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Biofilm Genetics Of Burkholderia Cenocepacia, Laura C. Benton

Master's Theses and Capstones

Burkholderia cenocepacia is a soil bacterium and opportunistic human pathogen found to infect the lungs of cystic fibrosis (CF) patients. One factor that may allow B. cenocepacia to persist in the CF lung and continue to cause a decline in lung function is its ability to form biofilms. Little is known about the genetic mechanisms allowing this bacterium to transition from an acute to a chronic (biofilm) lifestyle. I used both transposon mutagenesis and positive laboratory selection to identify mutations that increase biofilm production. Mutations affecting capsule polysaccharide synthesis were identified, among others, by random mutagenesis to confer an increased …

Regulation Of Polyamine Metabolism In Transgenic Poplar Cell Cultures, Smita Cherry

Master's Theses and Capstones

Polyamines (PA) are naturally occurring low molecular weight aliphatic amines found in all living organisms and essential for their growth and development. The present study uses the tool of transgenic manipulation to elucidate the regulation of PA pathway in poplar cells. This study was divided into two segments; the first segment provides insight into biochemistry of a putrescine overproducing cell line (HP) that overexpresses a mouse ornithine decarboxylase (mODC) under 35S-CaMV promoter, with respect to different treatments. The second segment focused on creation and biochemical characterization of a cell line (SOS1) that overexpresses ODC/SAMDC from Plasmodium falciparum controlled by the …

Effect Of Cholinergic Deafferentation Of Prefrontal Cortex On Working Memory For Familiar And Novel Odors, Emily Carter

Master's Theses and Capstones

The role of acetylcholine in the medial prefrontal cortex (mPFC) in working memory was investigated in aged rats. Subjects with cholinergic lesions of the prelimbic portion of the mPFC (pACh-lx) or a sham lesion of the same region were trained on an odor delayed non-match to sample paradigm. The effects of prefrontal cholinergic depletion and aging were assessed in task variations that manipulated mnemonic demand and stimulus novelty.

pACh-lx animals were impaired relative to sham-lx animals at memory for familiar stimuli over delays. This global impairment was not dependent on the length of the delay, suggesting that aged pACh-lx animals …

Nsu Fischler School Of Education And Human Services Undergraduate Education [2009], Nova Southeastern University

Abraham S. Fischler College of Education and School of Criminal Justice College Archive

No abstract provided.

An Assessment Of The Biodiversity And Bioremediation Potential Of Distromatic Ulva Spp (Chlorophyta) In The Great Bay Estuarine System Of New Hampshire And Maine, Usa, Laurie Carol Hofmann

Master's Theses and Capstones

Eutrophication of coastal ecosystems is a global problem, and algae have become an important resource for bioremediation. The goals of this study were (1) to assess the biodiversity of Ulva spp. in the Great Bay Estuarine System (GBES) of New Hampshire and Maine, and (2) to assess which Ulva populations are most appropriate for bioremediation by determining if environmental nutrient history and/or taxonomie differences affect ammonium uptake. Molecular analysis of the internal transcribed spacer nrDNA regions of Ulva spp. revealed four distinct distromatic taxa: Ulva lactuca Linnaeus, Ulva rigida C. Agardh, Ulva compressa Linnaeus, and U. pertusa Kjellman. The latter …

Fine-Scale Activity, Distribution And Habitat Utilization Of Atlantic Cod (Gadus Morhua) On The Ipswich Bay Spawning Ground, Laughlin Siceloff

Master's Theses and Capstones

Data storage tags (DSTs) and acoustic telemetry were applied to examine cod spawning habitat utilization in Ipswich Bay and compare seasonal activity patterns. I tagged 200 spawning cod in Ipswich Bay during April--May 2006 with DSTs recording depth and temperature. Twenty-six cod were also implanted with acoustic transmitters and relocated manually and with stationary listening stations during May and June. Twenty-five DSTs were returned, showing that most cod departed the spawning ground during May and June and dispersed throughout the western Gulf of Maine. Cod shared a low vertical activity pattern in Ipswich Bay, but adopted various site-specific vertical behaviors …

Estuarine Water Column Filtration By Zostera Marina L (Eelgrass) And Crassostrea Virginica (Eastern Oyster), Paul David Sokoloff

Master's Theses and Capstones

Zostera marina L., eelgrass, and Crassostrea virginica, the eastern oyster, atone or in combination, can have a significant effect on the clarity of estuarine waters. A mesocosm study was utilized to investigate the filtration capabilities, the rate of particle removal from the water column, using several fractions of the naturally occurring seston. A series of experimental seston additions were made to twelve mesocosm tanks with the four treatments of eelgrass atone, oysters atone, eelgrass + oysters and no eelgrass or oysters (control) to determine the rate of water column filtration. The results demonstrated differences in the capability of the four …

Effects Of Sedimentation And Periphyton Communities On Embryonic Rainbow Smelt, Osmerus Mordax, Lauren Helena Wyatt

Master's Theses and Capstones

The decline of anadromous rainbow smelt (Osmerus mordax) populations has been suspected to be linked to anthropogenic causes. Increased runoff from agriculture and urbanization has led to additional sediment inputs and eutrophying compounds in rivers. The aim of this study was to assess the survival of embryonic rainbow smelt from fertilization through hatching under varying levels of sedimentation (0.00, 0.25, 1.00, and 6.00 g per 45.6 cm 2) and with periphyton communities of different biomass and algal composition. Additionally, embryo survival was assessed when cultured on periphyton in combination with sterilized sediment or eutrophying compounds (nitrates and phosphates). Oxygen consumption …

Patterns Of Population Structure And Productivity In Saltmarsh Sparrows, Jennifer Walsh

Master's Theses and Capstones

The Saltmarsh Sparrow (Ammodramus caudacutus) is one of the few species globally that is exclusively restricted to coastal wetlands. Despite the high vagility characteristic of avian species, the highly patchy distribution of tidal marshes can often lead to fine scale genetic structure in salt marsh obligates. To elucidate patterns of population structure, we investigated the degree of genetic differentiation among nine Saltmarsh Sparrow populations along the northeastern coastline of the United States. Although overall FST values were small (0.008), population substructuring was detected along with a positive correlation between geographic distance and genetic differentiation, suggesting that Ammodramus caudacutus follow an …

Coiled-Coil-Mediated Dimerization Is Not Required For Myosin Vi To Stabilize Actin During Spermatid Individualization In Drosophila Melanogaster, Tatsuhiko Nogushi, Deborah J. Frank, Mamiko Isaji, Kathryn G. Miller

Biology Faculty Research

Myosin VI is a pointed-end-directed actin motor that is thought to function as both a transporter of cargoes and an anchor, capable of binding cellular components to actin for long periods. Dimerization via a predicted coiled coil was hypothesized to regulate activity and motor properties. However, the importance of the coiled-coil sequence has not been tested in vivo. We used myosin VI's well-defined role in actin stabilization during Drosophila spermatid individualization to test the importance in vivo of the predicted coiled coil. If myosin VI functions as a dimer, a forced dimer should fully rescue myosin VI loss of function …

The Mechanisms And Roles Of Feedback Loops For Visual Processing, Jing Shao

All Theses and Dissertations (ETDs)

Signal flow in the brain is not unidirectional; feedback represents a key element in neural signal processing. To address the question on how do neural feedback loops work in terms of synapses, microcircuitry, and systems dynamics, we developed a chick midbrain slice preparation to study and characterize one important feedback loop within the avian visual system: isthmotectal feedbackloop. The isthmotectal feedback loop consists of the optic tectum: OT) and three nucleus isthmi: Imc, Ipc and SLu. The tectal layer 10 neurons project to ipsilateral Imc, Ipc and SLu in a topographic way. In turn Ipc and SLu send back topographical: …

Functional Significance Of Glycoprotein Clearance By The Asialoglycoprotein Receptor And The Mannose/Galnac-4-So4 Receptor, Lindsay Steirer Taylor

All Theses and Dissertations (ETDs)

Glycosylation plays an important role in many biological functions. Two highly abundant, carbohydrate-specific, endocytic receptors reside in parenchymal and endothelial cells of the liver. Our lab has shown that the asialoglycoprotein receptor: ASGR) is capable of clearing glycoproteins bearing terminal Siaalpha2,6GalNAc as well as ones bearing terminal Gal/ GalNAc and that the Mannose/GalNAc-4-SO4 receptor: MR) is capable of clearing glycoproteins bearing terminal GalNAc-4-SO4. I am taking a genetic approach identifying endogenous ligands for the ASGR and the MR in vivo and establishing the biologic significance of clearing these glycoproteins from the blood. A number of glycosylated hormones such as luteinizing …

In Vivo Function Of Otopetrin 1 In The Vestibular Sensory Epithelium, Euysoo Kim

All Theses and Dissertations (ETDs)

Otopetrin family genes encode multi-transmembrane domain proteins with three highly conserved domains. In mice, three Otopetrin paralogues are found. One of its members, Otopetrin 1: Otop1) has been previously shown to be essential for the formation of otoconia in the vestibular system of the inner ear. Otoconia are calcium carbonate biominerals that are required for normal balance and the sensation of linear acceleration with respect to gravity. The mechanism by which OTOP1 mediates otoconia biosynthesis is not known, but the ability of OTOP1 to modulate [Ca2+]i in response to purinergic signals in heterologous systems suggest that OTOP1 may be involved …

Evolution Of Endosperm Starch Synthesis Pathway Genes In The Context Of Rice: Oryza Sativa) Domestication, Guoqin Yu

All Theses and Dissertations (ETDs)

The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized biosynthesis pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication and subsequent crop improvement. In this study, I have examined six key genes in the rice endosperm starch biosynthesis pathway to investigate the evolution of this pathway before rice domestication and during rice domestication. Oryza rufipogon is the wild ancestor of cultivated rice: Oryza sativa). Oryza sativa has five variety groups: aus, …

Microbial Diversity And Geochemical Energy Sources Of Tutum Bay, Ambitle Island, Papua New Guinea, An Arsenic-Rich, Shallow-Sea Hydrothermal System, Nancy Akerman

All Theses and Dissertations (ETDs)

I investigate the hydrothermal system located in Tutum Bay, Ambitle Island, Papua New Guinea, a shallow-sea system ~5 - 10 meters below sea level that is arsenic-rich. Hydrothermal vents in the bay expel fluids with arsenite: AsIII) concentrations as high as 950 μg/L. To determine the role that Tutum Bay microorganisms might play in mediating As-redox reactions, three approaches were used: analyzing the geochemical environment for energy sources, characterizing the archaeal community composition of the sediments, and conducting culture-dependent As-cycling experiments. The second chapter of this dissertation discusses an energetic study of potential chemolithotrophic metabolic reactions, including As-redox reactions. Results …

Computational And Experimental Investigation Of Allosteric Communication In The Transcriptional Regulator Nikr, Michael Bradley

All Theses and Dissertations (ETDs)

The Ni2+ and DNA binding protein NikR is involved in nickel regulation in Escherichia coli through transcriptional repression of the NikABCDE nickel permease. NikR is a homotetramer and each chain contains both a DNA binding ribbon-helix-helix: RHH) domain and a Ni2+ binding regulatory ACT: aspartokinase, chorismate mutase, TyrA) fold. Work herein combines computational modeling of NikR structure with experimental studies aimed at understanding allosteric communication between the ACT and RHH domains. Hydrogen/deuterium exchange mass spectrometry shows a Ni2+ specific NikR conformational change relative to bound Cu2+, Co2+, and Zn2+. Concurrent coordination geometry and in vivo repressor function studies show that …

A Phenotypic And Genetic Characterization Of The Cell Adhesion Molecules Echinoid And Friend-Of-Echinoid In The Directed Cell Movements Of Ommatidial Rotation During Drosophila Eye Development., Jennifer Fetting

All Theses and Dissertations (ETDs)

Correct development of multicellular organisms relies on the precise patterning of cells, which must respond to and interpret specific cues that instruct the cells to differentiate and often undergo directed cell movements and rearrangements to give rise to functional tissues and organs. Differential adhesion between the stationary and mobile cells permits and promotes these cellular movements, effecting patterning of cells and tissues. During Drosophila eye development, groups of cells, the ommatidial precursors, undergo a 90° rotational movement within a matrix of stationary cells, providing the cell motility readout of tissue polarity. The mechanisms that regulate ommatidial rotation are not well …

Aggregation & Localization Of A Disease-Associated Prion Protein (Prp) Mutant, Andrea Rhonda Medrano

All Theses and Dissertations (ETDs)

ABSTRACT OF THE DISSERTATION Aggregation & Localization of a Disease-Associated Prion Protein: PrP) Mutant by Andrea Rhonda Zaragoza Medrano Doctor of Philosophy in Biology and Biomedical Sciences: Genetics) Washington University in St. Louis, 2009 Professor David A. Harris, Chairperson Prion protein: PrP) is a GPI-anchored sialoglycoprotein involved in the pathogenesis of infectious and inherited forms of transmissible spongiform encephalopathies: TSEs). A nine-octapeptide insertional mutation in the prion protein: PrP) causes a fatal neurodegenerative disorder in both humans and transgenic mice. To determine the precise cellular localization of this mutant PrP: designated PG14), we have generated transgenic mice expressing PG14-EGFP, a …

Subunit Compositions Of Arabidopsis Dna-Dependent Rna Polymerases And The Roles Of The Plant-Specific Rna Polymerases Iv And V In Gene Silencing, Thomas Ream

All Theses and Dissertations (ETDs)

In addition to RNA polymerases I, II and III, the essential RNA polymerases present in all eukaryotes, plants have two additional nuclear RNA polymerases, abbreviated as Pol IV and Pol V, that play non-redundant roles in siRNA-directed DNA methylation and gene silencing. Using a combination of affinity purification and protein identification by mass spectrometry, my studies show that Arabidopsis Pol IV and Pol V are composed of subunits that are paralogous or identical to the twelve subunits of Pol II. Four subunits of Pol IV are distinct from their Pol II paralogs, six subunits of Pol V are distinct from …

Biology In Mathematics At The University Of Richmond, Lester Caudill

Department of Math & Statistics Faculty Publications

In an effort to meet the needs of science students for modeling skills, three new courses have been created at the University of Richmond: Scientific Calculus I and II, and Mathematical Models in Biology and Medicine. The courses are described, and lessons learned and future directions are discussed.

Eeg During Pedaling: Brain Activity During A Locomotion-Like Task In Humans, Sanket G. Jain

Master's Theses (2009 -)

This study characterized the brain electrical activity during pedaling, a locomotor-like task, in humans. We postulated that phasic brain activity would be associated with active pedaling, consistent with a cortical role in locomotor tasks. 64 channels of electroencephalogram (EEG) and 10 channels of electromyogram (EMG) data were recorded from 10 neurologically-intact volunteers while they performed active and passive (no effort) pedaling on a custom-designed stationary bicycle. Ensemble average waveforms, two dimensional topographic maps and amplitude of the beta (13-35 Hz) frequency band were analyzed and compared between active and passive trials. The absolute amplitude (peak positive-peak negative) of the EEG …

The Effect Of Office Chair Backrest Design On The Body's Metabolic Response To Office Work, Stephen H. Freier

Master's Theses (2009 -)

Most office chairs have a backrest that is wider at the shoulders than at the hips. Recently, a new office chair was developed that has a backrest that is narrower at the shoulders and wider at the hips (upwardly tapered backrest). The upwardly tapered backrest should allow users to increase their ventilatory efficiency, compared to a conventional, wide backrest. This new backrest design will hypothetically allow a user to retract their scapulae, increase expansion of the chest cavity, thus allowing the lungs more space to expand. Specific measures of improved ventilatory efficiency are an increase in tidal volume (V_{t …}

Teaching The Unifying Theory Of Biology : A Curriculum Unit On Evolution, Nell Blankfort

Capstone Projects and Master's Theses

This action research project developed an updated and expanded curriculum unit on the theory of evolution. The activities and assessments that were selected and designed for the curriculum followed the instructional theories of backward design and constructivism. Working as a community of learners, high school students were empowered to engage in experimentation, innovation, discovery, and problem solving as they participated in a series of lab activities designed to help them gain new understandings of the theory of evolution. The success of the unit was evaluated by looking at student work and assessing student levels of understanding, using both qualitative and …

The Distribution Of Beneficial Mutations And Their Pleiotropic Effects, Sarah Gaffney Wrocklage

Master's Theses and Capstones

Understanding the distribution of beneficial mutations is relevant to the understanding of virtually all aspects of the adaptive process. Data describing this distribution are limited, but even less well understood are the pleiotropic effects of adaptive mutations. Yet, the pleiotropy of beneficial mutations may play a role in numerous biological processes. In this thesis, we address this problem by measuring the distribution of beneficial mutations and their pleiotropic effects using mutants of Burkholderia cenocepacia and Escherichia coli. The fitness of each mutant was measured relative to its progenitor in several novel environments. We found that the effects of beneficial mutations …

Genetic Over-Expression Of Cytokeratin 18 In Bovine Luteal Cells: Effects On Intermediate Filament Formation And Fas Ligand-Induced Apoptosis, Jennifer J. Forcina

Master's Theses and Capstones

The receptor Fas and its ligand, FasL, are implicated in apoptosis of luteal cells during regression of the corpus luteum (CL). In some cell types, cytokeratin (CK) 8/18 filaments impair FasL-induced apoptosis. Here, we determined if genetic over-expression of CK18 filaments in luteal cells similarly prevents FasL-induced apoptosis. Luteal cell cultures were prepared from early and late stage bovine CL (day 5 and days 16-18 post-ovulation, respectively). The cells were transduced with media, mock vector containing GFP, or a CK18-containing vector, and then exposed to a cytokine cocktail containing FasL for 24 hours. Transduction of luteal cells with CK18 vector …

Feature Topography And Sound Intensity Level Encoding In Primary Auditory Cortex, Paul Watkins

All Theses and Dissertations (ETDs)

The primary auditory cortex: A1) in mammals is one of the first areas in the neocortex that receives auditory related spiking activity from the thalamus. Because the neocortex is implicated in regulating high-level brain phenomena, such as attention and perception, it is therefore important in regards to these high-level behaviors to understand how sounds are represented and transformed by neuronal circuits in this area. The topographic organization of neuronal responses to auditory features in A1 provides evidence for potential mechanisms and functional roles of this neural circuitry. This dissertation presents results from models of topographic organization supporting the notion that …

Orthotomicus Tridentatus Eggers: Distribution And Biology In Cedar Forests Of Turkey, Mustafa Avci, Oğuzhan Sarikaya

Turkish Journal of Agriculture and Forestry

Orthotomicus tridentatus Eggers, 1921 (Col.: Curculionidae, Scolytinae) is the most important forest pest of cedar stands in Turkey. Yet, very little is known about its distribution and biology. Therefore, the distribution and biological characteristics of O. tridentatus were studied in the Taurus Mountains in southern Turkey between 2006 and 2008. It was determined to be a species common to all cedar forests. The length of adults was between 2.5 and 3.9 mm and the main galleries were 'S' shaped. O. tridentatus was determined to be a monophagus species for Cedrus libani A. Rich. and as endemic to Turkey. It was …

Ngasp - The Nematode Genome Annotation Assessment Project, Avril Coghlan, Tristan J. Fiedler, Sheldon J. Mckay, Paul R. Flicek, Todd W. Harris, Darin Blasiar, Lincoln D. Stein

Biomedical Engineering and Sciences Faculty Publications

While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. Results: The most accurate gene-finders were …

Gene Expression Analysis Of Immobilized Saccharomyces Cerevisiae, Ryan Michael Summers

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Immobilization is an effective method to increase ethanol production, as proven by previous research. Results almost exclusively demonstrate an increase in ethanol production by and decrease in reproduction rate of immobilized Saccharomyces cerevisiae cells. Recently, research has been conducted to determine the cause of this change. The extreme variance in results due to lack of technology makes it difficult to determine the cellular changes induced by immobilization. With the advent of new technology, specifically gene expression analysis, the RNA content of cells can be easily and rapidly analyzed.

S. cerevisiae cells were immobilized in 3% (w/v) calcium alginate beads and …

Hydrological Characterization Of A Riparian Vegetation Zone Using High Resolution Multi-Spectral Airborne Imagery, Osama Zaki Akasheh

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The Middle Rio Grande River (MRGR) is the main source of fresh water for the state of New Mexico. Located in an arid area with scarce local water resources, this has led to extensive diversions of river water to supply the high demand from municipalities and irrigated agricultural activities. The extensive water diversions over the last few decades have affected the composition of the native riparian vegetation by decreasing the area of cottonwood and coyote willow and increasing the spread of invasive species such as Tamarisk and Russian Olives, harmful to the river system, due to their high transpiration rates, …