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Molecular Dynamics Studies Of Nucleic Acids And Ribonucleoprotein Complexes, Tyler James Mulligan

Master's Theses and Capstones

Molecular simulations of protein-nucleic acid complexes, as well as the HIV-1 Trans Activation Response Element (TAR) RNA molecule, were conducted. First, three different molecular dynamics techniques were studied on the molecule HIV-1 TAR RNA. The three techniques studied were classical molecular dynamics, steered molecular dynamics (SMD), and metadynamics. The classic molecular dynamics simulations were used to equilibrate the HIV-1 TAR RNA system, as well as every other system studied in this thesis. The SMD technique was used in order to observe the breaking force of the nucleotide interactions within TAR. This breaking force averaged to about 100pN. The metadynamics technique …

The Investigation Of Microbe-Nematode Interactions, Chelsea K. Crepeau

Honors Theses and Capstones

No abstract provided.

An Investigation Into Nosocomial Infection Using Data Mining, Alexander Rocke

Honors Theses and Capstones

The purpose of this study was to investigate potential risk factors and analyze trends that are associated with nosocomial infection using an inferential statistical methodology that would allow for the identification and future tracking of the aforementioned trends. The raw data on which statistical analyses were performed was collected and aggregated by the National Healthcare Safety Network for the year 2011 (5)

The results of the statistical analyses revealed that many factors should be taken into account when considering the causes of nosocomial infection, in paticular, that the amount of aggregated hours a certain type of ward (burn, medical, surgical, …

Interactions Of Shiga-Like Toxin-2 (Stx-2) From Escherichia Coli O157:H7 And The Bcl-2 Family Of Proteins During Host Cell Programmed Cell Death, Lia K. Jeffrey

Doctoral Dissertations

Stx-2 is a major contributor to the pathogenesis of Escherichia coli 0157:H7. Prior reports suggest that Stx-2 increases necrosis and apoptosis of a variety of host cells including those of endothelial origin as well as immune cells such as neutrophils (156). However, the role Stx-2 plays in delayed apoptosis of neutrophils is not fully understood given that previous studies have shown conflicting results (118, 51). The process of apoptosis is mediated by the Bcl-2 protein family (2, 46, 226). The purpose of this research was to define the molecular mechanisms of Stx-2 and Bcl-2 protein family interactions. These studies examined …

Characterization Of The Expression Profile Of Polyamine Biosynthetic Genes (Spermidine Synthase) And Polyamine Metabolic Regulation In Arabidopsis, Lin Shao

Doctoral Dissertations

Polyamines are ubiquitously distributed cationic compounds, which play important roles in numerous cellular functions in plants. This study was aimed at elaborating the regulation of polyamine biosynthetic gene expression and polyamine metabolism. The organ/tissue specific expression patterns of two genes encoding the polyamine biosynthetic enzyme spermidine synthase ( AtSPDS1 and AtSPDS2) were studied in Arabidopsis at different developmental stages using promoter::reporter approach. The two homologues showed similar ubiquitous expression with subtle differences being observed in certain tissues (e.g. root, siliques, and embryos). Neither transgenic manipulation by over-expression of AtSPDSI alone nor its concomitant expression with genes encoding other biosynthetic enzymes …

Regulation Of The Catalytic And Allosteric Properties Of Photoreceptor Phosphodiesterase (Pde6) By The Glutamic Acid-Rich Protein-2 (Garp2), Wei Yao

Doctoral Dissertations

The photoreceptor phosphodiesterase (PDE6) must be precisely regulated to control the sensitivity, amplitude, and kinetics of the photoresponse during excitation, termination and adaptation to light stimulation in rod and cone photoreceptors. The central hypothesis of this thesis is that one PDE6 binding partner, the glutamic acid-rich protein (GARP2), may regulate PDE6 to reduce its "dark noise", enhance its sensitivity and conserve metabolic energy during rod photoresponse saturation.

The first aim of this research is to better understand the unique biochemical and biophysical characteristics of GARP2 in order to reveal its functional attributes for regulating PDE6 during phototransduction in rod photoreceptors. …

Small Scale Raft Aquaponics: Evaluation Of Hybrid Striped Bass Growth And Plant Uptake Potential, Calvin Grant Diessner

Master's Theses and Capstones

Hybrid striped bass ([male]Morone saxatilis [female] Morone chrysopos) were successfully cultivated in two separate 48 day trials (t1 and t2) with seedlings of lettuce (Lactuca sativa cv. Rex) and pac choi (Brassica rapa cv. Win-Win) within a shared recirculating aquaponic system. It was determined that fish stocking density had no significant effect on the mean yield of lettuce and pac choi biomass in t1. Stocking density did have a significant effect on the elemental nutrients generated within the aquaponic systems. A nutrient deficiency was exhibited by the leaf tissue of pac choi grown with fish stocked at low a density …

Theoretical Analysis Of The Reaction Of Peroxymethyl Radical With Atomic Hydrogen And Of Dibenzofuran With Atomic Chlorine, Mikhail Zhukovskiy

Master's Theses and Capstones

Experimental determination of rate constants for gas phase radical reactions is challenging. When rate constants necessary for modeling complex processes in atmospheric and combustion science are unknown, theoretical predictions are useful. We used Variational Transition State Theory with Multidimensional Tunneling (VTST/MT) with Density Functional Theory (DFT) to calculate the rate constant and isotope effects for reaction between the peroxymethyl radical and the hydrogen atom.

Polychlorinated dibenzofurans (PCDFs) are a group of extremely toxic compounds formed during waste incineration. Currently, their chemical degradation in the atmosphere is poorly understood. While some experimental and theoretical results regarding the reaction of PCDFs with …

Calcium Homeostasis In Escherichia Coli, Muhammad Arif

Doctoral Dissertations

While the role of calcium ions as secondary chemical messengers has been well described in eukaryotic cells, little is known about calcium homeostasis in bacteria at the physiological and molecular level. No calcium influx gene has been identified so far. This dissertation focuses on calcium regulation of gene expression by (i) determining the effects of elevated and depleted calcium levels on global gene expression in wild-type cells (MG1655), (ii) employing transposon mutants (calcium-sensitive) and mutants that are defective in calcium transport, and (iii) performing quantitative analysis of a specific subset of 15 genes to elucidate their possible involvement in calcium …

Keratin 8/18 Filaments: Potential Modulators Of Death Signaling In Ovarian Granulosa Cells, Sarah E. Kinsman

Master's Theses and Capstones

Granulosa cell apoptosis is associated with follicular atresia; but the cellular mechanisms that drive this process, especially its cell specificity, are relatively unknown. Here, we determined that cultured granulosa cells abundantly express K8/K18 filaments and inhibition of protein synthesis enhances Fas-induced apoptosis. In this context, the roles of cFLIP, ERK1/2 and Akt are minimal but conversely, K8/K18 filaments have a prominent role in granulosa cell resistance to Fas-induced apoptosis. Keratin 8/18 filaments in granulosa cells provide a plausible mechanism to avoid Fas-induced apoptosis and this mechanism potentially involves the synthesis of labile proteins. The existence of K8/K18 filaments in granulosa …

Evolutionary Genomics And Ecoligical Interactions Of Biofilm Adaptation, Charles C. Traverse

Master's Theses and Capstones

How diversity evolves and persists in biofilms is essential for understanding much of microbial life, including the uncertain dynamics of chronic infections. We developed a novel biofilm model enabling long-term selection for daily adherence to and dispersal from a plastic bead in a test tube. Focusing on a pathogen of the cystic fibrosis (CF) lung, Burkholderia cenocepacia, we sequenced clones and metagenomes to unravel the mutations and evolutionary forces responsible for adaptation and diversification of a single biofilm community during 1050 generations of selection. The mutational patterns revealed recurrent evolution of biofilm specialists from generalist types and multiple adaptive alleles …

A Model Study Of Adlayer Pattern Formation Of A Linear Molecule On Square And Triangular Lattices, Gennadiy N. Berezutskiy

Master's Theses and Capstones

We have determined patterning and geometric properties of rigid-diatomic-molecular rotors, fixed on (square and triangular) the lattice site modeled by the Morse potential. Zero-K adlayer patterns were enhanced through the implementation of unconstrained multivariable function using derivative-free method (also known as simplex algorithm). Results have been obtained over wide geometry range for adlayer patterns composed of periodically repeated primary cell.

A primary focus of this work was the calculation of adlayer free energies and geometry at the ground state. Those were obtained from conformational search of the primary (2x2) cell to locate geometric configuration, which minimizes the total energy. The …

Identification And Characterization Of Photorhabdus Temperata Mutants Altered In Hemolysis And Virulence, Christine A. Chapman

Master's Theses and Capstones

Photorhabdus temperata is an invertebrate pathogen and nematode symbiont that is commonly used as a biological control agent in the management of commercial crop pests. The focus of this study was to investigate the poorly understood molecular elements involved in the expression of hemolysis and virulence in this bacterium. A 10,000 transposant library was screened using a blood agar plate assay to identify mutants altered in hemolytic activity. A total of 74 mutants displaying defective, delayed, or early hemolysis were identified and subsequently tested for altered virulence in the Greater Waxmoth, Galleria mellonella, using an in vitro mortality assay. Ten …

Analysis Of Arabidopsis Thaliana Protein Phosphatase 2a C Subunit Expression, Megan M. Thompson

Master's Theses and Capstones

Reversible protein phosphorylation is required for presumably most biological pathways. One of the major enzymes involved in eukaryotic dephosphorylation is Protein Phosphatase 2A (PP2A). PP2A is composed of three subunits: A (scaffolding), B (regulatory), and C (catalytic). Our lab is interested in determining the function of the five C subunits (C1, C2, C3, C4 and C5) in Arabidopsis thaliana. We have identified a Na+-induced altered root growth phenotype in c4 mutant plants. The goal of this project was to determine expression of the five C subunit genes throughout the life cycle of Arabidopsis with emphasis on correlating the location of …

Discovering Signaling Events In The Actinorhizal Symbiosis, Nicholas J. Beauchemin

Master's Theses and Capstones

Although the symbiosis between Frankia and actinorhizal host plants has been widely studied, very little is known about the initial molecular interactions. To address this issue, Casuarina cunninghamiana root exudates were collected and tested on Frankia Ccl3. Frankia growth yield was enhanced by root exudates but Frankia could not utilize them as a sole carbon and energy source. Exposure to root exudates caused Frankia hyphal curling and surface property changes in fatty acids and carbohydrates. Pre-exposure to root exudates also decreased the time required for nodule initiation. The results show that root exudates and Frankia physiological changes for symbiosis are …

Identification And Characterization Of Photorhabdus Temperata Mutants Altered In Cell Surface And Symbiosis, Cintia R. Felix

Master's Theses and Capstones

Photorhabdus temperata forms a mutualistic association with the entomopathogenic nematode Heterorhabditis bacteriophora. Nematode growth and development has an obligate requirement for the bacterial symbiont. The objective of this study was to identify and understand cell surface properties that are required for symbiosis. A previously generated library of 10,000 P. temperata transposon mutants was screened for altered surface properties via a calcofluor dye-binding assay. Seventeen mutants were identified and tested in vitro for symbiosis. Key mutants were tested for symbiosis and insect pathogenesis in vivo with Galleria mellonella larvae. Five mutants showed at least a 10-fold decrease of IJ yield. Four …

Truncated Mortalin In Animal Cancer, Katrina K. Olson

Master's Theses and Capstones

Hematopoetic neoplasia or clam hemocyte cancer (a leukemia-like disease) has been studied in a number of bivalve molluscs for the last 20 years. Recent molecular studies of the hemocytes of the soft shell clam, Mya arenaria, have demonstrated an interaction between p53 and mortalin, the mitochondrial Hsp70. The former protein is intimately involved in the initiation of cell-cycle arrest, apoptosis, DNA repair, and cell differentiation. In cancerous clams, wild-type p53 is sequestered in hemocyte cytoplasm by mortalin and cannot be translocated to the nucleus. This is critical because although p53 is functions properly, it is unable to enter the nucleus …

Genomic Resource Development For A Diploid Mint: Mentha Longifolia, Zahra Hadadian

Master's Theses and Capstones

This research project aimed to develop genomic resources needed to enable construction of a genetic linkage map of the diploid mint species Mentha longifolia. Such a map would facilitate identification of plant genes involved in resistance to Verticillium fungal infection. For this purpose, a small genomic library was constructed from germplasm accession CMEN 585, 279 genomic inserts were sequenced and annotated and 19 PCR primer pairs were designed and tested on two resistant and two susceptible accessions. The Cleaved Modified Polymorphic Sequence (CAPS) method of molecular marker genotyping was found to detect little variation between crossing parents CMEN 585 (resistant) …

Regulation Of Photoreceptor Phosphodiesterase By Prenyl Binding Protein And By Other Interacting Proteins In Photoreceptor Cells, Hannah J. Gitschier

Master's Theses and Capstones

Photoreceptor phosphodiesterase (PDE6) is a central component of the visual pathway. While initial PDE6 activation following light stimulation of photoreceptors is well understood, regulation of PDE6 during recovery and light adaptation may require additional components that interact with PDE6. Two approaches were taken to characterize these potential interactions. The first explored the interaction of PDE6 with prenyl binding protein (PrBP/delta) and demonstrated that changes in membrane localization of PDE6 may occur during light adaptation as a result of association with PrBP/delta. The second approach characterized the PDE6 "interactome" by a mass spectrometric identification of 75 proteins that co-purify with PDE6 …

Microbial Interactions With Oysters From The Great Bay Estuary: Characterization Of Endemic Vibrio Choleraeand Oyster Metagenetics, Brian Michael Schuster

Master's Theses and Capstones

Within the last two decades the number of gastroenteritis seafood-borne outbreaks due to Vibrio species has increased. These infections are usually caused by the consumption of raw or undercooked shellfish. I took two approaches to describe the ecology of Vibrios in the Great Bay Estuary, Durham, New Hampshire. First, I performed a phenotypic and multi-locus sequence analysis of 31 V. cholerae strains isolated from oysters, water and sediment in 2008 and 2009. I concluded that the V. cholerae population is endemic, diverse and highly recombinatory, but none of the isolates contain the virulence markers indicative of clinical strains. Next, I …

Using Pentaploids As Tools For Studying Genomic Composition And Allele Transmission Patterns In Octoploid Fragaria, Elizabeth Poulsen

Master's Theses and Capstones

A unique pentaploid population of Fragaria (strawberry) was developed to gain insight into octoploid genome composition and allele transmission patterns. This population was produced by crossing representatives of two divergent subspecies of octoploid F. virginiana and then by crossing an octoploid hybrid plant with diploid F. vesca. To enable examination of allele transmission patterns, the intergenic region of the gRGA1-Subtilase gene pair locus was amplified, and PCR products were cloned, sequenced, and compared to define the allele composition of the hybrid octoploid. The sequencing data revealed three distinct major haplotypes and additional subtypes. The pentaploids were genotyped utilizing the FEL-CAPS …

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 …

A System For Automating The Interpretation Of Analytical Ultracentrifuge Data, Bradley W. Langhorst

Doctoral Dissertations

In order to accelerate the development of knowledge about protein associations, further improvements to acquisition, sharing, and analysis of Analytical Ultracentrifugation (AU) data must be made. XML data formats have been defined to allow complete exchange of the information associated with an AU experiment. Extensible formats to record solution identity, instrument setup parameters, acquired data, and analysis of that data have been developed. A normalized relational database to allow storage and searching of this data has also been created. A computer program called PANDaS (Protein Association Network Data Server) was built to interact with any software conforming to the data …

Spawning Stock Identification Of Atlantic Cod (Gadus Morhua) In Us Waters Using Pan I And Microsatellite Genetic Markers, Timothy S. Breton

Master's Theses and Capstones

Most Atlantic cod (Gadus morhua) stocks within U.S. waters are currently in decline as a result of overexploitation and fishing pressure from commercial fisheries. A better understanding of the genetic structure of cod populations is essential to identify stocks for successful fisheries management. In this study, the genetic structure of cod from major temporally and geographically distinct spawning grounds in U.S. waters was investigated. Adult and juvenile cod were sampled from aggregations within the Gulf of Maine, Georges Bank, and southern New England waters in cooperation with commercial fishermen and state fishery biologists. Caudal fin clips were collected and analyzed …

Studies Of Verticillium Wilt And Characterization Of Candidate Verticillium Wilt Resistance Genes In The Mint Species Mentha Longifolia (L) Huds, Kelly Jean Vining

Doctoral Dissertations

To investigate the genetic basis of verticillium wilt resistance in mint (Mentha L., Lamiaceae), wild-collected germplasm obtained from the United States Department of Agriculture was employed to develop breeding populations for wilt resistance screening and molecular genetic study, including cloning of candidate verticillium wilt resistance genes.

A collection of fourteen Mentha longifolia accessions from Europe, Asia and South Africa was analyzed for morphological traits, oil composition, and verticillium wilt resistance. In addition, a preliminary molecular diversity assessment was conducted utilizing randomly amplified polymorphic DNA (RAPD) markers. The accessions were found to be diverse regarding all observed traits and the South …

Glycoprotein Hormone Receptors In Sea Lamprey (Petromyzon Marinus): Identification, Characterization And Implications For The Evolution Of The Vertebrate Hypothalamic-Pituitary-Gonadal/Thyroid Axes, Mihael Freamat

Doctoral Dissertations

The vertebrate hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) endocrine axes involve specific interaction between pituitary glycoprotein hormones GpH (lutropin LH, follitropin FSH, thyrotropin TSH) and glycoprotein hormone receptors GpH-R (LH-R, FSH-R and TSH-R respectively).

GpHs and GpH-Rs originate in a common ancestral ligand/receptor pair. Their duplications were followed by divergent evolution resulting in the emergence of a novel, pituitary/peripheral gland control level. It is estimated that this occurred more than 500 million years ago (mya), before or concomitant with the divergence of the jawed vertebrates (Gnathostomes) lineage from their jawless (Agnathan) ancestors. This coincides with the estimated time of divergence of …

The Development Of Tools To Allow Genetic And Genomic Analysis Of Frankia, Tania Rawnsley Spenlinhauer

Doctoral Dissertations

Frankia, a nitrogen-fixing actinomycete, forms a symbiotic association with a variety of woody dicotyledonous plants. The lack of standard genetic tools for this important bacterium has hindered studies on the molecular biology of this symbiosis. We are interested in developing tools for the genetic analysis of Frankia physiology and its interactions with its host plants. Our approach has focused on the development of a physical and genetic map of the Frankia chromosome by macrorestriction analysis. Agarose-embedded chromosomal DNA plugs were prepared from three Frankia isolates: Eul1c, EAN1pec and Ccl3. The genome sizes of the three strains were determined by pulse-field …

The Function Of Pab1 In Translation And In Puf3 Dependent Deadenylation, Darren J. Lee

Doctoral Dissertations

The involvement of the poly(A)-binding protein (PAB1) in deadenylation and translation is well known. How PAB1 inhibits deadenylation and promotes translation is not well understood. I have analyzed PAB1 variants, containing entire domain deletions and substitutions of yeast residues with human residues. Chapter I discusses and provides in vivo translation rates of strains containing PAB1 variants, defects in mRNA degradation proteins, and defects in translation components. In chapter II, I address the role of PAB1 in regulated deadenylation. For this analysis I studied the effect of PUF3, a member of the PUF family of proteins that bind specific 3' UTR …

Constitutive Expression Of Jagged-1 In 3t3-L1 Preadipocytes Suppresses Adipogenesis And Adipose Tissue Development, Jennifer Allen

Master's Theses and Capstones

The Notch signaling pathway regulates adipogenesis. To determine specific effects the Notch ligand Jagged-1 has on the regulation of adipogenesis, we transfected 3T3-L1 preadipocytes with either a constitutively expressed full-length human Jagged-1 construct or an empty vector control. These cells were grown in conditions promoting differentiation and then evaluated for lipid accumulation and gene expression. To test the role of Jagged-1 in adipose tissue development in vivo, transfected cells were examined for their ability to form fat pads after injection into nude mice. In vitro, cells constitutively expressing Jagged-1 accumulated less lipid and exhibited a delay in adipocyte protein expression. …

Mhc (B) Complex Recombinant Immune Response, Nicole Gay Wilkinson

Master's Theses and Capstones

Recombination between chicken major histocompatibility complex (MHC) class I B-F and class IV B-G genes has enabled more precise identification of genes controlling immune responses. Congenic lines, each containing a unique MHC recombinant, were developed with 99.9% genetic uniformity to inbred Line UCD 003 (B17B17). A new recombinant, R13 (BF17-BG23), originated in the tenth backcross generation for R1 (BF24-BG23). Two experiments tested the R13 immune response to bovine red blood .cells (BRBC) and Rous sarcoma virus (RSV).

A single R13B17 sire mated to five R131317 dams produced progeny segregating for R13R13, R13B17, and B17B17 genotypes. These progeny were injected with …