthrax infections and five deaths resulted from exposure to these spores, and decontamination of the affected buildings was both time consuming and costly. Since these attacks, interest in sporicidal disinfectants has increased greatly. Many chemical sporicidal disinfectants are available commercially, but the exposure time required to sterilize can be relatively long. In addition, some spores are simply injured or inhibited by chemical disinfectants, but not necessarily killed. Studies …

Characterization Of A Novel Nuclear Variant Of Bmp2 And Coordinate Regulation Of Col11a2 And Col27a1 By The Transcription Factor Lc-Maf, Jaime Lynn Mayo

Theses and Dissertations

ABSTRACT I CHARACTERIZATION OF A NOVEL NUCLEAR VARIANT OF BMP2

Bone morphogenetic protein 2 (Bmp2) is a signaling protein that was first detected by its ability to induce cartilage and bone formation. It has since been implicated in broad variety of developmental, patterning, and disease processes. To date, Bmp2 has only been known to function as an extracellular signaling molecule. However, we have obtained clear evidence for a nuclear form of Bmp2. This nuclear variant, nBmp2, contains a bipartite NLS that overlaps the site of proteolytic cleavage. The NLS remains intact and functional when translation of Bmp2 initiates from a …

An Infection Model For Examining The Effects Of Gender And Diabetic State On Proinflammatory Cytokine Secretion By Phagocytic Cells In Response To Infection With Burkholderia Pseudomallei, Laura L. Dickey

Theses and Dissertations

Burkholderia pseudomallei is an opportunistic soil pathogen that causes melioidosis, a life-threatening human disease prevalent in Southeast Asia, northern Australia, the Middle East, Africa, and South America. The organism also causes disease in plants and animals. Persons with severe melioidosis usually die of septicemia. Relatively little is known regarding the virulence mechanisms of B. pseudomallei; however, several putative virulence determinants have been identified. The organism is able to invade and replicate within phagocytic cells and is particularly pathogenic in males with diabetes mellitus. B. thailandensis is closely related to B. pseudomallei, but is not pathogenic. This study examines various in …

Inhibitory Effects Of Estrogen Receptor Beta On Specific Hormone-Responsive Gene Expression And Association With Disease Outcome In Primary Breast Cancer, Chin-Yo Lin, Anders Strom, Li Say Kong, Silke Kietz, Jane S. Thomsen, Jason B. S. Tee, Vinsensius B. Vega, Lance D. Miller, Johanna Smeds, Jonas Bergh, Jan-Ake Gustafsson, Edison T. Liu

Faculty Publications

The impact of interactions between the two estrogen receptor (ER) subtypes, ER(alpha) and ER(beta), on gene expression in breast cancer biology is not clear. The goal of this study was to examine transcriptomic alterations in cancer cells co-expressing both receptors and the association of gene expression signatures with disease outcome. Methods: Transcriptional effects of ER(beta) overexpression were determined in a stably transfected cell line derived from ER(alpha) -positive T-47D cells. Microarray analysis was carried out to identify differential gene expression in the cell line, and expression of key genes was validated by quantitative polymerase chain reaction. Microarray and clinical data …

Tandem Repeat Regions Within The Burkholderia Pseudomallei Genome And Their Application For High Resolution Genotyping, Richard A. Robison, Jana M. U'Ren, James M. Schupp, Talima Pearson, Heidie Hornstra, Christine L. Friedman Clark, Kimothy L. Smith, Rebecca R. Leadem Daugherty, Shane D. Rhoton, Ben Leadem, Shalamar Georgia, Michelle Cardon, Lynn Y. Huynh, David Deshazer, Steven P. Harvey, Daniel Gal, Mark J. Mayo, David Wagner, Bart J. Currie, Paul Keim

Faculty Publications

The facultative, intracellular bacterium Burkholderia pseudomalle is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine …

Ecology Of Culturable Organisms At Rozel Point, Great Salt Lake, Utah, Emily Sarah Haws

Theses and Dissertations

The study of organisms from extreme environments is an emerging field of research with applications to multiple scientific areas. One of these extreme environments is Great Salt Lake (GSL), whose microbiology has yet to be extensively studied. This dynamic and unique environment offers an excellent opportunity to increase understanding of hypersaline ecology. Cultivation of microorganisms remains an important part of ecology research, as it is essential for understanding microbial physiology. We report here the culturing and characterization of isolates from Rozel Point, located on the northeastern shore of Great Salt Lake. This site was chosen because of the presence of …

The Role Of Prolactin In Ccl28 Regulation, Jennie Hyde

Theses and Dissertations

Infants are born with naive immune systems, making them susceptible to a variety of infections. In order to protect the newborn infant it is important that mothers be able to pass protective IgA antibodies to their infants through breast milk. B cells that produce IgA enter the mammary tissue during lactation and secrete IgA into the milk. During pregnancy, the mammary tissue expresses high levels of chemokines, molecules that allow lymphocytes to selectively home to specific tissues. The chemokine CCL28 has been shown to be upregulated during both pregnancy and lactation, and is vital for the ability of IgA-producing B …

Computational Promoter Analysis Of Mouse, Rat, And Human Antimicrobial Peptide-Coding Genes, Chin-Yo Lin, Manisha Brahmachary, Christian Schonbach, Liang Yang, Enli Huang, Sin Lam Tan, Rajesh Chowdhary, S. P. T. Krishnan, David A. Hume, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B. Bajic

Faculty Publications

Mammalian antimicrobial peptides (AMPs) are effectors of the innate immune response. A multitude of signals coming from pathways of mammalian pathogen/pattern recognition receptors and other proteins affect the expression of AMP-coding genes (AMPcgs). For many AMPcgs the promoter elements and transcription factors that control their tissue cell-specific expression have yet to be fully identified and characterized. Results- Based upon the RIKEN full-length cDNA and public sequence data derived from human, mouse and rat, we identified 178 candidate AMP transcripts derived from 61 genes belonging to 29 AMP families. However, only for 31 mouse genes belonging to 22 AMP families we …

Phylogenetics Of North American Psoraleeae (Leguminosae): Rates And Dates In A Recent, Rapid Radiation, Ashley N. Egan

Theses and Dissertations

The scientific discipline of phylogenetics involves understanding the diversity of life in the context of history. Technological advances in molecular biology and computational power have created an exponential increase in the number and kind of phylogenetic studies, allowing exploration of all manner of questions concerning the evolutionary history of a group. This dissertation research is focused on phylogenetic theory and applying these methods to the plant tribe Psoraleeae (Leguminosae; Fabaceae) with an emphasis on North American (NAm) members. First, theory of phylogeny estimation is explored in a review chapter focusing on strengths and weaknesses of phylogenetic methodology. Second, methods are …

A Phylogeny Of Belonolaimus Populations In Florida Inferred From Dna Sequences, Byron J. Adams, U. Gozel, K. B. Nguyen, R. N. Inserra, R. M. Giblin-Davis

Faculty Publications

The D2-D3 and ITS regions of rDNA from 33 Florida populations of Belonolaimus spp. were sequenced and subjected to phylogenetic analysis. Our objective was to derive a theoretical evolutionary framework for interpreting phenotypic differences as they relate to the taxonomy of the genus. The most striking aspect of the phylogenetic analysis is that none of the three nominal species (B. longicaudatus, B. euthychilus, and B. gracilis) are monophyletic. Additionally, two taxa appear to have discordant ITS and LSU sequences. Three major clades of B. longicaudatus exhibited discernible, overlapping, geographic foci from east to west across the peninsula. Morphological character states …

Multiplatform Genome-Wide Identification And Modeling Of Functional Human Estrogen Receptor Binding Sites, Chin-Yo Lin, Vinsensius B. Vega, Koon Siew Lai, Li Say Kong, Min Xie, Xiaodi Su, Huey Fang The, Jane S. Thomsen, Ai Li Yeo, Wing Kin Sung, Guillaume Bourque, Edison T. Liu

Faculty Publications

Transcription factor binding sites (TFBS) impart specificity to cellular transcriptional responses and have largely been defined by consensus motifs derived from a handful of validated sites. The low specificity of the computational predictions of TFBSs has been attributed to ubiquity of the motifs and the relaxed sequence requirements for binding. We posited that the inadequacy is due to limited input of empirically verified sites, and demonstrated a multiplatform approach to constructing a robust model. Results: Using the TFBS for the estrogen receptor (ER)alpha (estrogen response element [ERE]) as a model system, we extracted EREs from multiple molecular and genomic platforms …

Co-Variation In Soil Biodiversity And Biogeochemistry In Northern And Southern Victoria Land, Antarctica, Byron J. Adams, J. E. Barrett, Ross A. Virginia, Diana H. Wall, S. C. Cary, A. L. Hacker, J. M. Aislabie

Faculty Publications

Data from six sites in Victoria Land (72-77degrees S) investigating co-variation in soil communities (microbial and invertebrate) with biogeochemical properties show the influence of soil properties on habitat suitability varied among local landscapes as well as across climate gradients. Species richness of metazoan invertebrates (Nematoda, Tardigrada and Rotifera) was similar to previous descriptions in this region, though identification of three cryptic nematode species of Eudorylaimus through DNA analysis contributed to the understanding of controls over habitat preferences for individual species. Denaturing Gradient Gel Electrophoresis profiles revealed unexpectedly high diversity of bacteria. Distribution of distinct bacterial communities was associated with specific …

The Phylogeography Of Prosopium In Western North America, Becky Akiko Miller

Theses and Dissertations

The mountain whitefish (Prosopium williamsoni) has been largely overlooked in population genetic analyses despite its wide distribution in discrete drainage basins in western North America for over four million years. Its closest sister taxa the Bear Lake whitefish (P. abyssicola), Bonneville cisco (P. gemmifer), and Bonneville whitefish (P. spilonotus) are found only in Bear Lake Idaho-Utah and were also included in the analyses. A total of 1,334 cytochrome b and 1,371 NADH dehydrogenase subunit 2 sequences from the Bonneville Basin, the Columbia River Sub-basin, the lower Snake River Sub-basin, the upper Snake River Sub-basin, the Green River Basin, the Lahontan …

Tumor Associated Macrophages In A Mafia Mouse Model, Adrianne Brown Clifford

Theses and Dissertations

Recent evidence has shown the important role of macrophages in both tumor development and progression. To investigate the role of macrophages we used a mouse model known as MaFIA (Macrophage Fas Induced Apoptosis) mice that allows for the selective deletion of macrophages. Mice were given melanoma cells at various stages of depletion. Tumor mass was measured and organs were processed for flow cytometry to measure melanoma cell migration. The results show that mice receiving depletion treatment have larger tumor sizes and weights than those mice retaining their macrophage population. We detect metastasis in both the lung and kidney in both …

Characterization Of The Role Of Sox9 In Cartilage-Specific Gene Regulation, Mary Ann Genzer

Theses and Dissertations

Although advances have been made toward understanding the complex mechanisms that regulate the process of DNA transcription, the specific mechanisms of activation for many individual genes remain unknown. In this study, we focus on the role the transcription factor SOX9 plays in activating cartilage-specific genes, specifically Col9a1 and Cartilage Link Protein (CRTL1). Previously, enhancers of these genes containing single SOX9 binding sites were shown to be activated through SOX9 binding. However, the hypothesis was made that in cartilage-specific genes dimeric SOX9, as opposed to monomeric SOX9, is necessary for activation. We identified a putative binding site adjacent to each of …

Homologous Strand Exchange And Dna Helicase Activities In Plant Mitochondria, Daqing Song

Theses and Dissertations

Homologous recombination is critical for generating genetic variation in living organisms by exchange and rearrangement of DNA. Most of our knowledge about homologous recombination is limited to processes in bacteria or in eukaryotic nuclei. In E. coli, homologous recombination is dependent on the RecA protein. Higher plant chloroplasts have RecA-like strand exchange activity. However, little is known about these mechanisms in higher plant mitochondria. I have detected a RecA-like strand exchange activity in soybean mitochondria. This activity forms joint molecules in the presence of ATP, Mg2+, and homologous DNA substrates. In addition, the E. coli single-stranded DNA binding (SSB) protein …

Genetic Analysis Of Conserved Residues In Phou Of Escherichia Coli, Stewart G. Gardner

Theses and Dissertations

The Pho regulon is controlled by the PstSCAB transporter, PhoU, and the two-component proteins, PhoB and PhoR. PhoU is a negative regulator of the Pho regulon under phosphate-replete conditions. How PhoU functions is unknown. Many PhoU homologues are found widely throughout prokaryotic domains. There are several conserved amino acid residues in the PhoU protein. It is hypothesized that these residues play an important role in the function of PhoU. To test this hypothesis, several site directed mutations in the phoU gene have been produced with single amino acid changes in conserved residues. After testing these mutants, it was found that …

Investigation Of The Mechanisms Of Ozone-Mediated Viral Inactivation, Seiga Ohmine

Theses and Dissertations

Previous studies have established that ozone-oxygen mixtures can be used to inactivate a variety of microorganisms including bacteria, fungi and viruses. Ozone is a potent reactive oxygen species (ROS) that rapidly decays into a variety of additional short half-life ROS which have been shown to cause oxidative damage to biological molecules. I hypothesize that controlled ozone exposure and the subsequent generation of additional ROS would reduce viral infectivity by lipid and/or protein peroxidation. A proprietary ozone-oxygen delivery system was used to inactivate a series of enveloped [herpes simplex virus type-1 strain McIntyre (HSV-1), vaccinia strain Elstree (VAC), vesicular stomatitis virus …

Crustacean Phylogenetic Systematics And Opsin Evolution, Megan L. Porter

Theses and Dissertations

Composed of a chromophore bound to an integral membrane protein (opsin), visual pigments are phenotypically characterized by the wavelength of maximal absorption (λmax). The underlying molecular mechanism controlling λmax is the interaction between the opsin amino acid sequence and the chromophore. While a plethora of studies have looked at structure/function relationships in vertebrate opsins, fewer studies have investigated similar issues in invertebrates. Furthermore, those few studies undertaken in invertebrate systems suggest different mechanisms of spectral tuning and photoactivation compared to vertebrate systems. This dissertation research is focused on expanding our knowledge of opsin evolution in invertebrate systems, particularly from non-insect …

Assessment Of Cell Death Parameters In Bovine Parvovirus-Infected Ebtr Cells, Lubna Salah Eldin Abdel Latif

Theses and Dissertations

Bovine parvovirus (BPV) is a helper-independent parvovirus. It has a small icosahedral capsid with a single stranded DNA genome. It is a highly stable virus with a narrow host range. It causes acute gastroenteritis in calves. It is considered to be a cytolytic virus because it kills the host cells. However, the mechanism by which the virus causes cell death is not known. The work described in this thesis assessed different parameters of cell death in BPV infected embryonic bovine tracheal (EBTr) cells. There are several ways for viruses to induce cell death. Viruses can induce apoptosis in the infected …

Identification Of Proteins Involved In Chloroplast Dna Replication, Matthew G. Lassen

Theses and Dissertations

Chapter 1

Chloroplast nucleoids (ct-nucleoids) are DNA/protein complexes involved in compacting the chloroplast genome, and may play a role in regulating DNA replication. Ct-nucleoids were isolated from young soybean plants and separated by 2-D gel electrophoresis. Gel spots were excised and analyzed by MALDI-ToF mass spectrometry, resulting in several protein identifications. The proteins identified all have functions unrelated to DNA replication. While some of these proteins may be due to contamination, it is possible that some of these proteins are dual-functional, playing direct roles in the regulation of DNA replication.

Chapter 2

A 28 kDa soybean protein was isolated by …