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(1 - 7 of 7)
- Title
- MODELING AND PARTITIONING THE NUCLEOTIDE EVOLUTIONARY PROCESS FOR PHYLOGENETIC AND COMPARATIVE GENOMIC INFERENCE.
- Creator
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Castoe, Todd, Parkinson, Christopher, University of Central Florida
- Abstract / Description
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The transformation of genomic data into functionally relevant information about the composition of biological systems hinges critically on the field of computational genome biology, at the core of which lies comparative genomics. The aim of comparative genomics is to extract meaningful functional information from the differences and similarities observed across genomes of different organisms. We develop and test a novel framework for applying complex models of nucleotide evolution to solve...
Show moreThe transformation of genomic data into functionally relevant information about the composition of biological systems hinges critically on the field of computational genome biology, at the core of which lies comparative genomics. The aim of comparative genomics is to extract meaningful functional information from the differences and similarities observed across genomes of different organisms. We develop and test a novel framework for applying complex models of nucleotide evolution to solve phylogenetic and comparative genomic problems, and demonstrate that these techniques are crucial for accurate comparative evolutionary inferences. Additionally, we conduct an exploratory study using vertebrate mitochondrial genomes as a model to identify the reciprocal influences that genome structure, nucleotide evolution, and multi-level molecular function may have on one another. Collectively this work represents a significant and novel contribution to accurately modeling and characterizing patterns of nucleotide evolution, a contribution that enables the enhanced detection of patterns of genealogical relationships, selection, and function in comparative genomic datasets. Our work with entire mitochondrial genomes highlights a coordinated evolutionary shift that simultaneously altered genome architecture, replication, nucleotide evolution and molecular function (of proteins, RNAs, and the genome itself). Current research in computational biology, including the advances included in this dissertation, continue to close the gap that impedes the transformation of genomic data into powerful tools for the analysis and understanding of biological systems function.
Show less - Date Issued
- 2007
- Identifier
- CFE0001548, ucf:47138
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0001548
- Title
- PHARMACOGENOMIC MANAGEMENT OF FAMILIAL HYPERCHOLESTEROLEMIA: AN INTEGRATIVE REVIEW OF THE LITERATURE.
- Creator
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Skibo, Brian V., Bushy, Angeline, Kubiet, Leslee, University of Central Florida
- Abstract / Description
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The purpose of this thesis is to examine familial hypercholesterolemia (FH) and emerging pharmacogenomics therapies that propose to lower serum low density lipid (LDL) levels. The search of various data bases resulted in nine research articles being selected for review. Syntheses of the articles suggest emerging phamacogenomic drug therapy can improve treatment outcomes for individuals with a diagnosis of FH. The Human Genome Project (HGP) has had far reaching applications for genomic...
Show moreThe purpose of this thesis is to examine familial hypercholesterolemia (FH) and emerging pharmacogenomics therapies that propose to lower serum low density lipid (LDL) levels. The search of various data bases resulted in nine research articles being selected for review. Syntheses of the articles suggest emerging phamacogenomic drug therapy can improve treatment outcomes for individuals with a diagnosis of FH. The Human Genome Project (HGP) has had far reaching applications for genomic technologies and pharmacagenomic interventions, tailored to human conditions associated with select genomic traits. Synthesis of nine research articles demonstrate that little is known on the topic and reveals extensive gaps in the evidence. This thesis concludes with implications for nursing education, practice, policy and research along with limitations are noted.
Show less - Date Issued
- 2016
- Identifier
- CFH2000076, ucf:45544
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFH2000076
- Title
- THE ACQUISITION OF STUDENT NURSES' KNOWLEDGE OF GENETICS AND GENOMICS AND ATTITUDES TOWARD THE APPLICATION OF THEIR KNOWLEDGE IN CLINICAL PRACTICE.
- Creator
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Munroe, Theresa, Loerzel, Victoria, University of Central Florida
- Abstract / Description
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BACKGROUND: Nurses have the opportunity to bring a unique perspective to genetic and genomic healthcare through their emphasis of health promotion, prevention, screening, caring, and patient, family, and community relationships. Nurses are expected to have genetic and genomic knowledge that can be integrated into clinical practice. However, researchers today are finding nursing students are not competent or comfortable in the clinical applications of genetics and genomics, even though these...
Show moreBACKGROUND: Nurses have the opportunity to bring a unique perspective to genetic and genomic healthcare through their emphasis of health promotion, prevention, screening, caring, and patient, family, and community relationships. Nurses are expected to have genetic and genomic knowledge that can be integrated into clinical practice. However, researchers today are finding nursing students are not competent or comfortable in the clinical applications of genetics and genomics, even though these students will soon be working in healthcare as it advances in these fields. The purpose of this research was to evaluate the genetic and genomic knowledge of nursing undergraduate students and explore their attitudes about using this knowledge in practice. METHOD: A pre- and posttest design was used. Student knowledge was measured online using the Genomic Nursing Concept Inventory (GNCI) in both tests. Demographic questions were included in the pretest and questions regarding attitudes toward comfort and readiness to apply that knowledge were included in the posttest. The pretest was administered at the beginning of the Spring 2014 semester. The posttest was administered at the end of the same semester, after the nursing students received the majority of genetic and genomic instruction from their program's curriculum. Descriptive statistics were used to examine all data. Total and subscale knowledge scores on the GNCI were computed for each test. A paired t-test was used to compare pre- and post-GNCI total and subscale scores. Correlations were calculated at both time points. A Spearman correlation was used to examine the relationship between prior experience with genetic education or exposure to people with a genetic condition and total pre-score knowledge on the pretest. For the posttest, a total attitude score was calculated to examine the relationship between attitude and post total knowledge scores using a Pearson's r correlation. FINDINGS: 109 undergraduate junior nursing students participated. Gains in total and subscale knowledge between the pre- and posttest were statistically significant (p [less than] 0.05), except for the Mutations subscale. For the pretest GNCI, the average mean score was 45%, which improved to 50% at the time of the posttest. Lowest scoring items were in the Genome Basics subscale, whereas highest scoring items were found within the Inheritance subscale for the posttest. Mean total attitude scores were 28.33 (SD = 5.17) indicating students had a relatively positive attitude towards using their knowledge base in practice. The majority of students (87.1%) agreed that it is important for the nurse to incorporate genetic and genomic knowledge into clinical practice although only 34.9% felt ready to do so. DISCUSSION: Genetics and genomic knowledge and preparedness were low among nursing students. This demonstrates a need for more integration of genetic and genomic content within nursing curriculum, including a review of basic concepts. Nurses are expected to perform comprehensive health assessments by incorporating knowledge of genetic, environmental, and genomic influences and risk factors. Lack of a basic understanding could lead to patient consequences related to inadequate risk assessment, referrals for genetic counseling, and patient education.
Show less - Date Issued
- 2014
- Identifier
- CFH0004648, ucf:45290
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFH0004648
- Title
- Computational Methods for Comparative Non-coding RNA Analysis: From Structural Motif Identification to Genome-wide Functional Classification.
- Creator
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Zhong, Cuncong, Zhang, Shaojie, Hu, Haiyan, Hua, Kien, Li, Xiaoman, University of Central Florida
- Abstract / Description
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Non-coding RNA (ncRNA) plays critical functional roles such as regulation, catalysis, and modification etc. in the biological system. Non-coding RNAs exert their functions based on their specific structures, which makes the thorough understanding of their structures a key step towards their complete functional annotation. In this dissertation, we will cover a suite of computational methods for the comparison of ncRNA secondary and 3D structures, and their applications to ncRNA molecular...
Show moreNon-coding RNA (ncRNA) plays critical functional roles such as regulation, catalysis, and modification etc. in the biological system. Non-coding RNAs exert their functions based on their specific structures, which makes the thorough understanding of their structures a key step towards their complete functional annotation. In this dissertation, we will cover a suite of computational methods for the comparison of ncRNA secondary and 3D structures, and their applications to ncRNA molecular structural annotation and their genome-wide functional survey.Specifically, we have contributed the following five computational methods. First, we have developed an alignment algorithm to compare RNA structural motifs, which are recurrent RNA 3D structural fragments. Second, we have improved upon the previous alignment algorithm by incorporating base-stacking information and devise a new branch-and-bond algorithm. Third, we have developed a clustering pipeline for RNA structural motif classification using the above alignment methods. Fourth, we have generalized the clustering pipeline to a genome-wide analysis of RNA secondary structures. Finally, we have devised an ultra-fast alignment algorithm for RNA secondary structure by using the sparse dynamic programming technique.A large number of novel RNA structural motif instances and ncRNA elements have been discovered throughout these studies. We anticipate that these computational methods will significantly facilitate the analysis of ncRNA structures in the future.
Show less - Date Issued
- 2013
- Identifier
- CFE0004966, ucf:49580
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004966
- Title
- BIOINFORMATIC ANALYSIS OF SOLANACEAE CHLOROPLAST GENOMES AND CHARACTERIZATION OF AN ARABIDOPSIS PROTEIN DISULFIDE ISOMERASE IN TRANSGENIC TOBACCO CHLOROPLASTS.
- Creator
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Grevich, Justin, Daniell, Henry, University of Central Florida
- Abstract / Description
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Throughout history, traditional plant breeding has been used to provide resistance to pests, disease and other forms of environmental stress, as well as to increase yield and improve upon quality and processing attributes. Over the last decade, the advancement in sequencing technology and bioinformatic analysis has unleashed a wealth of knowledge about chloroplast genetic organization and evolution. The lack of complete plastid genome sequences is one of the major limitations in advancing...
Show moreThroughout history, traditional plant breeding has been used to provide resistance to pests, disease and other forms of environmental stress, as well as to increase yield and improve upon quality and processing attributes. Over the last decade, the advancement in sequencing technology and bioinformatic analysis has unleashed a wealth of knowledge about chloroplast genetic organization and evolution. The lack of complete plastid genome sequences is one of the major limitations in advancing plastid genetic engineering to other useful crops. This is due to the fact that plastid genome sequences are essential for the identification of endogenous regulatory sequences and optimal sites for homologous recombination. Analysis of four Solanaceae genomes revealed significant genetic modifications in both coding and non-coding regions. Repeat analysis with Reputer revealed 33 to 45 direct and inverted repeats ? 30bp with at least 90% homology. All but five of the 42 repeats shared among all four genomes were located in the exact same genes or intergenic regions, suggesting a functional role. Intergenic analysis found four regions that are 100 percent identical in all four Solanaceae genomes. Such highly conserved intergenic regions are ideal targets for multi-species transformation cassettes. Protein disulfide isomerases (PDI) are a family of proteins known to function as molecular chaperones and aid in the formation of disulfide bonds during protein folding. They contain at least one thioredoxin domain used for the formation, isomerization, and reduction/oxidation of disulfide bonds. Bioinformatic analysis identified 13 PDI-like (PDIL) proteins found in Arabidopsis that contain at least one thioredoxin domain. In addition to the above-mentioned characteristics, PDIs have been shown to be directly involved in the translational regulation of the psbA mRNA in response to light and could potentially increase the efficiency of chloroplast engineering in plants. Human serum albumin (HSA) requires 17 disulfide bonds to be properly folded and is an ideal candidate for assessing the disulfide bond formation, protein folding, and other chaperone-like characteristics of PDIL proteins. Therefore, I have coexpressed HSA in order to further characterize an Arabidopsis PDIL protein, atPDIL5-4, and in particular, the redox control of the psbA 5'UTR. Interestingly, the polyclonal antibody used for identifying the PDIL protein cross-reacted and identified other proteins, but not the transgenic atPDIL5-4. Results of these investigations will be presented.
Show less - Date Issued
- 2006
- Identifier
- CFE0001083, ucf:46776
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0001083
- Title
- (UN)NATURAL BODIES, ENDANGERED SPECIES, AND EMBODIED OTHERS IN MARGARET ATWOOD'S ORYX AND CRAKE.
- Creator
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Galbreath, Marcy, Murphy, Patrick, University of Central Florida
- Abstract / Description
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The developing knowledge of life sciences is at the crux of Margaret Atwood's Oryx and Crake as she examines human promise gone awry in a near-future dystopia. This thesis examines aspects of posthumanism, ecocriticism, and feminism in the novel's scientific, cultural, and environmental projections. Through the trope of extinction, Atwood's text foregrounds the effects of human exceptionalism and instrumentalism in relation to the natural world, and engenders an analysis of human...
Show moreThe developing knowledge of life sciences is at the crux of Margaret Atwood's Oryx and Crake as she examines human promise gone awry in a near-future dystopia. This thesis examines aspects of posthumanism, ecocriticism, and feminism in the novel's scientific, cultural, and environmental projections. Through the trope of extinction, Atwood's text foregrounds the effects of human exceptionalism and instrumentalism in relation to the natural world, and engenders an analysis of human identity through its biological and cultural aspects. Extinction thus serves as a metaphor for both human development and human excesses, redefining the idea of human within the context of vulnerable species. Oryx and Crake reveals humanity's organic connections with non-human others through interspecies gene-splicing and the ensuing hybridity. In this perspective, Atwood's text provides a dialogue on humankind's alienation from the natural world and synchronic connections to the animal other, and poses timely questions for twenty-first century consumerism, globalism, and humanist approaches to nature. The loss of balance provoked by the apocalyptic situation in Oryx and Crake challenges commonplace attitudes toward beneficial progress. This imbalance signals the need for a new narrative: A consilient reimagining of humanity's role on earth as an integrated organism rather than an intellectual singularity.
Show less - Date Issued
- 2010
- Identifier
- CFE0003227, ucf:48552
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003227
- Title
- The Influence of Alloying Additions on Diffusion and Strengthening of Magnesium.
- Creator
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Kammerer, Catherine, Sohn, Yongho, Coffey, Kevin, Challapalli, Suryanarayana, Gordon, Ali, University of Central Florida
- Abstract / Description
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Magnesium alloys are being developed as advanced materials for structural applications where reduced weight is a primary motivator. Alloying can enhance the properties of magnesium without significantly affecting its density. Essential to alloy development, inclusive of processing parameters, is knowledge of thermodynamic, kinetic, and mechanical behavior of the alloy and its constituents. Appreciable progress has been made through conventional development processes, but to accelerate...
Show moreMagnesium alloys are being developed as advanced materials for structural applications where reduced weight is a primary motivator. Alloying can enhance the properties of magnesium without significantly affecting its density. Essential to alloy development, inclusive of processing parameters, is knowledge of thermodynamic, kinetic, and mechanical behavior of the alloy and its constituents. Appreciable progress has been made through conventional development processes, but to accelerate development of suitable wrought Mg alloys, an integrated Materials Genomic approach must be taken where thermodynamics and diffusion kinetic parameters form the basis of alloy design, process development, and properties-driven applications.The objective of this research effort is twofold: first, to codify the relationship between diffusion behavior, crystal structure, and mechanical properties; second, to provide fundamental data for the purpose of wrought Mg alloy development. Together, the principal deliverable of this work is an advanced understanding of Mg systems. To that end, the objective is accomplished through an aggregate of studies. The solid-to-solid diffusion bonding technique is used to fabricate combinatorial samples of Mg-Al-Zn ternary and Mg-Al, Mg-Zn, Mg-Y, Mg-Gd, and Mg-Nd binary systems. The combinatorial samples are subjected to structural and compositional characterization via Scanning Electron Microscopy with X-ray Energy Dispersive Spectroscopy, Electron Probe Microanalysis, and analytical Transmission Electron Microscopy. Interdiffusion in binary Mg systems is determined by Sauer-Freise and Boltzmann-Matano methods. Kirkaldy's extension of the Boltzmann-Matano method, on the basis of Onsager's formalism, is employed to quantify the main- and cross-interdiffusion coefficients in ternary Mg solid solutions. Impurity diffusion coefficients are determined by way of the Hall method. The intermetallic compounds and solid solutions formed during diffusion bonding of the combinatorial samples are subjected to nanoindentation tests, and the nominal and compositionally dependent mechanical properties are extracted by the Oliver-Pharr method.In addition to bolstering the scantly available experimental data and first-principles computations, this work delivers several original contributions to the state of Mg alloy knowledge. The influence of Zn concentration on Al impurity diffusion in binary Mg(Zn) solid solution is quantified to impact both the pre-exponential factor and activation energy. The main- and cross-interdiffusion coefficients in the ternary Mg solid solution of Mg-Al-Zn are reported wherein the interdiffusion of Zn is shown to strongly influence the interdiffusion of Mg and Al. A critical examination of rare earth element additions to Mg is reported, and a new phase in thermodynamic equilibrium with Mg-solid solution is identified in the Mg-Gd binary system. It is also demonstrated that Mg atoms move faster than Y atoms. For the first time the mechanical properties of intermetallic compounds in several binary Mg systems are quantified in terms of hardness and elastic modulus, and the influence of solute concentration on solid solution strengthening in binary Mg alloys is reported. The most significant and efficient solid solution strengthening is achieved by alloying Mg with Gd. The Mg-Nd and Mg-Gd intermetallic compounds exhibited better room temperature creep resistance than intermetallic compounds of Mg-Al. The correlation between the concentration dependence of mechanical properties and atomic diffusion is deliberated in terms of electronic nature of the atomic structure.
Show less - Date Issued
- 2015
- Identifier
- CFE0005815, ucf:50043
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0005815
