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Title: THE PROTEOMICS APPROACH TO EVOLUTIONARY COMPUTATION: AN ANALYSIS OF PROTEOME-BASED LOCATION INDEPENDENT REPRESENTATIONS BASEDON THE PROPORTIONAL GENETIC ALGORITHM.
Creator: Garibay, Ivan, Wu, Annie, University of Central Florida
Abstract / Description: As the complexity of our society and computational resources increases, so does the complexity of the problems that we approach using evolutionary search techniques. There are recent approaches to deal with the problem of scaling evolutionary methods to cope with highly complex difficult problems. Many of these approaches are biologically inspired and share an underlying principle: a problem representation based on basic representational building blocks that interact and self-organize into...
Show moreAs the complexity of our society and computational resources increases, so does the complexity of the problems that we approach using evolutionary search techniques. There are recent approaches to deal with the problem of scaling evolutionary methods to cope with highly complex difficult problems. Many of these approaches are biologically inspired and share an underlying principle: a problem representation based on basic representational building blocks that interact and self-organize into complex functions or designs. The observation from the central dogma of molecular biology that proteins are the basic building blocks of life and the recent advances in proteomics on analysis of structure, function and interaction of entire protein complements, lead us to propose a unifying framework of thought for these approaches: the proteomics approach. This thesis propose to investigate whether the self-organization of protein analogous structures at the representation level can increase the degree of complexity and ``novelty'' of solutions obtainable using evolutionary search techniques. In order to do so, we identify two fundamental aspects of this transition: (1) proteins interact in a three dimensional medium analogous to a multiset; and (2) proteins are functional structures. The first aspect is foundational for understanding of the second. This thesis analyzes the first aspect. It investigates the effects of using a genome to proteome mapping on evolutionary computation. This analysis is based on a genetic algorithm (GA) with a string to multiset mapping that we call the proportional genetic algorithm (PGA), and it focuses on the feasibility and effectiveness of this mapping. This mapping leads to a fundamental departure from typical EC methods: using a multiset of proteins as an intermediate mapping results in a \emph{completely location independent} problem representation where the location of the genes in a genome has no effect on the fitness of the solutions. Completely location independent representations, by definition, do not suffer from traditional EC hurdles associated with the location of the genes or positional effect in a genome. Such representations have the ability to self-organize into a genomic structure that appears to favor positive correlations between form and quality of represented solutions. Completely location independent representations also introduce new problems of their own such as the need for large alphabets of symbols and the theoretical need for larger representation spaces than traditional approaches. Overall, these representations perform as well or better than traditional representations and they appear to be particularly good for the class of problems involving proportions or multisets. This thesis concludes that the use of protein analogous structures as an intermediate representation in evolutionary computation is not only feasible but in some cases advantageous. In addition, it lays the groundwork for further research on proteins as functional self-organizing structures capable of building increasingly complex functionality, and as basic units of problem representation for evolutionary computation.
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Date Issued: 2004
Identifier: CFE0000311, ucf:46307
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0000311

Title: MULTISENSOR FUSION REMOTE SENSING TECHNOLOGY FOR ASSESSING MULTITEMPORAL RESPONSES IN ECOHYDROLOGICAL SYSTEMS.
Creator: Makkeasorn, Ammarin, Chang, Ni-Bin, University of Central Florida
Abstract / Description: Earth ecosystems and environment have been changing rapidly due to the advanced technologies and developments of humans. Impacts caused by human activities and developments are difficult to acquire for evaluations due to the rapid changes. Remote sensing (RS) technology has been implemented for environmental managements. A new and promising trend in remote sensing for environment is widely used to measure and monitor the earth environment and its changes. RS allows large-scaled measurements...
Show moreEarth ecosystems and environment have been changing rapidly due to the advanced technologies and developments of humans. Impacts caused by human activities and developments are difficult to acquire for evaluations due to the rapid changes. Remote sensing (RS) technology has been implemented for environmental managements. A new and promising trend in remote sensing for environment is widely used to measure and monitor the earth environment and its changes. RS allows large-scaled measurements over a large region within a very short period of time. Continuous and repeatable measurements are the very indispensable features of RS. Soil moisture is a critical element in the hydrological cycle especially in a semiarid or arid region. Point measurement to comprehend the soil moisture distribution contiguously in a vast watershed is difficult because the soil moisture patterns might greatly vary temporally and spatially. Space-borne radar imaging satellites have been popular because they have the capability to exhibit all weather observations. Yet the estimation methods of soil moisture based on the active or passive satellite imageries remain uncertain. This study aims at presenting a systematic soil moisture estimation method for the Choke Canyon Reservoir Watershed (CCRW), a semiarid watershed with an area of over 14,200 km2 in south Texas. With the aid of five corner reflectors, the RADARSAT-1 Synthetic Aperture Radar (SAR) imageries of the study area acquired in April and September 2004 were processed by both radiometric and geometric calibrations at first. New soil moisture estimation models derived by genetic programming (GP) technique were then developed and applied to support the soil moisture distribution analysis. The GP-based nonlinear function derived in the evolutionary process uniquely links a series of crucial topographic and geographic features. Included in this process are slope, aspect, vegetation cover, and soil permeability to compliment the well-calibrated SAR data. Research indicates that the novel application of GP proved useful for generating a highly nonlinear structure in regression regime, which exhibits very strong correlations statistically between the model estimates and the ground truth measurements (volumetric water content) on the basis of the unseen data sets. In an effort to produce the soil moisture distributions over seasons, it eventually leads to characterizing local- to regional-scale soil moisture variability and performing the possible estimation of water storages of the terrestrial hydrosphere. A new evolutionary computational, supervised classification scheme (Riparian Classification Algorithm, RICAL) was developed and used to identify the change of riparian zones in a semi-arid watershed temporally and spatially. The case study uniquely demonstrates an effort to incorporating both vegetation index and soil moisture estimates based on Landsat 5 TM and RADARSAT-1 imageries while trying to improve the riparian classification in the Choke Canyon Reservoir Watershed (CCRW), South Texas. The CCRW was selected as the study area contributing to the reservoir, which is mostly agricultural and range land in a semi-arid coastal environment. This makes the change detection of riparian buffers significant due to their interception capability of non-point source impacts within the riparian buffer zones and the maintenance of ecosystem integrity region wide. The estimation of soil moisture based on RADARSAT-1 Synthetic Aperture Radar (SAR) satellite imagery as previously developed was used. Eight commonly used vegetation indices were calculated from the reflectance obtained from Landsat 5 TM satellite images. The vegetation indices were individually used to classify vegetation cover in association with genetic programming algorithm. The soil moisture and vegetation indices were integrated into Landsat TM images based on a pre-pixel channel approach for riparian classification. Two different classification algorithms were used including genetic programming, and a combination of ISODATA and maximum likelihood supervised classification. The white box feature of genetic programming revealed the comparative advantage of all input parameters. The GP algorithm yielded more than 90% accuracy, based on unseen ground data, using vegetation index and Landsat reflectance band 1, 2, 3, and 4. The detection of changes in the buffer zone was proved to be technically feasible with high accuracy. Overall, the development of the RICAL algorithm may lead to the formulation of more effective management strategies for the handling of non-point source pollution control, bird habitat monitoring, and grazing and live stock management in the future. Soil properties, landscapes, channels, fault lines, erosion/deposition patches, and bedload transport history show geologic and geomorphologic features in a variety of watersheds. In response to these unique watershed characteristics, the hydrology of large-scale watersheds is often very complex. Precipitation, infiltration and percolation, stream flow, plant transpiration, soil moisture changes, and groundwater recharge are intimately related with each other to form water balance dynamics on the surface of these watersheds. Within this chapter, depicted is an optimal site selection technology using a grey integer programming (GIP) model to assimilate remote sensing-based geo-environmental patterns in an uncertain environment with respect to some technical and resources constraints. It enables us to retrieve the hydrological trends and pinpoint the most critical locations for the deployment of monitoring stations in a vast watershed. Geo-environmental information amassed in this study includes soil permeability, surface temperature, soil moisture, precipitation, leaf area index (LAI) and normalized difference vegetation index (NDVI). With the aid of a remote sensing–based GIP analysis, only five locations out of more than 800 candidate sites were selected by the spatial analysis, and then confirmed by a field investigation. The methodology developed in this remote sensing-based GIP analysis will significantly advance the state-of-the-art technology in optimum arrangement/distribution of water sensor platforms for maximum sensing coverage and information-extraction capacity. Effective water resources management is a critically important priority across the globe. While water scarcity limits the uses of water in many ways, floods also have caused so many damages and lives. To more efficiently use the limited amount of water or to resourcefully provide adequate time for flood warning, the results have led us to seek advanced techniques for improving streamflow forecasting. The objective of this section of research is to incorporate sea surface temperature (SST), Next Generation Radar (NEXRAD) and meteorological characteristics with historical stream data to forecast the actual streamflow using genetic programming. This study case concerns the forecasting of stream discharge of a complex-terrain, semi-arid watershed. This study elicits microclimatological factors and the resultant stream flow rate in river system given the influence of dynamic basin features such as soil moisture, soil temperature, ambient relative humidity, air temperature, sea surface temperature, and precipitation. Evaluations of the forecasting results are expressed in terms of the percentage error (PE), the root-mean-square error (RMSE), and the square of the Pearson product moment correlation coefficient (r-squared value). The developed models can predict streamflow with very good accuracy with an r-square of 0.84 and PE of 1% for a 30-day prediction.
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Date Issued: 2007
Identifier: CFE0001767, ucf:47267
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0001767

Title: ALAYZING THE EFFECTS OF MODULARITY ON SEARCH SPACES.
Creator: Garibay, Ozlem, Wu, Annie, University of Central Florida
Abstract / Description: We are continuously challenged by ever increasing problem complexity and the need to develop algorithms that can solve complex problems and solve them within a reasonable amount of time. Modularity is thought to reduce problem complexity by decomposing large problems into smaller and less complex subproblems. In practice, introducing modularity into evolutionary algorithm representations appears to improve search performance; however, how and why modularity improves performance is not well...
Show moreWe are continuously challenged by ever increasing problem complexity and the need to develop algorithms that can solve complex problems and solve them within a reasonable amount of time. Modularity is thought to reduce problem complexity by decomposing large problems into smaller and less complex subproblems. In practice, introducing modularity into evolutionary algorithm representations appears to improve search performance; however, how and why modularity improves performance is not well understood. In this thesis, we seek to better understand the effects of modularity on search. In particular, what are the effects of module creation on the search space structure and how do these structural changes affect performance? We define a theoretical and empirical framework to study modularity in evolutionary algorithms. Using this framework, we provide evidence of the following. First, not all types of modularity have an effect on search. We can have highly modular spaces that in essence are equivalent to simpler non-modular spaces. This is the case, because these spaces achieve higher degree of modularity without changing the fundamental structure of the search space. Second, for the cases when modularity actually has an effect on the fundamental structure of the search space, if left without guidance, it would only crowd and complicate the space structure resulting in a harder space for most search algorithms. Finally, we have the case when modularity not only has an effect in the search space structure, but most importantly, module creation can be guided by problem domain knowledge. When this knowledge can be used to estimate the value of a module in terms of its contribution toward building the solution, then modularity is extremely effective. It is in this last case that creating high value modules or low value modules has a direct and decisive impact on performance. The results presented in this thesis help to better understand, in a principled way, the effects of modularity on search. Better understanding the effects of modularity on search is a step forward in the larger issue of evolutionary search applied to increasingly complex problems.
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Date Issued: 2008
Identifier: CFE0002490, ucf:47680
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0002490

Title: PLANNING AND SCHEDULING FOR LARGE-SCALEDISTRIBUTED SYSTEMS.
Creator: Yu, Han, Marinescu, Dan, University of Central Florida
Abstract / Description: Many applications require computing resources well beyond those available on any single system. Simulations of atomic and subatomic systems with application to material science, computations related to study of natural sciences, and computer-aided design are examples of applications that can benefit from the resource-rich environment provided by a large collection of autonomous systems interconnected by high-speed networks. To transform such a collection of systems into a user's virtual...
Show moreMany applications require computing resources well beyond those available on any single system. Simulations of atomic and subatomic systems with application to material science, computations related to study of natural sciences, and computer-aided design are examples of applications that can benefit from the resource-rich environment provided by a large collection of autonomous systems interconnected by high-speed networks. To transform such a collection of systems into a user's virtual machine, we have to develop new algorithms for coordination, planning, scheduling, resource discovery, and other functions that can be automated. Then we can develop societal services based upon these algorithms, which hide the complexity of the computing system for users. In this dissertation, we address the problem of planning and scheduling for large-scale distributed systems. We discuss a model of the system, analyze the need for planning, scheduling, and plan switching to cope with a dynamically changing environment, present algorithms for the three functions, report the simulation results to study the performance of the algorithms, and introduce an architecture for an intelligent large-scale distributed system.
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Date Issued: 2005
Identifier: CFE0000781, ucf:46595
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0000781

Title: THE MIRRORED WALLS OF REALITY:A JOURNAL OF SHATTERED REFLECTION.
Creator: Bryant, Lisa, Ingram, Kate, University of Central Florida
Abstract / Description: ABSTRACT Theatre in its most crude, poignant, and honest form exists as the unapologetic mirror of our world. It houses the piercing reflections of mankind's hope, fear, self-doubt, passion, joy, despair, brilliance, destitution, and desire. It becomes the image of all that man hopes to be, yearns to achieve, and knows he has destroyed. Theatrical performance is without equal in its ability to conjure visible truth from the reflection man sees everyday and hopelessly fails to recognize....
Show moreABSTRACT Theatre in its most crude, poignant, and honest form exists as the unapologetic mirror of our world. It houses the piercing reflections of mankind's hope, fear, self-doubt, passion, joy, despair, brilliance, destitution, and desire. It becomes the image of all that man hopes to be, yearns to achieve, and knows he has destroyed. Theatrical performance is without equal in its ability to conjure visible truth from the reflection man sees everyday and hopelessly fails to recognize. Ultimately, theatre demands that man see himself without the masks of excuse, ignorance, or makeup. It is the vision of this journey to honor theatre's mask-less demand. Through the development of a multi-scene theatrical performance; the collection and analysis of relevant research material; and the cultivation of a comprehensive journal outlining the processes, the challenges, and the revelations that will travel the same road--from the cluttered moments of conception to the still air of an empty room after an exhausting final bow--only a mirror will remain. Each component--production, research, and journal--will function as equally essential elements. They will illuminate the evolution of fully realized theatre and detail the composition of a common theatrical message: Truth is both the seed of desperation and discovery.
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Date Issued: 2006
Identifier: CFE0001166, ucf:46872
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0001166

Title: AMERICAN AGRIBUSINESS AND BIOTECHNOLOGY: A NEW ERA OF FARMING.
Creator: Ryan, Nicole M, Sadri, Houman, University of Central Florida
Abstract / Description: In the past fifty years there has been an incredible amount of change made to the agrarian system of the United States. New discoveries in the realm of biotechnology led to the adoption of genetically modified organisms (GMOs) in agriculture, and transformed the industry. Due to regulatory policies set during the nineteen-eighties this technology was able to benefit from widespread commercialization. Today, we see the effects of this approach and are entering into a highly volatile political...
Show moreIn the past fifty years there has been an incredible amount of change made to the agrarian system of the United States. New discoveries in the realm of biotechnology led to the adoption of genetically modified organisms (GMOs) in agriculture, and transformed the industry. Due to regulatory policies set during the nineteen-eighties this technology was able to benefit from widespread commercialization. Today, we see the effects of this approach and are entering into a highly volatile political climate in regard to GMOs. This paper aims to provide an analysis of the regulatory system in place and the discrepancies that exist in US policy. The factors evaluated through this thesis include the current US regulatory approach, advancements in biotechnology, and a comparative perspective on US and EU systems. In each of these reviews it is also relevant to mention consumer opinion on GMOs and the role of interest groups. It is important for every American consumer to understand the politics and technology behind their meals. Through the analysis of recent judicial decisions and the enactment of new laws this thesis explains how the use of GMOs in agriculture is causing an unprecedented change to the political structures in place.
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Date Issued: 2016
Identifier: CFH2000035, ucf:45586
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFH2000035

Title: THE ACQUISITION OF STUDENT NURSES' KNOWLEDGE OF GENETICS AND GENOMICS AND ATTITUDES TOWARD THE APPLICATION OF THEIR KNOWLEDGE IN CLINICAL PRACTICE.
Creator: Munroe, Theresa, Loerzel, Victoria, University of Central Florida
Abstract / Description: 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.
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Date Issued: 2014
Identifier: CFH0004648, ucf:45290
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFH0004648

Title: Role of Kruppel-like Factor 8 (KLF8) in Cancer and Cardiomyopathy.
Creator: Lahiri, Satadru, Zhao, Jihe, Parthasarathy, Sampath, Masternak, Michal, Siddiqi, Shadab, University of Central Florida
Abstract / Description: Cancer and cardiovascular diseases are two most fatal diseases causing innumerable death each year. Understanding the mechanisms underlying these diseases is critical for developing proper therapeutic approach. Kr(&)#252;ppel-like factor 8 (KLF8) is a member of Kr(&)#252;ppel-like family transcription factors that is overexpressed in many types of cancers. There is no report on role of KLF8 in cardiovascular diseases to date. KLF8 transcriptionally activates or represses a host of target...
Show moreCancer and cardiovascular diseases are two most fatal diseases causing innumerable death each year. Understanding the mechanisms underlying these diseases is critical for developing proper therapeutic approach. Kr(&)#252;ppel-like factor 8 (KLF8) is a member of Kr(&)#252;ppel-like family transcription factors that is overexpressed in many types of cancers. There is no report on role of KLF8 in cardiovascular diseases to date. KLF8 transcriptionally activates or represses a host of target genes to promote cancer cell proliferation, migration, invasion and epithelial to mesenchymal transition during tumor progression. Studies proposed in this thesis identified a novel posttranslational modification of KLF8 essential for its role in promoting cancer cell migration and discovered a novel function of KLF8 in cardiomyopathy. In our first study, we identified serine 48 (S48) as a novel phosphorylation site on KLF8. Pharmacological and genetic manipulations of various potential kinases further revealed ERK2 as the kinase responsible for this novel phosphorylation. Functional studies indicated that this phosphorylation is crucial for protecting KLF8 protein from degradation in the nucleus and promoting cancer cell migration. Preclinical xenograft models have indicated an important role of KLF8 for tumor progression. To investigate role of KLF8 in spontaneous tumorigenesis better recapitulating pathology in patients, we established the first Cre-regulated conditional KLF8 transgenic mouse model. Upon induction of global expression of the KLF8 transgene, spontaneous mammary and testicular tumors were formed in a small population of the mice by their mid-age, as expected considering the long latency required for tumor progression. Surprisingly, however, nearly 100% of KLF8 the mice died with a significantly enlarged heart, which did not occur to any littermate control mouse. Further characterization of the mice revealed that the global expression of the transgene caused striking systolic dysfunction leading to fatal dilated cardiomyopathy. Importantly, these similar phenotypes were reproduced in heart-specific KLF8 transgenic mice. Cardiovascular disease PCR array identified a number of genes potentially mediating KLF8-induced cardiac pathology. These results identified a previously unimagined function of KLF8 in the heart, shed new light on the mechanisms of cardiac diseases and provide novel preclinical mouse models for future translational research.
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Date Issued: 2016
Identifier: CFE0006692, ucf:51914
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006692

Title: Analysis of large-scale population genetic data using efficient algorithms and data structures.
Creator: Naseri, Ardalan, Zhang, Shaojie, Hughes, Charles, Yooseph, Shibu, Zhi, Degui, University of Central Florida
Abstract / Description: With the availability of genotyping data of very large samples, there is an increasing need for tools that can efficiently identify genetic relationships among all individuals in the sample. Modern biobanks cover genotypes up to 0.1%-1% of an entire large population. At this scale, genetic relatedness among samples is ubiquitous. However, current methods are not efficient for uncovering genetic relatedness at such a scale. We developed a new method, Random Projection for IBD Detection (RaPID)...
Show moreWith the availability of genotyping data of very large samples, there is an increasing need for tools that can efficiently identify genetic relationships among all individuals in the sample. Modern biobanks cover genotypes up to 0.1%-1% of an entire large population. At this scale, genetic relatedness among samples is ubiquitous. However, current methods are not efficient for uncovering genetic relatedness at such a scale. We developed a new method, Random Projection for IBD Detection (RaPID), for detecting Identical-by-Descent (IBD) segments, a fundamental concept in genetics in large panels. RaPID detects all IBD segments over a certain length in time linear to the sample size. We take advantage of an efficient population genotype index, Positional BWT (PBWT), by Richard Durbin. PBWT achieves linear time query of perfectly identical subsequences among all samples. However, the original PBWT is not tolerant to genotyping errors which often interrupt long IBD segments into short fragments. The key idea of RaPID is that the problem of approximate high-resolution matching over a long range can be mapped to the problem of exact matching of low-resolution subsampled sequences with high probability. PBWT provides an appropriate data structure for bi-allelic data. With the increasing sample sizes, more multi-allelic sites are expected to be observed. Hence, there is a necessity to handle multi-allelic genotype data. We also introduce a multi-allelic version of the original Positional Burrows-Wheeler Transform (mPBWT).The increasingly large cohorts of whole genome genotype data present an opportunity for searching genetically related people within a large cohort to an individual. At the same time, doing so efficiently presents a challenge. The PBWT algorithm offers constant time matching between one haplotype and an arbitrarily large panel at each position, but only for the maximal matches. We used the PBWT data structure to develop a method to search for all matches of a given query in a panel. The matches larger than a given length correspond to the all shared IBD segments of certain lengths between the query and other individuals in the panel. The time complexity of the proposed method is independent from the number of individuals in the panel. In order to achieve a time complexity independent from the number of haplotypes, additional data structures are introduced.Some regions of genome may be shared by multiple individuals rather than only a pair. Clusters of identical haplotypes could reveal information about the history of intermarriage, isolation of a population and also be medically important. We propose an efficient method to find clusters of identical segments among individuals in a large panel, called cPBWT, using PBWT data structure. The time complexity of finding all clusters of identical matches is linear to the sample size. Human genome harbors several runs of homozygous sites (ROHs) where identical haplotypes are inherited from each parent. We applied cPBWT on UK-Biobank and searched for clusters of ROH region that are shared among multiple. We discovered strong associations between ROH regions and some non-cancerous diseases, specifically auto-immune disorders.
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Date Issued: 2018
Identifier: CFE0007764, ucf:52393
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0007764

Title: Expression of Trichoderma reesei (&)#223;-Mannanase in Tobacco Chloroplasts and its Utilization in Lignocellulosic Woody Biomass Hydrolysis.
Creator: Agrawal, Pankaj, Daniell, Henry, Kolattukudy, Pappachan, Self, William, University of Central Florida
Abstract / Description: Lignocellulosic ethanol offers a promising alternative to conventional fossil fuels. One among the major limitations in the lignocellulosic biomass hydrolysis is unavailability of efficient and environmentally biomass degrading technologies. Plant-based production of these enzymes on large scale offers a cost effective solution. Cellulases, hemicellulases including mannanases and other accessory enzymes are required for conversion of lignocellulosic biomass into fermentable sugars. ?...
Show moreLignocellulosic ethanol offers a promising alternative to conventional fossil fuels. One among the major limitations in the lignocellulosic biomass hydrolysis is unavailability of efficient and environmentally biomass degrading technologies. Plant-based production of these enzymes on large scale offers a cost effective solution. Cellulases, hemicellulases including mannanases and other accessory enzymes are required for conversion of lignocellulosic biomass into fermentable sugars. ?-mannanase catalyzes endo-hydrolysis of the mannan backbone, a major constituent of woody biomass. In this study, man1 gene encoding ?-mannanase was isolated from Trichoderma reesei and expressed via the chloroplast genome. PCR and Southern hybridization analysis confirmed the site-specific transgene integration into the tobacco chloroplast genomes and homoplasmy. Transplastomic plants were fertile and set viable seeds. Germination of seeds showed inheritance of transgenes into the progeny without Mendelian segregation. Expression of the endo-?-mannanase gene for the first time in plants facilitated its characterization for use in enhanced lignocellulosic biomass hydrolysis. Gel diffusion assay for endo-?-mannanase showed the zone of clearance confirming functionality of chloroplast-derived mannanase. Endo-?-mannanase expression levels reached up to 25 units per gram of leaf (fresh weight). Chloroplast-derived mannanase had higher temperature stability (40 (&)deg;C to 70 (&)deg;C) and wider pH optima (pH 3.0 to 7.0) than E.coli enzyme extracts. Plant crude extracts showed 6-7 fold higher enzyme activity than E.coli extracts due to the formation of disulfide bonds in chloroplasts, thereby facilitating their direct utilization in enzyme cocktails without any purification. Chloroplast-derived mannanase when added to the enzyme cocktail containing a combination of different enzymes yielded 20% more glucose equivalents from pinewood than the cocktail without mannanase. Our results demonstrate that chloroplast-derived mannanase is an important component of enzymatic cocktail for woody biomass hydrolysis and should provide a cost-effective solution for its diverse applications in the paper, oil, pharmaceutical, coffee and detergent industries.
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Date Issued: 2011
Identifier: CFE0004467, ucf:49309
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0004467

Title: Testing for Isolation in Florida Raccoons (Procyon lotor) Using Phylogenetics and Population Genetic Structure.
Creator: Trujillo, Alexa, Hoffman, Eric, Fedorka, Kenneth, Parkinson, Christopher, University of Central Florida
Abstract / Description: Molecular data are useful in determining if populations are isolated and for species delimitation. Researchers and managers currently recognize five subspecies of raccoons (Procyon lotor) in Florida, based largely on perceived geographic isolation due to the island ranges of four subspecies. In this study, I provide the first estimate of phylogenetic relationships and population divergences within Florida raccoons using a molecular dataset. I analyze the mitochondrial control region,...
Show moreMolecular data are useful in determining if populations are isolated and for species delimitation. Researchers and managers currently recognize five subspecies of raccoons (Procyon lotor) in Florida, based largely on perceived geographic isolation due to the island ranges of four subspecies. In this study, I provide the first estimate of phylogenetic relationships and population divergences within Florida raccoons using a molecular dataset. I analyze the mitochondrial control region, cytochrome b gene, and eight nuclear microsatellite loci to test two hypotheses: 1) the five, morphologically and geographically-defined subspecies of raccoon in Florida represent genetically distinct populations and (2) due to differing range sizes and habitat variation between island and mainland subspecies, the four island populations should exhibit reduced levels of genetic diversity and smaller effective population sizes compared to the mainland population. My results indicate no evidence of historical differentiation between the subspecies, but suggest a recent restriction of gene flow among three clusters of raccoons. The three clusters do not correlate to traditional geographies for subspecies identification. I provide evidence of reduced genetic diversity in island populations of raccoons compared to their mainland counterparts. These data stress the importance of using multiple lines of evidence when naming taxa to avoid misinforming the taxonomy.
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Date Issued: 2015
Identifier: CFE0006233, ucf:51069
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006233

Title: Dispersal, Gene Flow, and Adaptive Evolution During Invasion: Testing Range-Limit Theory with the Asian Tiger Mosquito.
Creator: Medley, Kimberly, Jenkins, David, Quintana-Ascencio, Pedro, Hoffman, Eric, Lounibos, Phil, University of Central Florida
Abstract / Description: Understanding the factors that make non-native species successful invaders is an important step towards mitigating spread. At the same time, species invasions can serve as natural experiments to test range-limit theory. Range-limit theory postulates declines in local abundance (abundant center model) and genetic diversity (central-peripheral hypothesis) towards range edges because of underlying environmental gradients. Such declines constrain adaptation to marginal habitats via gene swamping....
Show moreUnderstanding the factors that make non-native species successful invaders is an important step towards mitigating spread. At the same time, species invasions can serve as natural experiments to test range-limit theory. Range-limit theory postulates declines in local abundance (abundant center model) and genetic diversity (central-peripheral hypothesis) towards range edges because of underlying environmental gradients. Such declines constrain adaptation to marginal habitats via gene swamping. However, broader evolutionary theory predicts intermediate rates of immigration into range-edge populations can relieve genetic drift and improve adaptive potential. I tested hypotheses generated from theory while illuminating aspects affecting of the invasion of the Asian tiger mosquito (Aedes albopictus Skuse) into the US. Using reciprocal distribution modeling, I found US populations occupied significantly different climate and habitat than in their native range (SE Asia). Most inconsistencies were found in the northern US range, where Ae. albopictus has recently crept northward, providing an opportunity to test range-limit theory as the range reaches its limit. Because of its limited natural dispersal ability, rapid spread after the 1985 US introduction pointed to human-aided dispersal. I tested the current role of human-aided versus natural dispersal using a landscape genetics framework, and found that natural dispersal dominated current patterns. Some distant localities were highly genetically similar, indicating potential human-aided transport in limited cases. Asymmetric gene flow from core to edge localities supported the abundant center model, but uniformly high genetic diversity contrasted with the central-marginal hypothesis. I detected a significant signature of local adaptation by overwintering diapause-induced eggs in multiple field sites using reciprocal transplants. Surprisingly, most genotypes from throughout the range produced large offspring when overwintered at the range edge. Relative offspring mass between home and away winters peaked at an intermediate immigration rate. These results show that rapid adaptation has occurred in US populations of Ae. albopictus and highlight the potential for further spread. Genetic admixture from multiple introductions may explain high genetic diversity throughout the US range and contribute to high offspring size for all genotypes overwintered at the range edge. Finally, my work highlights the need for a better understanding of contemporary ecological and evolutionary processes leading to range-limits (or expansion) to more accurately reflect processes occurring in a human-dominated world.
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Date Issued: 2012
Identifier: CFE0004635, ucf:49891
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0004635

Title: FALCONET: FORCE-FEEDBACK APPROACH FOR LEARNING FROM COACHING AND OBSERVATION USING NATURAL AND EXPERIENTIAL TRAINING.
Creator: Stein, Gary, Gonzalez, Avelino, University of Central Florida
Abstract / Description: Building an intelligent agent model from scratch is a difficult task. Thus, it would be preferable to have an automated process perform this task. There have been many manual and automatic techniques, however, each of these has various issues with obtaining, organizing, or making use of the data. Additionally, it can be difficult to get perfect data or, once the data is obtained, impractical to get a human subject to explain why some action was performed. Because of these problems, machine...
Show moreBuilding an intelligent agent model from scratch is a difficult task. Thus, it would be preferable to have an automated process perform this task. There have been many manual and automatic techniques, however, each of these has various issues with obtaining, organizing, or making use of the data. Additionally, it can be difficult to get perfect data or, once the data is obtained, impractical to get a human subject to explain why some action was performed. Because of these problems, machine learning from observation emerged to produce agent models based on observational data. Learning from observation uses unobtrusive and purely observable information to construct an agent that behaves similarly to the observed human. Typically, an observational system builds an agent only based on prerecorded observations. This type of system works well with respect to agent creation, but lacks the ability to be trained and updated on-line. To overcome these deficiencies, the proposed system works by adding an augmented force-feedback system of training that senses the agents intentions haptically. Furthermore, because not all possible situations can be observed or directly trained, a third stage of learning from practice is added for the agent to gain additional knowledge for a particular mission. These stages of learning mimic the natural way a human might learn a task by first watching the task being performed, then being coached to improve, and finally practicing to self improve. The hypothesis is that a system that is initially trained using human recorded data (Observational), then tuned and adjusted using force-feedback (Instructional), and then allowed to perform the task in different situations (Experiential) will be better than any individual step or combination of steps.
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Date Issued: 2009
Identifier: CFE0002746, ucf:48157
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0002746

Title: Genetic structure and demographic analysis of Key deer (Odocoileus virginianus clavium).
Creator: Villanova, Vicki, Hoffman, Eric, Parkinson, Christopher, Fedorka, Kenneth, University of Central Florida
Abstract / Description: Recent improvements in genetic analyses have paved the way in using molecular data to answer questions regarding evolutionary history, genetic structure, and demography. Key deer are a federally endangered subspecies assumed to be genetically unique (based on one allozyme study), homogeneous, and have a female-biased population of approximately 900 deer. I used 985bp of the mitochondrial cytochrome b gene and 12 microsatellite loci to test two hypotheses: 1) if the Moser Channel is a barrier...
Show moreRecent improvements in genetic analyses have paved the way in using molecular data to answer questions regarding evolutionary history, genetic structure, and demography. Key deer are a federally endangered subspecies assumed to be genetically unique (based on one allozyme study), homogeneous, and have a female-biased population of approximately 900 deer. I used 985bp of the mitochondrial cytochrome b gene and 12 microsatellite loci to test two hypotheses: 1) if the Moser Channel is a barrier to gene flow, I should expect that Key deer are differentiated and have reduced diversity compared to mainland deer and (2) if isolation on islands leads to a higher probability of extinction, I should expect that Key deer exhibit a small population size and a high risk of extinction. My results indicate that Key deer are genetically isolated from mainland white-tailed deer and that there is a lack of genetic substructure between islands. While Key deer exhibit reduced levels of genetic diversity compared to their mainland counterparts, they contain enough diversity of which to uniquely identify individual deer. Based on genetic identification, I estimated a census size of around 1,000 individuals with a heavily skewed female-biased adult sex ratio. Furthermore, I combined genetic and contemporary demographic data to generate a species persistence model of the Key deer. Sensitivity tests within the population viability analysis brought to light the importance of fetal sex ratio and female survival as the primary factors at risk of driving the subspecies to extinction.
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Date Issued: 2015
Identifier: CFE0006058, ucf:50981
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006058

Title: EVOLVING MODELS FROM OBSERVED HUMAN PERFORMANCE.
Creator: Fernlund, Hans Karl Gustav, Gonzalez, Avelino J., University of Central Florida
Abstract / Description: To create a realistic environment, many simulations require simulated agents with human behavior patterns. Manually creating such agents with realistic behavior is often a tedious and time-consuming task. This dissertation describes a new approach that automatically builds human behavior models for simulated agents by observing human performance. The research described in this dissertation synergistically combines Context-Based Reasoning, a paradigm especially developed to model tactical...
Show moreTo create a realistic environment, many simulations require simulated agents with human behavior patterns. Manually creating such agents with realistic behavior is often a tedious and time-consuming task. This dissertation describes a new approach that automatically builds human behavior models for simulated agents by observing human performance. The research described in this dissertation synergistically combines Context-Based Reasoning, a paradigm especially developed to model tactical human performance within simulated agents, with Genetic Programming, a machine learning algorithm to construct the behavior knowledge in accordance to the paradigm. This synergistic combination of well-documented AI methodologies has resulted in a new algorithm that effectively and automatically builds simulated agents with human behavior. This algorithm was tested extensively with five different simulated agents created by observing the performance of five humans driving an automobile simulator. The agents show not only the ability/capability to automatically learn and generalize the behavior of the human observed, but they also capture some of the personal behavior patterns observed among the five humans. Furthermore, the agents exhibited a performance that was at least as good as agents developed manually by a knowledgeable engineer.
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Date Issued: 2004
Identifier: CFE0000013, ucf:46068
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0000013

Title: EXPRESSION OF GAL/GALNAC LECTIN OF ENTAMOEBA HISTOLYTICA IN TRANSGENIC CHLOROPLASTS TO DEVELOP A VACCINE FOR AMEBIASIS.
Creator: Chebolu, Seethamahalakshmi, Daniell, Henry, University of Central Florida
Abstract / Description: Amebiasis, also defined as invasive intestinal and extra intestinal amebiasis, is caused by Entameoba histolytica, an invasive protozoan parasite. World Health Organization (WHO) has reported that approximately 50 million people are infected each year causing an estimated 40 to 100 thousand deaths annually. Entameoba histolytica ranks only second to malaria as a protozoan cause of death. Amebiasis occurs world wide but people living in Central and South America, Africa and Asia are the...
Show moreAmebiasis, also defined as invasive intestinal and extra intestinal amebiasis, is caused by Entameoba histolytica, an invasive protozoan parasite. World Health Organization (WHO) has reported that approximately 50 million people are infected each year causing an estimated 40 to 100 thousand deaths annually. Entameoba histolytica ranks only second to malaria as a protozoan cause of death. Amebiasis occurs world wide but people living in Central and South America, Africa and Asia are the majority to suffer from morbidity and mortality. The enteric parasite has no zoonotic reservoirs and insect vectors for its transmission and infects humans and non-human primates. Therefore, anti-amebic vaccine could completely eradicate the disease. Entamoeba histolytica invades tissue and causes the disease in series of events. The disease is caused when the cyst form of the parasite is ingested with contaminated food or water. After excysting in the small intestine to form the trophozoite, the parasite adheres to the colonic mucus and epithelial cells through interaction of Gal/GalNAc lectin, an amebic surface adhesin with the host glycoconjugates. The parasite then secrets the proteolytic enzymes that disrupt the intestinal mucus and epithelial barrier facilitating tissue penetration. The trophozoite then kills the host epithelial and immune cells. Also, it resists the host's immune response causing the prolonged infection called the invasive amebiasis and causes colon or liver abscess. The symptoms include gradual onset of abdominal pain, diarrhea and bloody stools. Also, it can form cysts that are excreted with stools to start new cycle. The parasite recognition of the host glycoconjugates plays an important role in the pathogenesis. Therefore, the Gal/GalNAc lectin could be a possible vaccine candidate. The Gal/GalNAc lectin is composed of a 260-kDa heterodimer of disulfide-linked heavy (170 kDa) and light (35 kDa) subunits, which is non-covalently associated with an intermediate sub-unit of 150 kDa. The only recognized Carbohydrate recognition domain (CRD) was found in the heavy sub-unit. The CRD of the lectin is the potential target for colonization blocking vaccines and drugs. Preliminary studies have shown that the recombinant fragments of cysteine-rich region of LecA (lectin) containing the CRD (carbohydrate recognition domain) of the GalNAc lectin conferred protection against amebiasis. Therefore, production of LecA in plants using chloroplast genetic engineering would result in low cost vaccine because of high expression levels of vaccine antigens, and elimination of the cold-chain (low temperature, storage & transportation), hospitals and health professionals for their delivery. The LecA protein was expressed in transgenic chloroplasts of Nicotiana tabacum var. Petit havana by transforming the chloroplast genome using the LecA gene (1755 bp) by homologous recombination. The pLD-CtV has trnI and trnA genes that are used as flanking sequences for homologous recombination and the constitutive 16s rRNA promoter to regulate transcription. The aadA gene conferring spectinomycin resistance has been used for selection and gene10 regulatory sequence from T7 bacteriophage to enhance translation. The chloroplast integration of LecA was confirmed by PCR and Southern blot analysis. The expression of LecA protein in transgenic chloroplasts was analyzed by immunoblot analysis using anti-LecA antibodies. Maximum expression levels of LecA up to 6.3 % of the total soluble protein were observed in the old leaves. The evaluation of the immune response in animal model is underway. This is the first report of expression of LecA in a plant system.
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Date Issued: 2005
Identifier: CFE0000511, ucf:46467
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0000511

Title: MULTIGENE METABOLIC ENGINEERING VIA THE CHLOROPLAST GENOME.
Creator: Ruiz, Oscar Nemesio, Daniell PD, Henry h., University of Central Florida
Abstract / Description: The vast majority of valuable agronomic traits are encoded polygenetically. Chloroplast genetic engineering offers an alternate approach to multigene engineering by allowing the insertion of entire pathways in a single transformation event, while being an environmentally friendly approach.Stable integration into the chloroplast genome and transcription of the phaA gene coding for b-ketothiolase was confirmed by Southern and northern blots. Coomassie-stained gel and western blots confirmed...
Show moreThe vast majority of valuable agronomic traits are encoded polygenetically. Chloroplast genetic engineering offers an alternate approach to multigene engineering by allowing the insertion of entire pathways in a single transformation event, while being an environmentally friendly approach.Stable integration into the chloroplast genome and transcription of the phaA gene coding for b-ketothiolase was confirmed by Southern and northern blots. Coomassie-stained gel and western blots confirmed hyperexpression of b-ketothiolase in leaves and anthers, with high enzyme activity. The transgenic lines were normal except for the male sterile phenotype, lacking pollen. Scanning electron microscopy revealed a collapsed morphology of the pollen grains. Transgenic lines followed an accelerated anther developmental pattern, affecting their development and maturation, resulting in aberrant tissue patterns. Abnormal thickening of the outer wall, enlarged endothecium and vacuolation, decreased the inner space of the locules, affecting pollen grain and resulted in the irregular shape and collapsed phenotype. Reversibility of the male sterility phenotype was achieved by exposing the plants to continuous illumination, producing viable pollen and copious amounts of seeds. This is the first report of engineered cytoplasmic male sterility and offers a new tool for transgene containment for both nuclear and organelle genomes.Detailed characterization of transcriptional, posttranscriptional and translational processes of heterologous operons expressed via the chloroplast genome is reported here. Northern blot analyses performed on chloroplast transgenic lines harboring seven different heterologous operons, revealed that in most cases, only polycistronic mRNA was produced or polycistrons were the most abundant form and that they were not processed into monocistrons. Despite such lack of processing, abundant foreign protein accumulation was detected in these transgenic lines. Interestingly, a stable secondary structure formed from a heterologous bacterial intergenic sequence was recognized and efficiently processed, indicating that the chloroplast posttranscriptional machinery can indeed recognize sequences that are not of chloroplast origin, retaining its prokaryotic ancestral features. Processed and unprocessed heterologous polycistrons were quite stable even in the absence of 3'UTRs and were efficiently translated. Unlike native 5' UTRs, heterologous secondary structures or 5'UTRs showed efficient translational enhancement independent of any cellular control. Finally, we observed abundant read-through transcription in the presence of chloroplast 3'UTRs. Such read-through transcripts were efficiently processed at introns present within native operons. Addressing questions about polycistrons, as well as the sequences required for their processing and transcript stability are essential for future approaches in metabolic engineering.Finally, we have shown phytoremediation of mercury by engineering the mer operon via the chloroplast genome under the regulation of chloroplast native and heterologous 5'UTRs. These transgenenic plants hyperexpress were able to translate MerA and MerB enzymes to levels detectable by coomassie stained gel. The knowledge acquired from these studies offer guidelines for engineering multigene pathways via the chloroplast genome.
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Date Issued: 2004
Identifier: CFE0000115, ucf:46206
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0000115

Title: EXPRESSION OF HETEROLOGOUS PROTEINS IN TRANSGENIC TOBACCO CHLOROPLASTS TO PRODUCE A BIOPHARMACEUTICAL AND BIOPOLYMER.
Creator: Devine, Andrew, Daniell, Henry, University of Central Florida
Abstract / Description: The chloroplast has been demonstrated to be an ideal compartment to accumulate certain proteins or their biosynthetic products that would be harmful if they were accumulated in the cytoplasm. Hyper-expression of foreign proteins in chloroplast transgenics has accumulated up to 46% total soluble protein, this is possible due to the ~100 chloroplast genomes per chloroplast and ~100 chloroplasts per cell which can therefore, contain up to 10,000 copies of the transgene. Maternal gene inheritance...
Show moreThe chloroplast has been demonstrated to be an ideal compartment to accumulate certain proteins or their biosynthetic products that would be harmful if they were accumulated in the cytoplasm. Hyper-expression of foreign proteins in chloroplast transgenics has accumulated up to 46% total soluble protein, this is possible due to the ~100 chloroplast genomes per chloroplast and ~100 chloroplasts per cell which can therefore, contain up to 10,000 copies of the transgene. Maternal gene inheritance of plastids in most crop plants results in natural gene containment. Chloroplast transformation also eliminates positional effects that are frequently observed with nuclear transformation and no gene silencing has been observed so far at the level of transcription or translation. Consequently, independent chloroplast transgenic lines have very similar levels of foreign gene expression and there is no need to screen hundreds of transgenic events. The chloroplast genome has also been used in molecular farming to express human therapeutic proteins, vaccines for human or animal use and biomaterials. In this study we have produced a Nicotiana tabacum cv. petit Havana chloroplast transgenic line that expresses a cholera toxin B subunit (from Vibrio Cholerae)-human proinsulin (a,b and c chain) fusion protein, designated CTB-Pris. The pLD-PW vector contains the CTB-Pris gene cloned into the universal chloroplast transformation vector pLD-ctv in which the 16S rRNA promoter drives the aadA gene selectable marker, which confers resistance to spectinomycin; the psbA 5' untranslated region (UTR) which enhances translation of CTB-Pris in the presence of light and the psbA 3'UTR confers transcript stability. The trnI and trnA homologous flanking sequences facilitated site-specific integration of transgenes into the tobacco chloroplast genome. Site-specific integration was demonstrated by PCR and Southern blot analysis with probes for CTB-Pris. Western Blot analysis has demonstrated the presence of abundant CTB-Pris in transgenic plants with both CTB polyclonal and proinsulin monoclonal antibodies. Southern blot analysis has also confirmed that homoplasmy had been achieved in the T0 generation. The expression levels for CTB-Proinsulin varied between 270ìg/100mg to 364.8ìg/100mg of plant tissue which equates to ~30% total soluble protein. In the second study the E. coli ubiC gene that codes for chorismate pyruvate-lyase (CPL) was integrated in the tobacco chloroplast genome under the control of the light-regulated psbA 5' untranslated region. CPL catalyzes the direct conversion of chorismate – an important branch point intermediate in the shikimate pathway that is exclusively synthesized in plastids – to pHBA and pyruvate. pHBA is the major monomer in liquid crystal polymers (LCPs). These thermotropic polyesters have excellent properties, including high strength/stiffness, low melt viscosity, property retention at elevated temperatures, environmental resistance and low gas permeability. The leaf content of pHBA glucose conjugates in fully mature T1 plants exposed to continuous light (total pooled material) varied between 13-18% DW, while the oldest leaves had levels as high as 26.5% DW. The highest CPL enzyme activity observed in total leaf material was 50,783 pkat/mg of protein, which is equivalent to ~35% of the total soluble protein. Animal studies in the Daniell lab, suggest that the CTB-Proinsulin producing plants suppress insulitis and clinical symptoms of diabetes in NOD mice. These observations demonstrate the versatility of chloroplast gene expression for production of biopharmaceuticals and biopolymers.
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Date Issued: 2006
Identifier: CFE0001056, ucf:46794
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0001056

Title: AN INVERSE ALGORITHM TO ESTIMATE THERMAL CONTACT RESISTANCE.
Creator: Gill, Jennifer, Kassab, Alain, University of Central Florida
Abstract / Description: Thermal systems often feature composite regions that are mechanically mated. In general, there exists a significant temperature drop across the interface between such regions which may be composed of similar or different materials. The parameter characterizing this temperature drop is the thermal contact resistance, which is defined as the ratio of the temperature drop to the heat flux normal to the interface. The thermal contact resistance is due to roughness effects between mating surfaces...
Show moreThermal systems often feature composite regions that are mechanically mated. In general, there exists a significant temperature drop across the interface between such regions which may be composed of similar or different materials. The parameter characterizing this temperature drop is the thermal contact resistance, which is defined as the ratio of the temperature drop to the heat flux normal to the interface. The thermal contact resistance is due to roughness effects between mating surfaces which cause certain regions of the mating surfaces to loose contact thereby creating gaps. In these gap regions, the principal modes of heat transfer are conduction across the contacting regions of the interface, conduction or natural convection in the fluid filling the gap regions of the interface, and radiation across the gap surfaces. Moreover, the contact resistance is a function of contact pressure as this can significantly alter the topology of the contact region. The thermal contact resistance is a phenomenologically complex function and can significantly alter prediction of thermal models of complex multi-component structures. Accurate estimates of thermal contact resistances are important in engineering calculations and find application in thermal analysis ranging from relatively simple layered and composite materials to more complex biomaterials. There have been many studies devoted to the theoretical predictions of thermal contact resistance and although general theories have been somewhat successful in predicting thermal contact resistances, most reliable results have been obtained experimentally. This is due to the fact that the nature of thermal contact resistance is quite complex and depends on many parameters including types of mating materials, surface characteristics of the interfacial region such as roughness and hardness, and contact pressure distribution. In experiments, temperatures are measured at a certain number of locations, usually close to the contact surface, and these measurements are used as inputs to a parameter estimation procedure to arrive at the sought-after thermal contact resistance. Most studies seek a single value for the contact resistance, while the resistance may in fact also vary spatially. In this thesis, an inverse problem (IP) is formulated to estimate the spatial variation of the thermal contact resistance along an interface in a two-dimensional configuration. Temperatures measured at discrete locations using embedded sensors appropriately placed in proximity to the interface provide the additional information required to solve the inverse problem. A superposition method serves to determine sensitivity coefficients and provides guidance in the location of the measuring points. Temperature measurements are then used to define a regularized quadratic functional that is minimized to yield the contact resistance between the two mating surfaces. A boundary element method analysis (BEM) provides the temperature field under current estimates of the contact resistance in the solution of the inverse problem when the geometry of interest is not regular, while an analytical solution can be used for regular geometries. Minimization of the IP functional is carried out by the Levenberg-Marquadt method or by a Genetic Algorithm depending on the problem under consideration. The L-curve method of Hansen is used to choose the optimal regularization parameter. A series of numerical examples are provided to demonstrate and validate the approach.
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Date Issued: 2005
Identifier: CFE0000748, ucf:46582
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0000748

Title: THE GLYCINE AND PROLINE REDUCTASE SYSTEMS: AN EVOLUTIONARY PERSPECTIVE AND PRESCENCE IN ENTEROBACTERIACEAE.
Creator: Witt, Joshua, Self, William, University of Central Florida
Abstract / Description: The Glycine and Proline Reduction systems are two of the best characterized selenoenzymes in bacteria and have been found to occur in a wide variety of clostridia . These enzymes are utilized to reduce glycine or D-proline to obtain energy via substrate level phosporylation or membrane gradients, respectively [6, 7]. This includes the pathogens C. difficile and C. botulinum [5, 8]. Strains of C. difficile are activate toxigenic pathways whenever either of these pathways is active within the...
Show moreThe Glycine and Proline Reduction systems are two of the best characterized selenoenzymes in bacteria and have been found to occur in a wide variety of clostridia . These enzymes are utilized to reduce glycine or D-proline to obtain energy via substrate level phosporylation or membrane gradients, respectively [6, 7]. This includes the pathogens C. difficile and C. botulinum [5, 8]. Strains of C. difficile are activate toxigenic pathways whenever either of these pathways is active within the cell [5, 8]. Though evolutionary studies have been conducted on ammonia producing bacteria none has been done to directly characterize these two system by themselves. This includes an understanding of whether or not this system is transferred between organisms, as many of the clostridia that are to be studied are known to have an "open genome." [8, 10] With this information we were able to generate a phylogenic model of the proline and glycine reduction systems. Through this analysis, we were able to account for many clostridial organisms that contain the system, but also many other organisms as well. These included enterobacteriaceae including a strain of the model organism, Escherichia coli. It was further concluded that Glycine Reductase was a much less centralized system and included a wide range of taxa while Proline Reductase was much more centralized to being within the phyla of firmicutes. It was also concluded that the strain of E. coli has a fully functional operon for Glycine Reductase.
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Date Issued: 2013
Identifier: CFH0004506, ucf:45149
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFH0004506

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