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Title: Comparative Genotype-phenotype Mapping Reveals Distinct Modes of Venom Expression Evolution in the Sympatric Eastern Diamondback Rattlesnake (Crotalus adamanteus) and Eastern Coral SSnake (Micrurus fulvius).
Creator: Margres, Mark, McGivern, James J., Seavy, Margaret, Wray, Kenneth, Facente, Jack, Rokyta, Darin
Abstract/Description: Selection is predicted to drive diversification within species and lead to local adaptation, but understanding the mechanistic details underlying this process, and thus the genetic basis of adaptive evolution, requires the mapping of genotype to phenotype. Venom is complex and involves many genes, but the specialization of the venom-gland towards toxin production allows specific transcripts to be correlated with specific toxic proteins, establishing a direct link from genotype to phenotype....
Show moreSelection is predicted to drive diversification within species and lead to local adaptation, but understanding the mechanistic details underlying this process, and thus the genetic basis of adaptive evolution, requires the mapping of genotype to phenotype. Venom is complex and involves many genes, but the specialization of the venom-gland towards toxin production allows specific transcripts to be correlated with specific toxic proteins, establishing a direct link from genotype to phenotype. To determine the extent of expression variation and identify the processes driving patterns of phenotypic diversity, we constructed genotype-phenotype maps and compared range-wide toxin-protein expression variation for two species of snake with nearly identical ranges: the eastern diamondback rattlesnake (Crotalus adamanteus) and the eastern coral snake (Micrurus fulvius). We detected significant expression variation in C. adamanteus, identified the specific loci associated with population differentiation, and found that loci expressed at all levels contributed to this divergence. Contrary to expectations, we found no expression variation in M. fulvius, suggesting that M. fulvius populations are not locally adapted. Our results not only linked expression variation at specific loci to divergence in a polygenic, complex trait, but also have extensive conservation and biomedical implications. Crotalus adamanteus is currently a candidate for Federal listing under the Endangered Species Act, and the loss of any major population would result in the irrevocable loss of a unique venom phenotype. The lack of variation in M. fulvius has significant biomedical application because our data will assist in the development of effective antivenom for this species.
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Date Issued: 2014
Identifier: FSU_migr_bio_faculty_publications-0001, 10.1534/genetics.114.172437
Format: Citation

Title: The Microbiology and Pathology of Shell Disease in the Florida Spiny Lobster, Panulirus Argus with a Comparison to Shell Disease in the American Lobster, Homarus Americanus.
Creator: Porter, Lauren, Reeves, Robert H., Kostka, Joel, Herrnkind, William, Keller, Laura, Quadagno, David, Department of Biological Science, Florida State University
Abstract/Description: Shell disease is a common affliction in marine crustaceans. It manifests as necrotic lesions on the exoskeleton that are caused by bacteria producing extracellular enzymes capable of degrading crustacean cuticle. Prior to 1998, shell disease was not reported in the Florida spiny lobster, Panulirus argus. Since that time it has been seen in P. argus in the Florida Keys. In 1999, an outbreak of severe shell disease occurred in the American lobster, Homarus americanus. Shell disease has been...
Show moreShell disease is a common affliction in marine crustaceans. It manifests as necrotic lesions on the exoskeleton that are caused by bacteria producing extracellular enzymes capable of degrading crustacean cuticle. Prior to 1998, shell disease was not reported in the Florida spiny lobster, Panulirus argus. Since that time it has been seen in P. argus in the Florida Keys. In 1999, an outbreak of severe shell disease occurred in the American lobster, Homarus americanus. Shell disease has been reported in this species for almost a century. To determine if shell disease etiology is the same between the species, a comparative study was undertaken. Healthy and shell-diseased cuticle was sampled in P. argus and H. americanus to determine if a consistent culturable bacterial flora exists on the exoskeleton, and if it the same flora found in lesions. Bacteria were identified by 16S ribosomal DNA sequencing. At least 600 bases of the ribosomal RNA gene were aligned with sequences of identified marine bacteria and phylogenetic relationships were determined. Seven groups of bacteria, six of which are in the gamma proteobacteria, emerged consistently on healthy and diseased cuticle. No primary pathogen was isolated from either species. Six of the groups were isolated from both lobster species and one group was isolated only from P. argus. The association of the bacterial groups with both healthy and shell-diseased cuticle suggests that the normal bacterial flora is in part responsible for shell disease lesions. For each lobster species, histological, scanning electron microscope, and transmission electron microscope observations were made of lesions. In both species, Gram-negative rods were the predominant bacterial morphology present, but cocci and pleomorphic bacteria were also seen. The pathology of the disease appeared to be very different between the lobster species. In P. argus, lesions appear to spread laterally via formation of an extracellular matrix that encapsulates the bacteria. The bacteria seem to secrete degradative enzymes into the matrix, which breaks down surrounding cuticle. Many lesions appeared to be initiated by trauma in P. argus. In H. americanus, the lesions appear to spread by direct bacterial contact with and degradation of the cuticle.
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Date Issued: 2004
Identifier: FSU_migr_etd-0475
Format: Thesis

Title: Phylogeny and Historical Biogeography of Hadrosaurid Dinosaurs.
Creator: Prieto-Marquez, Albert, Erickson, Gregory M., Parker, William C., Steppan, Scott J., Swofford, David L., Ronquist, Fredrik, Department of Biological Science, Florida State...
Show morePrieto-Marquez, Albert, Erickson, Gregory M., Parker, William C., Steppan, Scott J., Swofford, David L., Ronquist, Fredrik, Department of Biological Science, Florida State University
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Abstract/Description: Hadrosaurids were the most diverse and abundant dinosaurs at the end of the Cretaceous. However, their phylogeny is incompletely known and the relationships of many taxa, particularly European and South American, remains unresolved. Questions remain regarding the timing of their origin and which attributes might have allowed these animals to diversify and colonize nearly all continents by the late Campanian. Likewise, the center of origin and subsequent biogeographical history of hadrosaurids...
Show moreHadrosaurids were the most diverse and abundant dinosaurs at the end of the Cretaceous. However, their phylogeny is incompletely known and the relationships of many taxa, particularly European and South American, remains unresolved. Questions remain regarding the timing of their origin and which attributes might have allowed these animals to diversify and colonize nearly all continents by the late Campanian. Likewise, the center of origin and subsequent biogeographical history of hadrosaurids has remained contentious. With the goal of elucidating the evolutionary history of hadrosaurids, I present the most comprehensive and resolved phylogeny of these animals ever estimated, using a complete taxonomic sampling at specific level. I also report the results of a biogeographic analysis seeking to establish the ancestral area of Hadrosauridae, testing whether they originated in Asia, North or South America. In addition I used the same method to track their diversification in relation to intercontinental connections throughout their tenure. Parsimony and Bayesian methods were implemented to elucidate the phylogenetic relationships of all hadrosaurid species. These included specimens of 41 hadrosaurids from Europe, Asia and North and South America. Outgroup taxa included twelve iguanodontoidean species from Europe, North America and Asia. New characters were defined and old ones revised on the basis of new data collected from first hand examination of specimens. Traditional and geometric morphometrics were applied to discover patterns of variation containing phylogenetic information. Continuous geometries were studied using the Analysis of Planar Shapes Using Geodesic Paths, a novel landmark-free method that considers the continuous non-linear geometry of the bones. In this way, a total of 299 phylogenetically informative characters (205 cranial and 94 postcranial) were defined and documented, the most extensive character data set ever constructed for hadrosaurid dinosaurs. In general, parsimony and Bayesian analyses confirmed the dichotomic evolution of hadrosaurids into Saurolophinae and the hollow-crested Lambeosaurinae. Saurolophines consisted of "saurolophs" and "kritosaurs". Lambeosaurines consisted of a succession of Eurasian outgroups to two major clades, "parasaurolophs" and "amurosaurs" ("hypacrosaurs" and "corythosaurs"). Hadrosauridae was redefined as the clade stemming from the most recent common ancestor of Hadrosaurus foulkii and Parasaurolophus walkeri. Its monophyly was unambiguously supported by an iliac supraacetabular process that projects lateroventrally between half and three quarters of the dorsoventral depth of the central plate of the ilium and a craniocaudally short supraacetabular process that is less than 55% the length of the central plate of the ilium. The closest outgroup taxa to Hadrosauridae lived in eastern North America. The hadrosaurid radiation and the divergence of saurolophines from lambeosaurines occurred no later than the Santonian and was coincident with the evolution of a suite of mandibular characters (i.e., increased number of tooth families, presence of three teeth forming the dentary occlusal plane, ventral offset of the oral predentary-premaxilla contact). These characters may have been key innovations. These results suggest that feeding adaptations might have played a central role in the diversification of hadrosaurids. Circumnarial fossae and cranial crests evolved prior to the hadrosaurid radiation. Both of these characters were reconstructed to have evolved at the same time. Ancestral areas were reconstructed on the phylogeny derived from the weighted parsimony analysis of Hadrosauridae. Fitch parsimony and the Dispersal-Vicariance (DIVA) method were implemented to reconstruct ancestral areas for all clades of Hadrosauria. The results show that the genesis of Hadrosauridae occurred in eastern North America during the late Santonian. Soon after their origin, hadrosaurids dispersed to Asia, the ancestral area for the major Saurolophinae-Lambeosaurinae divergence. Lambeosaurines and saurolophines dispersed to North America and underwent major cladogenesis during the late Campanian. Within Saurolophinae, "maiasaurs" and "saurolophs" returned to Asia, while "kritosaurs" colonized South America by the late Campanian. Within Lambeosaurinae, "tsintaosaurs" dispersed to Europe no later than the late Campanian. The North American radiations of "hypacrosaurs", "parasaurolophs" and "corythosaurs" may have represented independent dispersal events from the Asian continent or, alternatively, were part of a single dispersal in the late Campanian with posterior occupations of Asia by a few species from those clades. Vicariant events may have occurred following several of the inferred hadrosaurid dispersals. Thus, both vicariance and dispersal may have been instrumental in shaping the recorded distribution of hadrosaurids. Two additional studies were conducted on European and South American hadrosaurids. Although well represented in Asia and North America, the presence of this animals in Europe and South America is known only from rare and fragmentary remains that are poorly documented and mostly unstudied. As a result, the impact of these animals on the phylogenetics and biogeography of hadrosaurids as a whole are not known. Here, I provide a revised and complete osteology of the type specimens and hypodigms for the only two taxa known from South America, Secernosaurus koerneri and Kritosaurus australis. K. australis is regarded as a junior synonym of S. koerneri, based on a combination of iliac and pubic characters unique to these two taxa. Inclusion of S. koerneri within the genus Kritosaurus is not supported by the phylogenetic analysis. S. koerneri is inferred to be a member of the "kritosaur" clade within Saurolophinae, as the sister taxon to the Argentinean OTU from Salitral Moreno. Another unnamed hadrosaurid, an OTU from Big Bend National Park, Texas, is positioned as the closest outgroup to the South American clade. The results of this biogeographical analysis indicates that the Secernosaurus clade originated in South America during the late Campanian after a dispersal event (probably followed by vicariance) from southern North America before the end of that geologic stage. Finally, and regarding European hadrosaurids, the observation of previously unrecognized characters in the maxilla and dentary of Tsintaosaurus spinorhinus (Campanian of China) and Pararhabdodon isonensis (Maastrichtian of Spain) led to a revision of the taxonomy and phylogenetic relationships of the latter. In particular, the extreme elongation of the symphyseal region of the type and only material of Koutalisaurus kohlerorum (a dentary from the Maastrichtian of Spain) was also observed in T. spinorhinus. This implied that K. kohlerorum is indistinct from T. spinorhinus. This, in combination with the fact that P. isonensis and T. spinorhinus share a maxilla with elevated jugal joint continuous with the ectopterygoid ridge (a character not seen among Iguanodontoidea), led me to the conclusion that K. kohlerorum as a junior synonym of P. isonensis. The incorporation of those new characters in Bayesian and parsimony phylogenetic analyses of Hadrosauridae resulted in the inference that Pararhabdodon isonensis and Tsintaosaurus spinorhinus form a clade of basal lambeosaurines—the "tsintaosaurs". Fitch parsimony and Dispersal-Vicariance reconstruction of ancestral areas on the resulting phylogeny indicated that "tsintaosaurs" originated in eastern Asia during the middle or late Campanian and that P. isonensis represents a dispersal event (followed by vicariance) to Europe that occurred before the end of that geologic stage.
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Date Issued: 2008
Identifier: FSU_migr_etd-0460
Format: Thesis

Title: Cell Signaling and the Regulation of Axis Formation, Cell Proliferation, and Differentiation in Drosophila Melanogaster.
Creator: Poulton, John, Deng, Wu-Min, Horabin, Jamila I., Epstein, Lloyd, III, Thomas Keller, Tang, Hengli, Department of Biological Science, Florida State University
Abstract/Description: The development of multicellular animals involves a diverse array of cellular processes, including cell differentiation, proliferation, and polarization. The control of these processes is largely governed by communication between different cells. This intercellular communication, known as cell signaling, is therefore a fundamental aspect of developmental and cellular biology. Despite a wealth of knowledge regarding the canonical cell signaling pathways, many questions remain regarding the...
Show moreThe development of multicellular animals involves a diverse array of cellular processes, including cell differentiation, proliferation, and polarization. The control of these processes is largely governed by communication between different cells. This intercellular communication, known as cell signaling, is therefore a fundamental aspect of developmental and cellular biology. Despite a wealth of knowledge regarding the canonical cell signaling pathways, many questions remain regarding the mechanistic nature of the communication taking place during specific developmental events, as well as questions regarding the control of activation of cell signaling. In this dissertation I will use the egg chamber of Drosophila melanogaster as a model system to investigate the genetics and cellular biology surrounding two important developmental events involving cell signaling. In the first part I describe a role for an adhesion molecule, Dystroglycan (DG), in the communication between two important cell types present in the egg chamber (the follicle cells and the oocyte). This communication is of great developmental significance because it creates the foundation for the polarization of the oocyte. The finding that DG is involved in this process suggests that changes in cell adhesion are important in the communication that establishes oocyte polarity. In the second part of the dissertation I identify a novel role for the gene, Belle (Bel), in controlling the activation of a key cell signaling pathway known as Notch. Notch activation in the follicle cells is essential for many aspects of egg chamber development. I also demonstrate that the regulation of Notch by Bel occurs through Bel's role in the microRNA pathway, possibly through regulation of levels of another protein, Delta. Together my research sheds new light on two key facets of egg chamber development that will potentially elucidate similar mechanisms present in other aspects of development in Drosophila, as well as other organisms.
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Date Issued: 2009
Identifier: FSU_migr_etd-0459
Format: Thesis

Title: Studies of the Capacity for Creatine Biosynthesis in the Protochordate Ciona Intestinalis.
Creator: Deligio, James Thomas, Ellington, W. Ross, Chase, P. Bryant, Moerland, Timothy S., Department of Biological Science, Florida State University
Abstract/Description: Creatine kinase (CK) catalyzes the reversible transfer of the gamma-terminal phosphate of MgATP to the guanidine creatine (Cr) forming MgADP and phosphocreatine (PCr). The CK reaction plays a central role in both temporal and spatial ATP buffering in cells displaying high and variable rates of ATP turnover. There is a constant, non-enzymatic conversion of Cr to creatinine that must be compensated for by biosynthesis and/or dietary uptake. In all true vertebrate craniates, there is a capacity...
Show moreCreatine kinase (CK) catalyzes the reversible transfer of the gamma-terminal phosphate of MgATP to the guanidine creatine (Cr) forming MgADP and phosphocreatine (PCr). The CK reaction plays a central role in both temporal and spatial ATP buffering in cells displaying high and variable rates of ATP turnover. There is a constant, non-enzymatic conversion of Cr to creatinine that must be compensated for by biosynthesis and/or dietary uptake. In all true vertebrate craniates, there is a capacity for de novo biosynthesis of Cr as evidenced by the presence of the two enzymes of the biosynthetic pathway- arginine:glycine amidinotransferase (AGAT) and guanidinoacetate methyltransferase (GAMT). In these organisms the bulk of Cr biosynthesis is partitioned between the pancreas, kidney and liver for subsequent transport to muscle fibers and other cells expressing CK. Many protochordates and a broad spectrum of invertebrates, including the basal metazoan sponges, express CK and contain significant pools of Cr/PCr, particularly in primitive-type spermatozoa. However, repeated attempts at demonstrating the enzymes of Cr biosynthesis in these organisms have failed and it has been suggested that Cr is derived from the diet and/or by direct uptake from seawater. I show in this thesis that the protochordate tunicate Ciona intestinalis expresses what appear to be three unique, but very similar to one another, transcripts for GAMT. To validate that these transcripts code for GAMT, the full length cDNA for one of these was generated by PCR amplification and ligated into an expression vector. Expression resulted in the production of a large amount of soluble protein that was purified to homogeneity by low pressure chromatography. The resulting recombinant enzyme had an experimentally determined N-terminal amino acid sequence and relative molecular mass as predicted by the deduced amino acid sequence from the cDNA. Catalytic studies of this recombinant GAMT showed that it indeed had the capacity to methylate guanidinocetate to Cr with an apparent Km and maximal velocity comparable to GAMTs from vertebrates. Real-time PCR showed that this GAMT is primarily expressed in the stomach and gonad but also is expressed in two other tissue complexes. Analysis of the C. intestinalis genome and EST sequencing projects showed that the AGAT gene is present and is expressed demonstrating that this species has the complete Cr biosynthetic pathway. Perusal of other EST and genome sequencing projects reveal that true GAMTs are present in the lancelet Branchiostoma, the sea urchin Strongylocentrotus and the hydroid Hydractinia and AGAT genes are present in both Branchiostoma and Strongylocentrotus. Given the present experimental results and the emerging EST/genome sequencing data, it is clear that the capacity for de novo Cr biosynthesis is widespread in organisms expressing CK and that the genes for GAMT/AGAT evolved coincident with CK.
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Date Issued: 2005
Identifier: FSU_migr_etd-0777
Format: Thesis

Title: Self-Organization and the Superorganism: Functional Ecology of the Obligate Mutualism Between a Fungus Gardening Ant and Its Symbiotic Fungus.
Creator: Seal, Jon Nicholas, Tschinkel, Walter R., Johnson, Frank, James, Frances C., Levitan, Don R., Winn, Alice A., Department of Biological Science, Florida State University
Abstract/Description: This dissertation investigated the evolutionary ecology of a type of obligate mutualism, the form of agriculture found in ants. It presents the results of two laboratory experiments with the fungus-gardening ant species, Trachymyrmex septentrionalis, a species occurring in the Apalachicola National Forest in Florida that is closely related to mostly tropical leaf-cutting ants in the genera Atta and Acromyrmex. Fungus-gardening ants supply substrates to their fungus garden and feed the...
Show moreThis dissertation investigated the evolutionary ecology of a type of obligate mutualism, the form of agriculture found in ants. It presents the results of two laboratory experiments with the fungus-gardening ant species, Trachymyrmex septentrionalis, a species occurring in the Apalachicola National Forest in Florida that is closely related to mostly tropical leaf-cutting ants in the genera Atta and Acromyrmex. Fungus-gardening ants supply substrates to their fungus garden and feed the products of the fungus to their larvae. Because ants make choices in the substrates they collect, an interesting topic is the relationship between the choice of substrates and the quality and amounts of fungus and ants produced. No previous studies have measured the consequences of these choices on the relative sizes of fungus gardens or the quality and quantity of ants produced. The first experiment indicated a positive relationship between subtrate preference and both ant and fungal performance but it was not perfect. The ants preferred bluejack oak (Quercus incana) catkins and caterpillar frass over oak leaves or flowers (Gaylussacia dumosa). Colonies on the high catkin diet produced more fungal biomass than could be subsequently used, indicating only indirect feedback between forager activity and the colony's nutritional demands. The biomass of ant produced was similarin all groups, with the exception of being low in colonies that received only flowers. Colonies that had rejected tussock caterpillar frass were later able to produce as much ant biomass on a low catkin diet as those on the high catkin diet. In the second experiment, the successful replacement of T. septentrionalis's fungal cultivar, with a foreign fungus obtained in Louisiana from colonies of A. texana, did not change the substrate preference of the ants or the amount or quality of the ants produced. However, T. septentrionalis colonies with A. texana fungus produced more fungal biomass. Under the conditions of these experiments, the relationship between T. septentrionalis and its native fungal cultivar appear to be mutually adaptive, but that mutualism does not seem to be the product of a tight feedback mechanism on an ecological scale.
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Date Issued: 2006
Identifier: FSU_migr_etd-0289
Format: Thesis

Title: Florida Harvester Ants and Their Charcoal.
Creator: Smith, Christopher Ryan, Tschinkel, Walter R., Winn, Alice A., Inouye, Brian D., Department of Biological Science, Florida State University
Abstract/Description: Harvester ants of the genus Pogonomyrmex collect and deposit many items on top of their nests. Although these deposits, or depots, may be colossal there is very little known about them. This research is a case study of the depots in the Florida harvester ant, P. badius, describing the depot contents, distributions of different components within the depots, the ontogeny of the depots, a stimulus for their creation, testing hypotheses of their function, evaluating their effect on a measure of...
Show moreHarvester ants of the genus Pogonomyrmex collect and deposit many items on top of their nests. Although these deposits, or depots, may be colossal there is very little known about them. This research is a case study of the depots in the Florida harvester ant, P. badius, describing the depot contents, distributions of different components within the depots, the ontogeny of the depots, a stimulus for their creation, testing hypotheses of their function, evaluating their effect on a measure of colony level fitness, and providing an overview of information on depots of other species throughout the genus. The depots of P. badius consist mostly of small charcoal fragments, while those of other species are primarily pebbles. Mature colonies can have millions of objects in their depot, each of which is the result of a single foraging trip by a worker. In P. badius, the distributions of midden and charcoal about the mound are not completely overlapping, but are positively correlated in areas of overlap. Charcoal depots are isometric with colony size, increasing proportionately with the number of mature workers in the nest. Moreover, the amount of charcoal per colony size varies with season (they are larger in fall compared to spring), and site. The absence of the depot stimulates collection of non-food objects. The depots do not appear to function as territorial markers, roofs (preventing chamber collapse), or mulch (preventing water evaporation). Depots had a moderate effect on temperature (2°C, but only in the top 2cm), but it is not known whether the ants exploit this temperature difference. And finally, the effect of charcoal on the seasonal fitness of colonies was not statistically significant, but colonies with charcoal depots did produce more sexuals and workers, indicating that the effect of charcoal on fitness may accumulate over multiple seasons.
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Date Issued: 2004
Identifier: FSU_migr_etd-0340
Format: Thesis

Title: Ecological Relationships of Turtles in Northern Florida Lakes: A Study of Omnivory and the Structure of A Lake Food Web.
Creator: Aresco, Matthew Joseph, James, Frances C., Deyle, Robert, Travis, Joseph, Miller, Thomas, Houpt, Thomas, Means, D. Bruce, Department of Biological Science, Florida State University
Abstract/Description: Lakes in the southeastern United States support a high diversity of reptiles and amphibians, including many species of turtles. Reptilian omnivores are abundant and their role in lake food webs must be important. In Leon County, Florida, I studied 17 lakes and the abundances of 3 species of turtles - yellow-bellied slider, Trachemys scripta, Florida cooter, Pseudemys floridana, and Florida softshell, Apalone ferox. I found that lakes in northern Florida range from low-nutrient, sand-bottom...
Show moreLakes in the southeastern United States support a high diversity of reptiles and amphibians, including many species of turtles. Reptilian omnivores are abundant and their role in lake food webs must be important. In Leon County, Florida, I studied 17 lakes and the abundances of 3 species of turtles - yellow-bellied slider, Trachemys scripta, Florida cooter, Pseudemys floridana, and Florida softshell, Apalone ferox. I found that lakes in northern Florida range from low-nutrient, sand-bottom lakes to moderately eutrophic, muck-bottom lakes with abundant macrophytes, but one of the best predictors of turtle abundances was periphyton. Abundances of all three focal species were strongly correlated with a mud and muck substrate and both top-down (no alligator predation) and bottom-up (high periphyton productivity) factors. On a finer scale, abundances of the individual species were correlated with additional factors that may be related to trophic position: T. scripta – high phosphorus and high chironomid abundance, P. floridana – low macrophyte cover and high chironomid abundance, and A. ferox – high macroinvertebrate abundance, high snail abundance, and high phosphorus. An experiment revealed that intraspecific competition may be more important than interspecific competition in partitioning resources between the omnivorous, T. scripta, and specialist algivore, P. floridana. In low resource environments, inefficient digestive physiology and intraspecific competition may limit density of an omnivore compared to that of a low trophic position specialist. Stable isotope analysis of the entire food web of Lake Jackson, Leon County, Florida, revealed that filamentous macroalgae were the foundation of the web despite the much greater biomass of macrophytes. The turtle assemblage consisted of one herbivore and five omnivores. The diets of the three focal species differed: P. floridana was a specialist algivore (trophic position [TP] = 2.3), T. scripta was a generalist omnivore (TP = 3.3), and A. ferox was an omnivore with some specialization on insects and snails (TP = 3.8). There were few specialists (TP ³ 4.0) and few strict primary consumers. Omnivory was prevalent (90% of consumers), and the food web is one trophic level shorter than those in fish-dominated, north temperate lake webs that have few turtles, less species diversity, and lower productivity.
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Date Issued: 2005
Identifier: FSU_migr_etd-0230
Format: Thesis

Title: Allergenic Cross-Reactivity Between Cashew and Pistachio Nuts.
Creator: Tawde, Pallavi D., Roux, Kenneth, Sathe, Shridhar, Keller, Tom, Department of Biological Science, Florida State University
Abstract/Description: Title: Allergenic cross-reactivity between cashew and pistachio nuts Rationale: Cashew and pistachio belong to Anacardiaceae family and strong allergenic cross-reactivity between nuts of these two species has been reported. The aim of our study was to identify the cross-reactive allergenic proteins from cashew and pistachio nuts. Methods: Extracted cashew and pistachio nut proteins were separated by means of 1- and 2-dimensional PAGE. Pooled human sera from cashew-allergic patients was tested...
Show moreTitle: Allergenic cross-reactivity between cashew and pistachio nuts Rationale: Cashew and pistachio belong to Anacardiaceae family and strong allergenic cross-reactivity between nuts of these two species has been reported. The aim of our study was to identify the cross-reactive allergenic proteins from cashew and pistachio nuts. Methods: Extracted cashew and pistachio nut proteins were separated by means of 1- and 2-dimensional PAGE. Pooled human sera from cashew-allergic patients was tested for reactivity to soluble cashew and pistachio proteins by IgE immunoblotting after one-dimensional (1-D) and 2-D electrophoresis. The identities of the IgE-reactive bands from the pistachio immunoblot were further analyzed by means of N-terminal amino acid sequencing and comparison to previously published data from the cashew. ELISAs were performed using individual sera from subjects with cashew and tree nut allergy to assess the degree of IgE reactivity to cashew and pistachio nut extracts. Inhibition ELISA studies were conducted to assess the degree of allergenic cross-reactivity between cashew and pistachio nuts. Results: IgE immunoblots of cashew and pistachio extract probed with cashew-allergic sera identified proteins of 35kDa, 22kDa, and 7-9kDa. N-terminal amino acid sequencing of the IgE-reactive spots from pistachio immunoblot identified them as the acidic subunit, basic subunit of 11S globulin and 2S albumin seed storage proteins respectively. Seed storage proteins are known food allergens in cashew and have been designated as Ana o 1 (7S globulin), Ana o 2 (11S globulin) and Ana o 3 (2S albumin). ELISA results with ten individual cashew-allergic sera (two out of the ten patients have pistachio allergy, and the remaining eight patients had never eaten pistachio) showed IgE reactivity to both cashew and pistachio nut. Inhibition ELISA demonstrated that pre-incubation of sera with pistachio extract resulted in a marked decrease in IgE binding to cashew extract, and vice versa indicating allergenic cross-reactivity. Conclusion: The results demonstrate the presence of cross-reactive B cell epitopes on cashew and pistachio nut allergens. The plant taxonomic classification of cashew and pistachio nuts does appear to predict allergenic cross-reactivity.
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Date Issued: 2004
Identifier: FSU_migr_etd-0358
Format: Thesis

Title: Hypoallergenic Mutants of Ana O 2, a Major Cashew Allergen & Identification and Characterization of Tree Nut Allergens.
Creator: Tawde, Pallavi Dattatray, Roux, Kenneth H., Sathe, Shridhar K., III, Thomas C.S. Keller, Blaber, Michael, Reeves, Robert, Department of Biological Science, Florida State University
Abstract/Description: Allergic diseases are a heterogeneous group of type I IgE-mediated hypersensitivity reactions affecting more than 25% of the world's population of developed countries becoming a major clinical and public health issue. According to the American Academy of Allergy, Asthma and Immunology (AAAAI), allergies affect as many as 40-50 million people in the United States, making it the sixth most common cause of chronic illness. Recent studies have estimated that food allergies occur in 6 - 8% of...
Show moreAllergic diseases are a heterogeneous group of type I IgE-mediated hypersensitivity reactions affecting more than 25% of the world's population of developed countries becoming a major clinical and public health issue. According to the American Academy of Allergy, Asthma and Immunology (AAAAI), allergies affect as many as 40-50 million people in the United States, making it the sixth most common cause of chronic illness. Recent studies have estimated that food allergies occur in 6 - 8% of children under 3 years of age and in 4% of adults in the US population. The Food and Agriculture Organization (FAO) and the World Health Organization (WHO) proposed that milk, shellfish, egg, fish, peanut, soybean, tree nuts and wheat are eight major sources of food allergens and the causes of most food allergies. Peanut, tree nuts, and seafood allergies predominate in adults, whereas milk and egg allergies are important in children. Tree nut allergies, in particular, affect about 0.5% of the US population. The commonly consumed tree nuts in the US include walnuts, almonds, cashews, pistachios, and pecans, all of which are allergenic to predisposed individuals of the consuming population. The major allergenic proteins associated with tree nut allergies include the seed storage proteins belonging to the 7S and 11S globulin, and 2S albumin gene families. Complementary DNA expression libraries were created from English walnut, cashew and almond. To identify the almond profilin, almond and walnut 60S ribosomal protein P2, 7S and 11S globulin genes in cashew and pistachio nuts, the libraries were used either directly as targets for degenerate primers in PCR 'fishing' experiments or transferred to nitrocellulose membranes and screened with tree nut allergenic patient sera. Upon identification and amplification of the respective coding genes, they were modified with restriction enzymes, ligated into an expression vector, and expressed as fusion proteins. These purified fusion proteins were used to screen for tree nut-allergic patient IgE-reactivity in direct immunoblots and to identify the native counterparts of these proteins in crude nut extracts via inhibition immunoblots and/or inhibition ELISA. Information on the linear epitopes and homology modeling of 7S and 11S globulins from cashew and pistachio would provide structural insight into the issue of serological and clinical cross-reactivity between these two nuts from the Anacardiaceae family. The 11S globulins represent a family of most abundant seed storage proteins, and have been shown to be the most allergenic (i.e., react with high percentage of patients sera) of the seed storage proteins (allergenic in cashew, pistachio, almond, walnut, Brazil nut, and hazelnut). Linear IgE-reactive epitopes on the primary amino acid sequence of major cashew allergen and protein --11S globulin, Ana o 2 were located by overlapping synthetic peptide analysis using cashew allergic sera. Additionally, alanine scanning mutagenesis of the immunodominant IgE reactive linear epitopes was used in the identification of key amino acid residues critical for IgE binding. The identified critical amino acids would serve as targets to create hypoallergenic variants of Ana o 2, by introducing point mutations of those critical amino acids using site-directed mutagenesis in the Ana o 2 cDNA and unaltering the overall structural fold of the molecule. The biological potential of the hypoallergenic engineered Ana o 2 mutants would be analyzed using an ex vivo basophil activation assay. Thus, by reducing the anaphylactic potential of Ana o 2 while preserving T cell epitopes, we could potentially use these hypoallergens for allergen specific immunotherapy in cashew sensitized individuals.
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Date Issued: 2008
Identifier: FSU_migr_etd-0346
Format: Thesis

Title: Conformational Change of Troponin I Upon Muscle Activation.
Creator: Zhang, Xiaojun, Fajer, Piotr G., Logan, Timothy, Chase, P. Bryant, III, Thomas Keller, Blaber, Michael, Department of Biological Science, Florida State University
Abstract/Description: Unraveling the detailed molecular mechanisms involved in muscle contraction is a prerequisite for understanding the molecular basis of muscular disorders. Troponin (Tn) plays a key role in muscle regulation, and it is composed of three subunits: TnC, TnI and TnT. This study is aimed at understanding conformational changes occurring in TnI during muscle activation and force generation. The primary experimental technique used is site specific spin labeling combined with electron paramagnetic...
Show moreUnraveling the detailed molecular mechanisms involved in muscle contraction is a prerequisite for understanding the molecular basis of muscular disorders. Troponin (Tn) plays a key role in muscle regulation, and it is composed of three subunits: TnC, TnI and TnT. This study is aimed at understanding conformational changes occurring in TnI during muscle activation and force generation. The primary experimental technique used is site specific spin labeling combined with electron paramagnetic resonance (SDSL-EPR). In present study, we used SDSL EPR technique to observe the orientational changes of TnI-TnT coiled-coil domain and the conformational changes of TnI C-terminal domain between different thin filament states. The fiber tilts spectra of TnI133-MTSSL reconstituted fibers showed that in this domain, TnI is well ordered and oriented at a specific angle with respect to the actin filament. After simulations using a nonlinear-least-squares (NLS) approach, we found that TnI-TnT coiled-coil undergoes a significant orientational change between different states: from "Blocked" to "Closed" state, TnI re-orients itself ~50° axially; from "Closed" to "Open" state, TnI re-orients itself 90° azimuthally. In order to examine the conformational change of TnI C-terminal region upon Ca2+ binding, DEER distance measurements between two residues in TnI C-terminal region (residue 170 and residue 202) were performed. The broad distance distribution between residue 170 and 202 indicates that the TnI C-terminal region is flexible. Unlike TnC and other regions of TnI, in solution, this region is not affected by Ca2+ binding. The reconstitution of the troponin complex to Tm/actin does not change the flexibility of the TnI C-terminal region. By using both DEER and FRET techniques to monitor the distance change between TnI and actin upon Ca2+ binding, we discovered that this region shifts away from actin in thin filaments when Ca2+ is bound. This is the first direct observation of such a conformational change.
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Date Issued: 2008
Identifier: FSU_migr_etd-0539
Format: Thesis

Title: Elucidation of the Catalytic Mechanism of Two Fatty Acid-Metabolizing Enzymes Using EPR Spectroscopy.
Creator: Wu, Fayi, Gaffney, Betty J., Levenson, Cathy W., Fadool, Debra A., Outlaw, William H., Roux, Kenneth H., Department of Biological Science, Florida State University
Abstract/Description: Coral allene oxide synthase (cAOS), a hemoprotein with sequence similarity to bovine liver catalase (BLC), is the N-terminal domain of a fusion protein with an 8R-lipoxygenase in coral Plexaura homomalla. A radical having a g-value of 2.004-2.005 is formed in cAOS upon reaction with peracetic acid. The radical has been shown to be tyrosyl by deuterium substitution of tyrosines and by EPR. The radical site was located at Y193 by mutagenesis of several tyrosines, which are included in the...
Show moreCoral allene oxide synthase (cAOS), a hemoprotein with sequence similarity to bovine liver catalase (BLC), is the N-terminal domain of a fusion protein with an 8R-lipoxygenase in coral Plexaura homomalla. A radical having a g-value of 2.004-2.005 is formed in cAOS upon reaction with peracetic acid. The radical has been shown to be tyrosyl by deuterium substitution of tyrosines and by EPR. The radical site was located at Y193 by mutagenesis of several tyrosines, which are included in the regions of sequence similarity of cAOS and BLC. The kinetics of enzyme reacting with peracetic acid and 13R-HPODE, a nonoptimal substrate, demonstrated that oxidized heme intermediates form and radical formation has a role in recovery of the enzyme. The heme ligand of cAOS was determined to be Y353 by mutagenesis, based on the changed UV-vis spectra of the mutant. Lipoxygenase (LOX) is a family of non-heme iron-containing enzymes that catalyze the dioxygenation of polyunsaturated fatty acids. How LOX interacts with fatty-acid substrates is still not clear although the interaction is critically important in determining the regio- and stereo-specificity of the enzyme. We employed an EPR spectroscopic approach, combined with fatty-acid spin labels, to obtain insight into this question. The fatty-acid spin labels are labeled on carbons 5-, 8-, 10-, 12- and 16- of stearic acid (doxyl stearic acid, DSA). The affinity of DSA for soybean lipoxygenase-1 (LOX-1) increases as the chain length between the labeled carbon and the methyl end increases except in the case of the one labeled on carbon 16. The EPR lineshape suggests that 16-DSA binds to the cavity in a different mode from the others. Iron in LOX-1 enhances relaxation of all the DSA probes similarly. Enzyme kinetics showed that 5-DSA is a competitive inhibitor of LOX-1 with a Ki 9 ?M while the dissociation constant Kd determined by EPR is 10 ?M. These results indicate that all the probes bind to the fatty acid substrate-binding site of LOX-1 or to a portion of it. Room-temperature EPR spectra show local mobility of probes bound to LOX-1. Those probes labeled at the methyl or carboxyl end experienced more motion than those labeled in the middle of the chain. This suggests that the binding site does not accommodate the whole chain, but that doxyl portion resides near the entrance to the substrate cavity, with only the hydrocarbon portion of the spin label occupying the substrate site.
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Date Issued: 2006
Identifier: FSU_migr_etd-0706
Format: Thesis

Title: Phylogeography of the Sigmodontine Rodent, Phyllotis Xanthopygus, and a Test of the Sensitivity of Nested Clade Analysis to Elevation-Based Alternative Distances.
Creator: Albright, James Christopher, Steppan, Scott, Levitan, Don, Swofford, David, Department of Biological Science, Florida State University
Abstract/Description: I undertook a phylogenetic and phylogeographic study of the widespread Andean rodent, Phyllotis xanthopygus. My goals were to obtain general information about the history of the species and to explore some issues of Nested Clade Analysis (NCA) sensitivity in an empirical framework. The mitochondrial marker, cytochrome-b, was sequenced to produce an intraspecific maximum-likelihoo phylogeny of Phyllotis xanthopygus. I assessed the sensitivity of NCA to alternative distances by incorporating...
Show moreI undertook a phylogenetic and phylogeographic study of the widespread Andean rodent, Phyllotis xanthopygus. My goals were to obtain general information about the history of the species and to explore some issues of Nested Clade Analysis (NCA) sensitivity in an empirical framework. The mitochondrial marker, cytochrome-b, was sequenced to produce an intraspecific maximum-likelihoo phylogeny of Phyllotis xanthopygus. I assessed the sensitivity of NCA to alternative distances by incorporating physiognomic information in the form of two elevation distances based on isolines. The elevation distances were largely congruent, but they both differed from the standard great-circle distance metrics. Only three out of nine phylogeographic inferences were the same for the different approaches.
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Date Issued: 2004
Identifier: FSU_migr_etd-0026
Format: Thesis

Title: The Life History, Reproductive Ecology, and Demography of the Red Porgy, Pagrus Pagrus, in the Northeastern Gulf of Mexico.
Creator: Devries, Douglas Alan, Travis, Joseph, Koenig, Christopher C., Meeter, Duane, Elam, John S., Grimes, Churchill B., Levitan, Don R., Department of Biological Science, Florida...
Show moreDevries, Douglas Alan, Travis, Joseph, Koenig, Christopher C., Meeter, Duane, Elam, John S., Grimes, Churchill B., Levitan, Don R., Department of Biological Science, Florida State University
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Abstract/Description: This study examined the reproductive ecology of the red porgy Pagrus pagrus (Sparidae) in the NE Gulf of Mexico and the temporal, bathymetric, and small scale spatial variability of its life history traits and demographics. Almost 4000 specimens were collected using standardized hook and line gear year-round, Mar 1998-Sep 2001, in the NE Gulf - most (n=2,586) at 9 sites off NW Florida in 30-68 m. Spawning grounds were widespread, spawning occurred primarily Dec – Feb, and 50% of females...
Show moreThis study examined the reproductive ecology of the red porgy Pagrus pagrus (Sparidae) in the NE Gulf of Mexico and the temporal, bathymetric, and small scale spatial variability of its life history traits and demographics. Almost 4000 specimens were collected using standardized hook and line gear year-round, Mar 1998-Sep 2001, in the NE Gulf - most (n=2,586) at 9 sites off NW Florida in 30-68 m. Spawning grounds were widespread, spawning occurred primarily Dec – Feb, and 50% of females matured at 211 mm and sites, and were 206 - 417 mm TL and ages 2 - 9 yr, strong evidence the process is socially controlled. Red porgy are permanently sexually dichromatic, pair spawners, and do not form large, predictable spawning aggregations. Neither protogyny nor their reproductive ecology appears to make them more sensitive than gonochorists to exploitation - they are probably less so in some cases. Traits such as widespread spawning grounds, no tendency to form spawning aggregations, absence of behaviorally-related size or sex selectivity, socially controlled sex change, co-occurrence of sexes year-round, and an extended period of transition, should stabilize or enable rapid compensation of sex ratios in red porgy (preventing sperm limitation or disruption of mating). Size and age composition, size at age, survival rates, transition rates, sizes and ages at transition, and sex ratios all differed significantly at a scale of only 10's of km. Environmental heterogeneity and site fidelity probably explain most of those differences, which likely reflect phenotypic, not genetic, effects. Habitat patches likely have variable hydrological, geological, biological, exploitation, and ecological characteristics. Once recruited to a patch, philopatric adults are exposed to a unique suite of factors which could affect growth, mortality, and reproduction. Such small spatial scale differences in many traits suggests a complex structure of local subpopulations; these resemble Crowder et al.'s (2000) sources and sinks or the broadly - defined metapopulation of Kritzer and Sale (2004). Pooled data from such a complex population structure could introduce excessive variability to parameter estimates and bias stock assessments.
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Date Issued: 2006
Identifier: FSU_migr_etd-0076
Format: Thesis

Title: Dendritic Spines and Deacetylases.
Creator: Dietz, Karen C., Ouimet, Charles C., Wang, Zuoxin, Kabbaj, Mohamed, Trombley, Paul Q, III, Thomas C.S. Keller, Department of Biological Science, Florida State University
Abstract/Description: The work presented in this dissertation represents investigations into the mechanism of two neurological disorders. The first set of experiments was aimed at examining the morphology of post-synaptic structures called dendritic spines in a mouse model of Down's syndrome. The second set of experiments was aimed at examining the regional pattern and cellular distribution of possible therapeutic targets, histone deacetylases, in treating the symptoms of Huntington's disease. In the first set of...
Show moreThe work presented in this dissertation represents investigations into the mechanism of two neurological disorders. The first set of experiments was aimed at examining the morphology of post-synaptic structures called dendritic spines in a mouse model of Down's syndrome. The second set of experiments was aimed at examining the regional pattern and cellular distribution of possible therapeutic targets, histone deacetylases, in treating the symptoms of Huntington's disease. In the first set of experiments, we examined a mouse model of Down's syndrome, the Ts65Dn mouse, to determine if it mimics the dendritic spine abnormalities in area CA1 of hippocampus that have been documented in human individuals with the disorder. The Ts65Dn mouse represents a partial trisomy of the murine chromosome homologous to a large portion of human chromosome 21, which is present in 3 copies rather than 2 in Down's syndrome. These mice show behavioral abnormalities and learning deficits that are thought to replicate the mental retardation that is a prominent characteristic of Down's syndrome. As many of the behavioral and learning paradigms used to test these mice require hippocampal function, and neurons from hippocampal tissue taken from Down's syndrome individuals show a reduction in the density of dendritic spines, we sought to determine if Ts65Dn mice exhibit the same morphological abnormality. Dendritic spine densities on the apical branches of CA1 hippocampal neurons in Ts65Dn animals were not significantly different when compared to those from euploid (normal chromosome number) littermates. In addition, morphological analysis of dendritic spine shape demonstrated that the proportion of dendritic spines in each of the four major spine shape categories (stubby, thin, filopodia and mushroom) was not different between the two conditions. As the environment for cells in a cultured slice are most likely very different from those experienced in the intact animal, we examined if neurons in the intact brain exhibited signs of abnormal dendritic spine density in the Ts65Dn mouse. Analysis of dendritic spine densities on apical branches of CA1 hippocampal neurons from mice sacrificed at 2 weeks, 3 months or 6 months of age showed no significant differences between the euploid and trisomic conditions. Furthermore, Western blot analysis showed that Ts65Dn do not have reduced expression of a dendritic spine protein, drebrin, as has been reported in Down's syndrome. The second set of experiments that are described concern the immunohistochemical localization of two enzymes involved in the transcriptional regulation of genes. These enzymes, called histone deacetylases, or HDACs, aid in the regulation of histone acetylation levels as a mechanism to control access of transcription factors to gene sequences. Recently, it was found that compounds that inhibit enzymes that remove acetyl groups demonstrate therapeutic effects in animal models of Huntington's disease, a neurodegenerative disorder that targets brain regions important for movement control. The work presented here describes the immunohistochemical localization of a HDAC2 and HDAC7. HDAC7 immunohistochemistry was consistent with biochemical studies demonstrating that HDAC7 can be present in both the cytoplasm and the nucleus. A finding of interest is that not all neurons of the murine brain express HDAC7, nor is it localized to the same subcellular compartment in all cell types. Granule cells of the hippocampal dentate gyrus and of the cerebellum showed very little immunoreactivity for HDAC7. Apical dendrites of the CA1 and CA3 regions of hippocampus showed very heavy cytoplasmic staining. Deeper cortical layers showed pyramidal neurons with heavier staining than superficial pyramidal layers in almost all cortical regions, except for the orbital, insular and piriform cortices which showed heavy staining in superficial layers as well. In general, staining of the olfactory system appeared more intense than other sensory system regions. Fibers along the striatonigral bundle, from the caudate to the substantia nigra reticulata showed heavy immunoreactivity. These data suggest that targeting therapeutics to HDAC7 activity may indeed be useful, as the striatonigral pathway is a key component of movement control. HDAC2 immunoreactivity confirmed that HDAC2 is strictly a nuclear localized protein. In addition, it appeared that HDAC2 is ubiquitously expressed throughout the murine brain in all brain regions. Interestingly, HDAC2 staining occurred only in neurons that showed NeuN staining, demonstrating that it is a neuron-specific protein. Therefore, therapeutic inhibition of HDACs that include inhibition of HDAC2 may affect many aspects of neurologic functioning in multiple brain regions. It is our hope that this work will provide some added detail and knowledge to the greater neuroscience community, and will aid in the greater understanding of the organization and function of the brain and ultimately aid in development of treatments for and ultimately the cure of neurological diseases and disorders.
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Date Issued: 2008
Identifier: FSU_migr_etd-0082
Format: Thesis

Title: Construction and Analysis of a Transgenomic Cytogenetic Sorghum (Sorghum Propinquum) BAC Fish Map of Maize (Zea Mays L.) Pachytene Chromosome 9.
Creator: Amarillo, Ferdinand Enginco, Bass, Hank W., Levenson, Cathy W., Bates, George W., Fadool, James M., Keller, Laura R., Department of Biological Science, Florida State University
Abstract/Description: Large-scale cytogenetic mapping in maize has been a major challenge primarily due to fact that the maize genome has a low gene density and an abundance of repetitive sequence elements. Using a unique combination of biological and genome resources for maize, sorghum, and oat, we have solved this problem and produced a cytogenetic FISH map of maize pachytene-stage chromosome 9 with 32 maize markers. The genetically mapped markers used are distributed along the linkage maps at an average spacing...
Show moreLarge-scale cytogenetic mapping in maize has been a major challenge primarily due to fact that the maize genome has a low gene density and an abundance of repetitive sequence elements. Using a unique combination of biological and genome resources for maize, sorghum, and oat, we have solved this problem and produced a cytogenetic FISH map of maize pachytene-stage chromosome 9 with 32 maize markers. The genetically mapped markers used are distributed along the linkage maps at an average spacing of 5 centiMorgans. Each locus was mapped by means of multicolor direct FISH with a fluorescently labeled probe mix containing a whole chromosome paint, a single sorghum BAC clone, and the centromeric sequence, CentC. A maize-chromosome-addition line of oat was used for bright unambiguous identification of the maize 9 fiber within pachytene chromosome spreads. The locations of the sorghum BAC FISH signals were determined, and each new cytogenetic locus was assigned a centiMcClintock position on the short (9S) or long (9L) arm. Nearly all of the markers appeared in the same order on linkage and cytogenetic maps but at different relative positions on the two. The CentC FISH signal was localized between tda66 (at 9S.03) and cdo17 (at 9L.03). Several regions of genome hyperexpansion on maize chromosome 9 were found by comparative analysis of relative marker spacing in maize and sorghum. This transgenomic cytogenetic FISH map creates anchors between various maps of maize and sorghum integrating genetic markers, BAC fingerprints, and BAC hybridization data. It will provide tools for validating sequenced genomes, a foundation for exploring genomic diversity among related species, and a framework for comparative mapping of other plants with large and complex genomes.
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Date Issued: 2007
Identifier: FSU_migr_etd-0189
Format: Thesis

Title: Gene Expression Profiling of Flagellar Length Control in Chlamydomonas Reinhardtii.
Creator: Chamberlain, Kara Lista, Keller, Laura R., Levenson, Cathy W., Bass, Hank W., Epstein, Lloyd M., Houpt, Thomas A., Department of Biological Science, Florida State University
Abstract/Description: Complex organelles, such as cilia and flagella, play an integral part in how a cell interacts with the environment. The model system Chlamydomonas reinhardtii is a biflagellate alga that uses its flagella for swimming and sensing the environment. C. reinhardtii monitor and respond to environmental cues through changes in cellular morphology and gene expression. I used gene expression profiling to characterize the global response of stimulus-induced changes in flagellar morphology and gene...
Show moreComplex organelles, such as cilia and flagella, play an integral part in how a cell interacts with the environment. The model system Chlamydomonas reinhardtii is a biflagellate alga that uses its flagella for swimming and sensing the environment. C. reinhardtii monitor and respond to environmental cues through changes in cellular morphology and gene expression. I used gene expression profiling to characterize the global response of stimulus-induced changes in flagellar morphology and gene expression in C. reinhardtii. Previous investigations have demonstrated coordination between changes in flagellar morphology with changes in gene expression. When C. reinhardtii encounters various stimuli the cell responds through changes in flagellar length, such as assembly, disassembly, and elongation. I created a custom microarray assay to examine the transcript regulation associated with these changes in flagellar length. Using this technique, approximately 1000 genes were evaluated in a single experiment to create a global gene expression profile. While the transcriptional regulation of flagellar assembly is well characterized, that of flagellar disassembly and elongation is less understood. Using high throughput microarrays, I analyzed the changes in gene expression associated with flagellar assembly, disassembly and elongation. Microarrays were probed with fluorescently labeled cDNAs synthesized from RNA extracted from cells before and during stimulation. Evaluation of the gene expression profiles identified ~100 clones showing at least a 2-fold change in expression during changes in flagellar length. Products of these genes are associated not only with flagellar structure and motility but also with other cellular responses including signal transduction and metabolism. Expression of specific genes from each category was further characterized with high resolution quantitative real-time PCR (qRT-PCR). Comparison of the gene expression profiles demonstrated coordinate expression of cell motility component genes during flagellar assembly and disassembly; whereas comparison of the assembly and elongation expression profiles demonstrated that these morphological changes are very different responses at a transcriptional level. Furthermore, transcript regulation of genes involved in other cellular activities revealed a new and uncharacterized whole cell response to stimulation. This analysis lays the groundwork for a more comprehensive understanding of the cellular and molecular networks regulating flagellar length changes.
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Date Issued: 2007
Identifier: FSU_migr_etd-0158
Format: Thesis

Title: Sexual Selection, Fertilization Dynamics and the Use of Alternative Mating Tactics in the Hermaphroditic Seabass Serranus Subligarius.
Creator: Adreani, Mia Susan, Levitan, Don, Travis, Joseph, Wang, Zuoxin, Houle, David, Koenig, Christopher, Department of Biological Science, Florida State University
Abstract/Description: The use of an alternative male mating tactic is frequently discussed as an option that makes the best of a bad situation for disadvantaged males and not as part of an adaptive system that can produce equal average levels of reproductive success for individuals using each tactic. It is easy to develop scenarios in which some combinations of tactics produce greater success than others; the difficulty of testing hypotheses about these scenarios and the optimal distribution of tactics revolves...
Show moreThe use of an alternative male mating tactic is frequently discussed as an option that makes the best of a bad situation for disadvantaged males and not as part of an adaptive system that can produce equal average levels of reproductive success for individuals using each tactic. It is easy to develop scenarios in which some combinations of tactics produce greater success than others; the difficulty of testing hypotheses about these scenarios and the optimal distribution of tactics revolves around the difficulty of understanding how tactics are expressed. To be specific, it is unknown whether alternative behaviors are conditional and if conditional, how an individual assesses and ultimately chooses which tactic to use in any given context. Under conditions of limited mate availability, variable resource allocation or altered physiological response (e.g. temperature or poor food quality), one might expect variation in mating patterns, but the direction and extent of these variations is relatively unknown. In the simultaneously hermaphroditic marine fish, Serranus subligarius, male role individuals are known to pair spawn, group spawn and streak spawn. These mating strategies are common among marine reef fish and their behavior has been well studied. What is unclear is how each behavior translates into reproductive success and how these competing strategies are maintained within the same population. This research will focus on the use of alternative mating tactics among simultaneous hermaphrodites. The majority of simultaneous hermaphrodites mate in pairs, often cross-fertilizing each other. Alternative tactics among external fertilizers include group spawning, sneak spawning (males mimic females), or streak spawning, in which a male releases sperm over a spawning event already in progress. In this dissertation I examined the ecological and social contexts under which alternative tactics are utilized and their resulting outcomes with respect to mating behavior and fertilization success. Chapter one investigates the role of simultaneous hermaphrodites in sexual selection and reviews several studies in which sexual selection is revealed in systems with equal allocation to sex. I discuss ways in which sexual selection has been measured and suggest ways in which this may be modified in hermaphrodites. I also indicate ways in which males compete and females are chosen in these systems, despite their ability to mate with any other individual. Finally, I implicate some of the potential causes of sexual conflict in my study system; namely, that individuals vie for the male role and larger fish spawn more frequently in the male role. In chapter two, I explored the ecological and physiological contexts under which streak spawning occurs and discuss their relative importance. Size structure was characterized at each of three sites within the field study site and was subsequently used as the impetus for the experiments performed in Chapter 3 to tease out its relevance. Size structure appears to play an important role in the occurrence of streak spawning, as more streaking appears in the sites, which have greater than 20% of individuals comprised of the small size class (measured by density transects at three sites). This chapter also aims to quantify the type of habitat over which a pair spawns and whether or not this differs when additional males participate. I found that at one of the sites, there was a preference for streak spawners when macroalgae was present than when the rocks were bare. In addition, this chapter demonstrates the peak spawning times to be July and August, which were confirmed by both field observations and investigation of the gonads of actively mating individuals. In chapter three, I investigated the fertilization success of animals spawning with and without streakers participating, both in the field and in a controlled manipulation experiment. In the field I find that fertilization rates are lower in fish spawning with multiple males participating. I confirmed this finding under more controlled conditions in a field manipulation experiment. Rock rubble reef plots provided substrate on which I tested the role of density and size structure on the frequency of streak spawning and resulting fertilization success. Spawns with additional males resulted in lower fertilization success and the number of streak spawns was significantly greater when small size-class individuals were present. Thus, both field and experimental evidence suggest that small individuals predict the incidence of streak spawning and their participation lowers fertilization success. Reduced fertilization success means that both males and females incur a fitness cost. The mechanism for lowered success remains unclear but likely includes the physical disturbance created in the water column by the activity of additional males. The results of this dissertation suggest that there may be a cost to certain mating systems and the contexts under which these different tactics are utilized are dependent on ecological, social and physiological factors. It points to the complexities of individual variation in behavior and the need for more rigorous experimental work to tease apart the factors associated with variation in mating tactic. Interactions among environment, social group, and ontogeny are not often addressed simultaneously in study systems and more empirical work in these areas would help elucidate the mechanisms associated with the use of alternative mating tactics.
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Date Issued: 2011
Identifier: FSU_migr_etd-0122
Format: Thesis

Title: The Batoid Tree of Life: Recovering the Patterns and Timing of the Evolution of Skates, Rays and Allies (Chondrichthyes: Batoidea).
Creator: Aschliman, Neil C., Naylor, Gavin J.P., Steppan, Scott J., Parker, William C., Mast, Austin R., Department of Biological Science, Florida State University
Abstract/Description: Batoid fishes (skates, stingrays and allies) comprise the majority of species diversity and morphological disparity among chondrichthyans, one of the two primary divisions of extant jawed vertebrates. The largely recent and growing interest in batoid evolution has emphasized the need for a well-supported phylogeny against which evolutionary changes in traits can be interpreted. While batoids are morphologically well characterized and have an excellent fossil record, there is currently no...
Show moreBatoid fishes (skates, stingrays and allies) comprise the majority of species diversity and morphological disparity among chondrichthyans, one of the two primary divisions of extant jawed vertebrates. The largely recent and growing interest in batoid evolution has emphasized the need for a well-supported phylogeny against which evolutionary changes in traits can be interpreted. While batoids are morphologically well characterized and have an excellent fossil record, there is currently no consensus on the interrelationships of family-level taxa. Patterns of evolution within the two largest groups of batoids, skates and stingrays, also remain obscure. This dissertation presents novel frameworks for interpreting the patterns and timing of batoid evolution based on molecular data, morphology, and fossils. I recovered a resolved and time-calibrated phylogeny of the major extant groups of batoids using mitochondrial genomes, two independent nuclear markers, and fossil ages. Taxon sampling included 37 ingroup species from 22 of 23 families. Data partitioning schemes, potential biases in the sequence data, the relative informativeness of each fossil, and ancestral state reconstructions were explored. The molecular data set was then expanded with additional species in order to address questions at a finer taxonomic scale, in particular among skates and stingrays. Two nuclear and two mitochondrial markers were sequenced for 87 batoid species across 52 of 81 genera. A similar analytical approach was applied to this larger data set. I also performed a morphology-based phylogenetic analysis in order to interpret accurately coded morphological characters against the molecular frameworks. I updated the data set of McEachran and Aschliman (2004) with a number of corrections and modifications, and added new characters from the synarcual and other chondroskeletal structures. The molecular phylogenies indicate that the major lineages of batoids originated in relatively rapid sequence, followed by long periods of independent evolution. These trees corroborate morphology-based hypotheses in many respects, but have strongly divergent implications in others. Lineages inferred to be distantly related, such as skates and stingrays, or sawfishes and sawsharks, are indicated to have achieved very similar, specialized body plans through convergence. Skates and stingrays are unique among batoids in exhibiting a highly depressed disc supported to the apex by fin rays, and swim by passing waves along the lateral margin of the pectoral fin without additional propulsion by lateral motion of the tail and caudal fin. The plesiomorphic mode of locomotion and body plan for most batoid groups was probably not shark-like, as in sawfishes. Instead, it is inferred to be a combination of pectoral fin undulation and shark-like axial locomotion, which is correlated with a broader pectoral disc and reduced tail compared to the sawfish body plan. The higher-resolution molecular phylogeny is in many cases congruent with previous morphological studies or biogeography. Exceptions typically suggested a potential weakness in the molecular data, suggested that a morphology-based classification scheme is likely based on convergent characters or ignores a highly divergent morphotype nested within otherwise similar taxa, or helped resolve taxonomic confusion based on informal re-assignment by authority. Potentially non-monophyletic families and genera were identified for future study with expanded taxon sampling, additional sequence data and morphological re-evaluation. The origin of Batoidea is estimated to have occurred in the Late Triassic, with the major groups diverging throughout the Jurassic and possibly into the Cretaceous. Radiations of each major crown group are indicated to have occurred from the Late Cretaceous to the Cenozoic. The tree shape recovered for all major batoid groups, with long internal branches subtending subsequent radiations around the Cretaceous/Tertiary boundary, suggests that batoid standing diversity may be due in large part to lineage pruning and/or rapid radiation into vacated niche space. This is consistent with the fossil record, which suggests that batoids were more severely affected by the end-Cretaceous extinction event than were the other neoselachians. The updated morphological phylogeny included several key changes from earlier hypotheses and more closely approximates the molecular frameworks. There remain conflicts between morphological and molecular trees, such as the phylogenetic placements of skates and thornbacks, which currently appear to be difficult to reconcile. Future attempts to reconcile molecules and morphology will require expanded data sets and investigation of potential sources of error in each.
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Date Issued: 2011
Identifier: FSU_migr_etd-0242
Format: Thesis

Title: Analysis of Chromatin Structure Indicates a Role for Fluoxetine in Altering Nucleosome Distribution.
Creator: Gracia, Ely
Abstract/Description: An interesting stimulus for chromatin structural changes is the generic and popular anti-depressant drug Fluoxetine, commonly known as Prozac. Generally accepted as a Selective Serotonin Reuptake Inhibitors (SSRI's), recent work has emerged suggesting that this antidepressant also functions as a Histone Deaceylase Inhibitors (HDIs). Studies have also come out indicating that Fluoxetine acts as an immunosuppressant drug. Treatment with Fluoxetine is believed to reduce the over-activation of...
Show moreAn interesting stimulus for chromatin structural changes is the generic and popular anti-depressant drug Fluoxetine, commonly known as Prozac. Generally accepted as a Selective Serotonin Reuptake Inhibitors (SSRI's), recent work has emerged suggesting that this antidepressant also functions as a Histone Deaceylase Inhibitors (HDIs). Studies have also come out indicating that Fluoxetine acts as an immunosuppressant drug. Treatment with Fluoxetine is believed to reduce the over-activation of the immune system associated with depression. We have used an innovative microarray technology to measure changes in nucleosomal positioning that stem from Fluoxetine treatment. With the use of the microarray, we were able to show that Fluoxetine regulated chromatin structure, that Fluoxetine induced nucleosomal changes show time-dependent kinetics, and targeted genes responsible for the regulation of immune system processes. These results give new and important insights into non-SSRI roles of this highly prescribed class of drugs.
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Date Issued: 2012
Identifier: FSU_migr_uhm-0087
Format: Thesis

Title: Phosphorylation of the Transcription Factor YY1.
Creator: Rizkallah, Raed, Hurt, Myra M., Levenson, Cathy W., Epstein, Lloyd Mark, Keller, Thomas C. S., Bass, Hank, Department of Biological Science, Florida State University
Abstract/Description: Reversible phosphorylation plays an integral role in the regulation of eukaryotic cellular proteins, especially transcription factors. YY1 is a multifunctional transcription factor involved in the regulation of a wide spectrum of essential cellular processes. YY1 has been proposed to be a phosphoprotein and several studies have reported that phosphorylation affects its DNA binding activity. However, these results were indirect and contradictory. In this study, we provide direct evidence that...
Show moreReversible phosphorylation plays an integral role in the regulation of eukaryotic cellular proteins, especially transcription factors. YY1 is a multifunctional transcription factor involved in the regulation of a wide spectrum of essential cellular processes. YY1 has been proposed to be a phosphoprotein and several studies have reported that phosphorylation affects its DNA binding activity. However, these results were indirect and contradictory. In this study, we provide direct evidence that YY1 is a phosphoprotein in normally cycling HeLa cells. Using purified YY1, we present direct evidence that phosphorylation has a negative effect on its DNA binding activity, using several binding sites. We have mapped three phosphorylated sites on YY1 in vivo. The phosphorylated serine residue 247 was detected in asynchronously growing HeLa cells. A phosphomimetic substitution at this site had no effect on the sub-cellular localization of YY1 and only a moderate negative effect on the DNA binding activity of YY1. The other two phosphorylated sites, at threonines 348 and 378, were detected in nocodazole–arrested HeLa cells. Threonines 348 and 378 are located in the linker peptides between the zinc finger motifs of the DNA binding domain of YY1. Phosphorylation at these two residues was correlated with cytoplasmic distribution of YY1 away from the condensed DNA. Moreover, diminished DNA binding activity was observed for YY1 in whole cell extracts from nocodazole-arrested HeLa cells, in in vitro electrophoretic mobility shift assays (EMSA). This diminished binding activity was reversed by dephosphorylation of YY1 with phosphatases. Consistent with these results, phosphomimetic substitutions at threonines 348 and 378 resulted in the loss of YY1 DNA binding activity. However, these mutations caused no observable effect on the subcellular localization of YY1 in interphase HeLa cells. We also show that YY1 is excluded from the condensing chromosomes at prophase in normally growing cells and it remains dispersed away from DNA until telophase. At this stage of mitosis, YY1 is recruited back to DNA in the nucleus at the same time of chromosome decondensation. These observations propose a mechanism for the inactivation of YY1 DNA binding activity in mitosis, through phosphorylation of its DNA binding domain. To identify kinases that phosphorylate YY1, we have tested bacterially expressed and purified YY1 against one hundred kinases in vitro. Several kinases were shown to highly phosphorylate YY1. Polo-like kinase 1 (Plk1) and Casein Kinase 2á1 (CK2á1) showed the highest activity in phosphorylating YY1 of the kinases examined. Using deletion and point-substitution mutants of YY1, we have shown that Plk1 specifically phosphorylates threonine 39 in the acidic trans-activation motif in the N-terminal domain of YY1. Phosphorylation at this site could play a role in the regulation of the transcriptional activity of YY1. In addition, CK2á1 was shown to phosphorylate YY1 at serine 118, located in the caspase consensus cleavage site. Phosphorylation at serine 118 may play an important role in regulating the cleavage of YY1 during apoptosis.
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Date Issued: 2008
Identifier: FSU_migr_etd-4622
Format: Thesis

Title: Characterization of Dopamine and Kainate Receptors in Olfactory Bulb Neurons and Their Efffects on Glutamatergic Transmission.
Creator: Davila, Gabriel Nestor, Trombley, Paul, Ouimet, Charles, Freeman, Marc, Gaffney, Betty, Meredith, Michael, Department of Biological Science, Florida State University
Abstract/Description: The main olfactory bulb (OB) receives odorant information from the nasal epithelium, interprets much of that information, and transmits the results to higher cortical regions. The predominant excitatory neurotransmitter in the OB and throughout the brain is glutamate. Modulators of glutamatergic activity influence synaptic transmission of intrabulbar circuits profoundly; therefore, the effects of neuromodulators must be thoroughly characterized in order to understand fully how OB circuits...
Show moreThe main olfactory bulb (OB) receives odorant information from the nasal epithelium, interprets much of that information, and transmits the results to higher cortical regions. The predominant excitatory neurotransmitter in the OB and throughout the brain is glutamate. Modulators of glutamatergic activity influence synaptic transmission of intrabulbar circuits profoundly; therefore, the effects of neuromodulators must be thoroughly characterized in order to understand fully how OB circuits function. Investigations performed here address the capacity of dopamine receptor (DAR) and kainate receptor (KAR) activation to modulate glutamate transmission from principal cells to interneurons in OB primary cultures. Initially, I obtained immunocytochemical evidence for DARs expressed in principal cells. Subsequent electrophysiological analyses revealed that the D2-like receptor subtype (D2Rs) attenuated both spontaneous and evoked glutamatergic transmission. Information gleaned from studies of input resistances and calcium currents allowed me to determine that the site of modulation is located on the presynaptic cell. My research into KARs demonstrated the existence of functional KARs in OB neurons and began to elucidate their physiological roles in OB neurotransmission. First, I gathered immunocytochemical evidence to visualize KARs expressed both at and near synapses. In situ hybridization (ISH) was employed to map which OB neurons express mRNA for each KAR subunit. Expression levels for each subunit were quantified in parallel studies using the reverse transcriptase-polymerase chain reaction (RT-PCR). Electrophysiological approaches were used to determine whether or not KARs participate in synaptic transmission between OB neurons in primary cultures. I provide evidence for KAR-mediated modulation of both spontaneous and evoked glutamatergic transmission between OB neurons. Taken together, this work supports the notion that synaptic transmission of OB neurons can be modulated by either metabotropic or ionotropic ligand-gated ion channels. In addition, this is the first thorough characterization of KAR expression and physiology in OB neurons.
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Date Issued: 2003
Identifier: FSU_migr_etd-0817
Format: Thesis

Title: The Effects of D-Cycloserine, an Nmda Receptor Agonist, on Conditioned Taste Aversion Learning.
Creator: Davenport, Rachel A., Houpt, Thomas A., Ouimet, Charles C., III, Thomas C. S. Keller, Department of Biological Science, Florida State University
Abstract/Description: Conditioned taste aversion (CTA) learning occurs as a result of the pairing of a novel taste with a malaise-inducing substance. This is a robust associative learning paradigm that has been shown to be N-methyl-D-Aspartic acid (NMDA) receptor-mediated, as NMDA receptor antagonists attenuate CTA learning. This work presents four experiments that examine the role of an NMDA receptor agonist, d-Cycloserine (DCS), in CTA learning. The first experiment showed that DCS enhanced CTA learning but only...
Show moreConditioned taste aversion (CTA) learning occurs as a result of the pairing of a novel taste with a malaise-inducing substance. This is a robust associative learning paradigm that has been shown to be N-methyl-D-Aspartic acid (NMDA) receptor-mediated, as NMDA receptor antagonists attenuate CTA learning. This work presents four experiments that examine the role of an NMDA receptor agonist, d-Cycloserine (DCS), in CTA learning. The first experiment showed that DCS enhanced CTA learning but only under certain constraints. Namely, DCS enhanced CTA when there was a short delay between the taste and toxin pairing (10 minutes), but not when there was a longer delay (45 minutes). We next tried to explain this phenomenon by probing three possibilities: (1) DCS fails to enhance CTA after a long delay because its activity is short-lived, (2) during the long delay, DCS enhances learned safety towards the taste that would counteract CTA acquisition or (3) enhancement of CTA by DCS depends upon the temporal proximity of taste and toxin. Our data showed that DCS was effective at enhancing short-delay CTA for at least one hour after administration; thus a short half-life is not sufficient to explain why DCS fails to enhance long-delay CTA. DCS did not enhance learned safety, even though learned safety is NMDA receptor-mediated; therefore it is unlikely that learned safety during the long delay masked enhancement of CTA learning. DCS enhanced CTA only when there was a short period of taste processing; longer temporal delays between initial taste processing and LiCl, even with an immediate taste-toxin pairing, did not support DCS enhancement. Thus the lack of an effect of DCS on long-delay CTA is not due to a short half-life of DCS nor a build-up of learned safety during the long-delay, nor the temporal distance between the taste and toxin stimuli. The duration of time since initiation of the taste stimuli appears critical, however. There are a few potential neural mechanisms that may explain this short- vs. long-delay phenomenon. The most relevant finding in recent literature suggests that NMDA receptors can become internalized after activation. It is possible that NMDA receptors become activated after the initial taste and may internalize during the delay between taste and toxin causing less enhancement of DCS on long-delay CTA.
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Date Issued: 2006
Identifier: FSU_migr_etd-0826
Format: Thesis

Title: Molecular Events Underlying the Enhancement of Conditioned Taste Aversion by D-Cycloserine.
Creator: Davenport, Rachel A., Houpt, Thomas A., Kelley, Colleen M., III, Thomas C. S. Keller, Ouimet, Charles C., Trombley, Paul Q., Department of Biological Science, Florida State...
Show moreDavenport, Rachel A., Houpt, Thomas A., Kelley, Colleen M., III, Thomas C. S. Keller, Ouimet, Charles C., Trombley, Paul Q., Department of Biological Science, Florida State University
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Abstract/Description: Conditioned taste aversion (CTA) is a form of associative learning in which an animal avoids and reacts aversively to a taste (conditioned stimulus, CS) that has been previously paired with a toxin or other malaise-inducing stimulus (unconditioned stimulus, US). CTA is unique among Pavlovian learning paradigms because conditioning is supported across long delays (minutes to hours) between taste and toxin [Garcia et al., 1966; Kalat & Rozin, 1973; Smith & Roll, 1967] and is robust in that an...
Show moreConditioned taste aversion (CTA) is a form of associative learning in which an animal avoids and reacts aversively to a taste (conditioned stimulus, CS) that has been previously paired with a toxin or other malaise-inducing stimulus (unconditioned stimulus, US). CTA is unique among Pavlovian learning paradigms because conditioning is supported across long delays (minutes to hours) between taste and toxin [Garcia et al., 1966; Kalat & Rozin, 1973; Smith & Roll, 1967] and is robust in that an animal can form a strong aversion that can last for months [Houpt et al., 1996; Martin & Timmins, 1980; Steinert et al., 1980] after only a single trial of a taste-toxin pairing [Garcia & Koelling, 1967]. CTA learning is easily manipulated, as the strength or magnitude of the aversion is dependent on the concentration, saliency, and duration of the CS, as well as the amount or strength of the US [Barker, 1976; Dragoin, 1971; Nachman & Ashe, 1973]. The anatomical pathway involved in CTA is well characterized and includes the nucleus of the solitary tract, parabrachial nucleus, amygdala, and gustatory cortex [for a review, see Yamamoto, 2006]. The two forebrain regions, the amygdala and gustatory cortex, are particularly important as lesions of these areas cause deficits in CTA learning [Josselyn et al., 2004; Nerad et al., 1996], and both structures exhibit cellular changes during and after CTA acquisition, such as induction of long-term potentiation [Escobar & Bermudez-Ratoni, 2000], activation of immediate early genes such as c-fos [Lamprecht and Dudai, 1995], phosphorylation of markers such as MAPK [Berman et al., 1998], phosphorylation of NMDAR subunits such as NR2B [Rosenblum et al., 1997], and changes in the activation and expression of genes such as CREB, fra-2, and fen-1 [Desmedt et al., 2003; Kwon et al., 2008; Saavedra-RodrÃguez et al., 2009]. As with other forms of associative learning, CTA is N-methyl-D-aspartate receptor (NMDAR)-dependent [Jimenez & Tapia, 2004]. Pharmacological inactivation of NMDARs attenuates or blocks CTA [e.g. Gutierrez et al., 1999] while activation by NMDAR agonists enhances CTA learning [Land & Riccio, 1997]. Data from our lab show that the NMDAR agonist, D-cycloserine (DCS), dose-dependently enhances taste learning, but only under certain parameters [Nunnink et al., 2007].
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Date Issued: 2011
Identifier: FSU_migr_etd-0825
Format: Thesis

Title: The Dynamics of the Distribution of Predeators in an Enclosed Reserve in South Africa.
Creator: Engbretsen, Kirstin, Department of Biological Sciences
Abstract/Description: Siyafunda Conservation Initiative conducts wildlife research on the Greater Makalali Private Game Reserve, a 61,000 acre fenced reserve in South Africa. Their objective is to reintroduce native species to the reserve and reestablish the natural ecosystem that was once present across much of South Africa. The purpose of my research trip was to examine the activities of mammalian predators and create GIS-based maps that show predator distribution in the reserve. The predators I focused on were...
Show moreSiyafunda Conservation Initiative conducts wildlife research on the Greater Makalali Private Game Reserve, a 61,000 acre fenced reserve in South Africa. Their objective is to reintroduce native species to the reserve and reestablish the natural ecosystem that was once present across much of South Africa. The purpose of my research trip was to examine the activities of mammalian predators and create GIS-based maps that show predator distribution in the reserve. The predators I focused on were lion, cheetah, leopard and hyena. My goals were to receive training and field experience in conservation research and to provide Siyafunda with information that could help with decisions for future management. During my six weeks living in the reserve, we took daily monitoring drives to collect information, such as demographic statistics, prey selection, reproductive behavior, and habitat usage for multiple species. Using the predator information I collected in six weeks, as well as eight years of Siyafunda's previous data, I created maps to visualize predatory home ranges in the reserve. I also helped with updating the identification system for individual animals and creating family trees that help identify the bloodline of individual predators. I studied the past data to help analyze predator movement and population dynamics throughout the years. I also investigated the ways that adding or removing animals from the system affects already established populations. I am working with the director of Siyafunda, Michael Job, to develop a GIS-based distribution model that can be continuously updated. My research should assist the managers of the GMPGR as they continue to assure the health of the ecosystem, especially regarding the challenges within a closed system of overpopulation or species decline from competition.
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Date Issued: 2013
Identifier: FSU_migr_undergradresearch-0011
Format: Citation

Title: Protecting Against Photoreceptor Degeneration in a Model of Retinitis Pigmentosa.
Creator: Lebowitz, Joseph, Department of Biological Sciences
Date Issued: 2013
Identifier: FSU_migr_undergradresearch-0023
Format: Citation

Title: Zymosan Fungal Infection Induces Necleosome Distributions During the Innate Immune Response on a Time Dependent Manner.
Creator: Gruder, Olivia, Department of Biological Sciences
Abstract/Description: Chromatin structure plays a critical role in the regulation of the human genome. An understanding of the role of chromatin structure and its relationship to gene regulation is critical to developing new strategies to prevent and treat diseases. We chose to investigate the anti-inflammatory response of human macrophage-like cell line (THP1) to Zymosan, in order to elucidate the regulation of chromatin. Zymosan is a component of the fungal cell wall that induces an innate immune response. After...
Show moreChromatin structure plays a critical role in the regulation of the human genome. An understanding of the role of chromatin structure and its relationship to gene regulation is critical to developing new strategies to prevent and treat diseases. We chose to investigate the anti-inflammatory response of human macrophage-like cell line (THP1) to Zymosan, in order to elucidate the regulation of chromatin. Zymosan is a component of the fungal cell wall that induces an innate immune response. After THP1 were treated with Zymosan, we hypothesized that the fungal infection would initiate an inflammatory response by altering nucleosome redistribution and/or altering chromatin structure in a time dependent manner. Based on previous results that showed rapid, widespread, transient changes in nucleosome distribution in the innate immune response, we chose to look at multiple time points at high temporal resolution: 0 (control), 20', 40', 60', 80', 100', 2h, 3h, 4h and 12h. We measured nucleosome distribution at each of these time points at hundreds of genes transcription start sites involved in the immune response. We saw the greatest changes in nucleosome positioning from 20 to 60 minutes, and it appeared that these changes were transient since they reverted back to their original after the 60-minute time point. These results support our prediction that all cells have the same nucleosome distributions during their resting states, but can be altered with the addition of an insult. In response to a stimulus, a biochemical "yawn" occurs to provide accessibility to genes needed to provide a response. The data indicates that widespread but transient changes occur to the entire genome upon response to an environmental stimulus.
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Date Issued: 2013
Identifier: FSU_migr_undergradresearch-0006
Format: Citation

Title: Determining by use of Nested Deletions what Maintains Proper Replication Timing.
Creator: Davis, Caroline, Department of Biological Sciences
Date Issued: 2013
Identifier: FSU_migr_undergradresearch-0020
Format: Citation

Title: Protecting Against Rod Degeneration In A Model Of Retinitis Pigmentosa.
Creator: Lebowitz, Joseph, Department of Biological Science
Abstract/Description: Retinitis Pigmentosa (RP) is a heritable disease that affects the retina, the photosensitive neural tissue lining the back of the eye. RP results in the gradual degeneration of rod photoreceptor cells, but secondarily cone cells degenerate and all visual input is lost. Mutations in nearly 100 genes have been associated with this disease and related disorders, however little is known about the series of cellular events that precede photoreceptor death. Taking advantage of a transgenic...
Show moreRetinitis Pigmentosa (RP) is a heritable disease that affects the retina, the photosensitive neural tissue lining the back of the eye. RP results in the gradual degeneration of rod photoreceptor cells, but secondarily cone cells degenerate and all visual input is lost. Mutations in nearly 100 genes have been associated with this disease and related disorders, however little is known about the series of cellular events that precede photoreceptor death. Taking advantage of a transgenic zebrafish model of rod degeneration, a small molecule screen and morpholino injections were used to identify modifiers of the cell death typically observed in RP. Rod photoreceptors in the developing zebrafish larvae express a fluorescent reporter gene. This leads to rod degeneration similar to that seen in RP, but cell death can easily be observed under a microscope. Live larvae were observed under the fluorescence microscope to determine if a compound has slowed or altered the degeneration of the rod cells at 4 days post fertilization. A gene-dosage dependent rate of degeneration was uncovered when comparing larvae that were hetero- and homozygous for the transgene. Modulation of the retinoic acid pathway modestly altered cell death. Knocking down Nr2e3 and p53 expression also showed protective effects that were stronger than those following chemical treatment. p53 codes for a key regulator of apoptosis, and Nr2e3 codes for a transcription factor of the rhodopsin gene. These results suggest further study of genetic and chemical manipulation of photoreceptor degeneration, and genotype-phenotype correlations in such diseases.
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Date Issued: 2013
Identifier: FSU_migr_uhm-0269
Format: Thesis

Title: Phylogeographic Patterns in the Eastern Diamondback Rattlesnake (Crotalus adamanteus).
Creator: Aronow, Karalyn, Biological Science
Abstract/Description: The aim of this project was to analyze relationships among populations of Crotalus adamanteus (Eastern Diamondback Rattlesnake) and to compare phylogeographic patterns across different classes of genes. The objective was to determine the effect of selective pressures on the detection of barriers to gene flow. For example, venom genes are under strong positive selection and allow an analysis of the rate of allele exchange in a gene that directly affects the fitness of an individual. This...
Show moreThe aim of this project was to analyze relationships among populations of Crotalus adamanteus (Eastern Diamondback Rattlesnake) and to compare phylogeographic patterns across different classes of genes. The objective was to determine the effect of selective pressures on the detection of barriers to gene flow. For example, venom genes are under strong positive selection and allow an analysis of the rate of allele exchange in a gene that directly affects the fitness of an individual. This selection might drive alleles through phylogeographic barriers that limit the spread of neutral alleles. The relationship between nontoxin genes and fitness is not as clear and can be difficult to establish. However, most variation in these genes is neutral and determined by stochastic events. The type of selection on a gene will affect the phylogeographic pattern displayed. Prior phylogeographic studies have used either neutral markers (e.g., microsatellites) or genes not directly involved in specific adaptations (e.g., mitochondrial genes). One venom gene, two mitochondrial genes, one nuclear gene, and one pseudogene were compared for patterns of adaptation and the presence of geographic barriers to gene flow. This novel approach to studying gene flow could have an impact on defining taxonomic groups and conservation efforts, as well as serve as a guide for choosing appropriate genetic markers for other species. In the venom gene that was analyzed, it appeared the high level of selection led to alleles being driven across the barriers to gene flow of alleles under neutral selection.
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Date Issued: 2011
Identifier: FSU_migr_uhm-0002
Format: Thesis

Title: Retinal gene profile.
Creator: Thornton, Kimberley
Date Issued: 2005-08-03
Identifier: 160469, FSDT160469, fsu:18925
Format: Document (PDF)

Title: Histone Deacetylase Inhibitors Prevent Nucleosome Redistribution at Transcription Start Sites.
Creator: Pickeral, Crystal, Biological Science
Date Issued: 2011
Identifier: FSU_migr_uhm-0034
Format: Thesis

Title: Analysis of the length control mechanism in Chlamydomonas reinhardtii.
Creator: Smith, Felicia
Date Issued: 2005-08-03
Identifier: 160529, FSDT160529, fsu:18953
Format: Document (PDF)

Title: Patterns of genetic variation and covariation in Viola septemloba.
Creator: Ransom, David Glenn
Date Issued: 2007-07-13
Identifier: 160757, FSDT160757, fsu:19061
Format: Document (PDF)

Title: The linking of coral disturbance, specifically the formation of "chimneys" on Acropora palmata, to the threespot damselfish Stegastes planifrons.
Creator: Clapp, Francis
Date Issued: 2005-12-09
Identifier: 160587, FSDT160587, fsu:18983
Format: Document (PDF)

Title: Amygdala Mechanisms Involved in Chemosensory Communication.
Creator: Stroe, Ioana, Biological Science
Abstract/Description: The amygdala is an almond-shaped region of the brain present in many vertebrates such as human, hamsters and mice. The amygdala is composed of several parts, of which the following are most relevant to my research: the basolateral amygdala (BLA) and the posterior medial amygdala (MeP). The BLA functions in learning and shows increased activation after the mouse has learned a behavior. The lateral paracapsular nuclei of the intercalated nucleus (ICNlpcn) project inhibitory neurons into the BLA...
Show moreThe amygdala is an almond-shaped region of the brain present in many vertebrates such as human, hamsters and mice. The amygdala is composed of several parts, of which the following are most relevant to my research: the basolateral amygdala (BLA) and the posterior medial amygdala (MeP). The BLA functions in learning and shows increased activation after the mouse has learned a behavior. The lateral paracapsular nuclei of the intercalated nucleus (ICNlpcn) project inhibitory neurons into the BLA and mediate its activity. Dopamine has been shown to inhibit the lpcn group and therefore relieve inhibition of the BLA (disinhibition). Dopamine also acts directly in the BLA to increase activation. Therefore, if a mouse is conditioned to prefer a particular odor (in this case steer urine), dopamine injection will cause an increase in BLA activation after learning due to both disinhibition and direct excitatory response. The medial posterior amygdala in the mouse mostly responds to olfactory stimuli from the same species (conspecific stimuli). The MeP is also thought to be under control of another ICN group, the caudal ICN (ICNc). If the same inhibitory relationship is seen between ICNc and MeP, the dopamine injection may cause disinhibition in the MeP and therefore the conditioned steer urine stimulus may show increased activation in the MeP despite being a stimulus from another species (heterospecific stimulus). My experiment tests whether the ICNc has inhibitory control over the MeP, and whether dopamine will cause inhibition in the ICNc and therefore cause disinhibition in the MeP.
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Date Issued: 2011
Identifier: FSU_migr_uhm-0040
Format: Thesis

Title: The Cost of Safety: Negotiating the Trade-Off between Safety and Growth.
Creator: Matechik, Christopher, Biological Science
Abstract/Description: To avoid the threat of predation, prey can alter their behavior such as moving from habitats where predation risk is high to those where it is low. However, such behaviors may involve a tradeoff if the low risk habitats are suboptimal feeding locations for the prey compared to the high risk ones. In seagrass, pinfish (Lagodon rhomboides) often move from low- to high-blade density patches in the presence of the predatory Gulf flounder (Paralichthys albigutta). However, restricted movements in...
Show moreTo avoid the threat of predation, prey can alter their behavior such as moving from habitats where predation risk is high to those where it is low. However, such behaviors may involve a tradeoff if the low risk habitats are suboptimal feeding locations for the prey compared to the high risk ones. In seagrass, pinfish (Lagodon rhomboides) often move from low- to high-blade density patches in the presence of the predatory Gulf flounder (Paralichthys albigutta). However, restricted movements in high-blade habitats may lead to reduced foraging efficiency and growth rates. I used a field experiment that ran for 28 days to examine this potential tradeoff between survival and growth. Neither predator presence nor seagrass blade density affected survival or growth in pinfish. However, after accounting for the loss of experimental replicates at lower grass-blade densities, the change in pinfish biomass was greater in the predator-present treatment compared to the controls, suggesting higher mortality, increased vigilance or both when flounder were present. Unfortunately, loss of experimental replicates and high variance in the measured responses hindered my ability to address the potential tradeoff, but suggestive results support further examination.
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Date Issued: 2011
Identifier: FSU_migr_uhm-0025
Format: Thesis

Title: Characterization of Maize Transgene-Reactivated Mutants.
Creator: Mills, Erica, Biological Science
Abstract/Description: Epigenetic gene regulation results from heritable changes in chromatin structure, DNA methylation, and/or histone modifications associated with different expression levels for endogenous genes and transgenes. The silent b1 transgene (Btg-s) can be used to study epigenetic gene regulation in maize. A forward genetics screen based on the reactivation of Btg-s was conducted using EMS mutagenized maize. Through this screen, several mutants reactivating the transgene, designated transgene...
Show moreEpigenetic gene regulation results from heritable changes in chromatin structure, DNA methylation, and/or histone modifications associated with different expression levels for endogenous genes and transgenes. The silent b1 transgene (Btg-s) can be used to study epigenetic gene regulation in maize. A forward genetics screen based on the reactivation of Btg-s was conducted using EMS mutagenized maize. Through this screen, several mutants reactivating the transgene, designated transgene reactivated (tgr), were identified. Published work demonstrates that mutations affecting proteins involved in the RNA-dependent DNA methylation pathway cause transgene reactivation. Such mutations result in characteristic phenotypes, such as a loss of DNA methylation, loss of siRNA accumulation, and loss of transcriptional silencing. To investigate Btg promoter methylation in the tgr mutants, bisulfite sequencing was performed on plants with silenced and reactivated transgenes from four lines of tgr mutants (tgr1-3,11). Results show that in three mutant lines, the promoter region had higher methylation levels in silenced plants compared to reactivated plants, while another mutant had similar levels of methylation in both phenotypes. For tgr2, siRNA levels were assayed and transcript abundance was evaluated for genes encoding proteins possibly involved in the methylation pathway. It was found that tgr2 showed no loss of siRNA production and no difference in transcript levels were observed between silenced and reactivated individuals for the genes evaluated. This work aided in characterizing the tgr mutants which are potentially strong tools for understanding epigenetic regulation of transgenes.
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Date Issued: 2011
Identifier: FSU_migr_uhm-0028
Format: Thesis

Title: Chromatin Structural Changes Linking Retinoic Acid Function to Genomic Targets.
Creator: Hood, Preston
Abstract/Description: Eukaryotic DNA is organized into chromatin, which serves as the ultimate substrate for all nuclear events including transcription, replication, recombination and repair. Alterations to chromatin and its modes of remodeling serve as the basis for understanding gene regulation. Chromatin structure can be analyzed to identify the mechanics and regulation associated to genome response. All-trans retinoic acid (atRA), a metabolite of Vitamin A, uses a direct route to control gene expression within...
Show moreEukaryotic DNA is organized into chromatin, which serves as the ultimate substrate for all nuclear events including transcription, replication, recombination and repair. Alterations to chromatin and its modes of remodeling serve as the basis for understanding gene regulation. Chromatin structure can be analyzed to identify the mechanics and regulation associated to genome response. All-trans retinoic acid (atRA), a metabolite of Vitamin A, uses a direct route to control gene expression within the nucleus. Retinoic acid (RA) binds DNA via coactivating RA receptors that function through a type 2 nuclear receptor pathway. This binding is believed to stimulate a shift in the structure of DNA that could possibly result from alterations to proteins associated with specific locations (Wan et al., 2012). The GM12878 cell line was treated with atRA for different lengths of time and the resulting changes in chromatin structure were mapped. We sought to understand if this chromatin structure mechanism is more broadly used to facilitate RA-induced regulation in the human genome. Here we show that changes can be mapped using the R console computer program created by the Dennis Lab. Genes were analyzed and can be categorized into three different categories of change: consistent changes through all three time points in the same location; changes through all three time points in different locations; and transient stage changes that do not appear in the early or late treatment times.
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Date Issued: 2012
Identifier: FSU_migr_uhm-0082
Format: Thesis

Title: Rescue of a Chlamdydomonas Reinhardtii Mutant.
Creator: Crumbley, Christine, Biological Science
Abstract/Description: This research focuses on the signal transduction pathway involved in acid-induced deflagellation in the green algae Chlamydomonas reinhardtii. A wild type copy of the 2L15 gene will be amplified and used to create a plasmid. This plasmid will contain a wild type copy of the nitrate reductase gene of Chlamydomonas reinhardtii, which will serve as a selectable marker, as well as the 2L15 gene. The plasmid will be used to transform Chlamydomonas reinhardtii mutants with the hope of rescuing the...
Show moreThis research focuses on the signal transduction pathway involved in acid-induced deflagellation in the green algae Chlamydomonas reinhardtii. A wild type copy of the 2L15 gene will be amplified and used to create a plasmid. This plasmid will contain a wild type copy of the nitrate reductase gene of Chlamydomonas reinhardtii, which will serve as a selectable marker, as well as the 2L15 gene. The plasmid will be used to transform Chlamydomonas reinhardtii mutants with the hope of rescuing the mutant phenotype.
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Date Issued: 2007
Identifier: FSU_migr_uhm-0044
Format: Thesis

Title: Restoration and Control of Circadian Rhythmicity in a Novel Transgenic Mouse.
Creator: Abich, Estela, Department of Biological Science
Abstract/Description: Previous biochemical findings from our lab revealed that PERIOD (PER) proteins globally regulate the molecular oscillator through both transcriptional and posttranslational mechanisms. Furthermore, our lab demonstrated that PER rhythms define a critical rhythmic nodal point in the generation of circadian rhythms. Deciphering the phase shifting mechanism is important for developing effective pharmacological or environmental (e.g., phototherapy) interventions to treat many circadian diseases,...
Show morePrevious biochemical findings from our lab revealed that PERIOD (PER) proteins globally regulate the molecular oscillator through both transcriptional and posttranslational mechanisms. Furthermore, our lab demonstrated that PER rhythms define a critical rhythmic nodal point in the generation of circadian rhythms. Deciphering the phase shifting mechanism is important for developing effective pharmacological or environmental (e.g., phototherapy) interventions to treat many circadian diseases, including sleep disorders in shift workers. Our novel inducible Per2 transgenic mouse in Per1/2-null background provides a unique opportunity to address how perturbations in Per expression can cause phase shifts and the opportunity to delve into whether the clock can be reset to a desirable phase by manipulating PER rhythms in a calculated manner. Although photic stimuli acutely induces both Per1 and Per2, manipulation of Per2 alone should be enough to mimic light-induced phase shifts, because Per-deficient mice are similar to wild type mice in their phase delays and advances in response to light pulses. This experiment aimed to demonstrate how we could use this novel genetic construct to gain an in-depth understanding of how we can artificially regulate rhythms in humans.
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Date Issued: 2014
Identifier: FSU_migr_uhm-0288
Format: Thesis

Title: Quantifying locomotor activity by computer video analysis.
Creator: Liu, Yang
Date Issued: 2005-04-18
Identifier: 160778, FSDT160778, fsu:19070
Format: Document (PDF)

Title: The varnished conk and the forked fungus beetle: predation vs. mutualism in the relationship between Ganoderma lucidum and Bolitotherus cornutus.
Creator: Seitzman, Brian H.
Date Issued: 2007-07-13
Identifier: 160747, FSDT160747, fsu:19057
Format: Document (PDF)

Title: Crosstalk between Chromatin Structure and DNA Methylation and the Regulation of DNA Templated Processes.
Creator: Noori, Tarreq, Biological Science
Abstract/Description: Methylation of DNA is one of the earliest described epigenetic modifications. Hypermethylation is associated with gene silencing, while the inhibition of methylation is generally associated with reactivating silenced genes. The packaging of DNA in the nucleus into chromatin also plays a role in regulating gene expression. We sought to understand the crosstalk between changes in methylation status of the genome and changes in chromatin structure. 5-azacytidine (5-azaC), a potent DNA...
Show moreMethylation of DNA is one of the earliest described epigenetic modifications. Hypermethylation is associated with gene silencing, while the inhibition of methylation is generally associated with reactivating silenced genes. The packaging of DNA in the nucleus into chromatin also plays a role in regulating gene expression. We sought to understand the crosstalk between changes in methylation status of the genome and changes in chromatin structure. 5-azacytidine (5-azaC), a potent DNA methytransferase inhibitor, has recently generated interest as a potential anti-cancer drug, possibly functioning by reactivating silenced tumor suppressor genes. We treated the hematologic cancer cell lines U-937 and T-HP1 with 5-aza for varying lengths of time. We then harvested DNA for methylation studies, RNA for gene expression studies and chromatin for nuclease accessibility studies. The chromatin accessibility was further measured at two different levels of resolution; the domain level (10s of kb) and nucleosome position (10s of bp). This was achieved using an innovative DNA microarray assay. Results were analyzed to correlate changes in chromatin structure with changes in methylation and gene expression. We have identified that the class II, major histocompatibility complex, transactivator (CIITA) shows chromatin structural changes. The results provide a model for understanding the regulatory chromatin structure involved in the immune response.
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Date Issued: 2011
Identifier: FSU_migr_uhm-0032
Format: Thesis

Title: Identification of residues in budding yeast RAD53 kinase that are crucial for regulating histone protein level S.
Creator: Adair, Abigail
Date Issued: 2007-02-01
Identifier: 160306, FSDT160306, fsu:18849
Format: Document (PDF)

Title: Binding interactions between intron RNA and the spliceosomal proteins SF3b155 and p14.
Creator: Cherkis, Karen A.
Date Issued: 2006-05-18
Identifier: 160576, FSDT160576, fsu:18977
Format: Document (PDF)

Title: Exploring the Function of 14-3-3 Proteins in Neurodegenerative Disease.
Creator: Vogt, Peggy, Biological Science
Abstract/Description: The two pathological hallmarks of Parkinson's are neurodegeneration in the substantia nigra parc compacta and the presence of Lewy bodies in the surviving neurons. Recent evidence indicates that Lewy bodies share biochemical and morphological similarities with aggresomes, a large juxtanuclear aggregate. In previous studies, we observed that 14-3-3 proteins promote the aggresome formation of α-Synuclein, the main component of Lewy bodies. In this study, we determined 14-3-3 to have a...
Show moreThe two pathological hallmarks of Parkinson's are neurodegeneration in the substantia nigra parc compacta and the presence of Lewy bodies in the surviving neurons. Recent evidence indicates that Lewy bodies share biochemical and morphological similarities with aggresomes, a large juxtanuclear aggregate. In previous studies, we observed that 14-3-3 proteins promote the aggresome formation of α-Synuclein, the main component of Lewy bodies. In this study, we determined 14-3-3 to have a generalized aggresome promoting function by examining two known aggregation-prone proteins, including a mutant form of CFTR and the GFP-250 protein. To assess the isoform specificity of 14-3-3 proteins in this process, we compared the extent of increase in aggresome formation promoted by overexpression of two different 14-3-3 isoforms. Furthermore, we utilized two different mutants to demonstrate that dimerization of 14-3-3 may not be required for its function in the aggresome formation cascade. Taken together, our data indicate that 14-3-3 proteins may play essential critical role in the aggresome formation process. The discovery of the mechanism by which 14-3-3 participates in the aggresome formation cascade may help us to understand pathogenesis of neurodegenerative diseases, such as Parkinson's disease.
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Date Issued: 2011
Identifier: FSU_migr_uhm-0042
Format: Thesis

Title: Indirect Genetic Effects and the Growth of Juvenile Eastern Mosquitofish (Gambusia holbrooki).
Creator: Buncy, Adam Timothy, Department of Biological Science
Abstract/Description: The purpose of this study was to discover if indirect genetic effects (IGEs) affect male mosquitofish juvenile growth. IGEs can be defined as the environmental effect on an individual's phenotype due to the variation in the genotypes of its social partners (Wolf et al 1998). Indirect genetic effects can impact a variety of phenotypic traits. Specifically, I asked: what are the effects of IGEs on the growth (length and weight) of male juvenile siblings reared in different social environments?...
Show moreThe purpose of this study was to discover if indirect genetic effects (IGEs) affect male mosquitofish juvenile growth. IGEs can be defined as the environmental effect on an individual's phenotype due to the variation in the genotypes of its social partners (Wolf et al 1998). Indirect genetic effects can impact a variety of phenotypic traits. Specifically, I asked: what are the effects of IGEs on the growth (length and weight) of male juvenile siblings reared in different social environments? I tested the hypothesis that indirect genetic effects act during development to affect the growth of juvenile male mosquitofish. The weight and standard length of pairs of sibling males reared in the same physical environment, but different social environments, were measured once per month to assess physical condition. If physical condition differs in response to social environment, this is evidence that indirect genetic effects do play a role. Specifically, mottled and silver juvenile males were reared with two adult females and two adult males, both of which were either silver or mottled. I measured the length and weight of these pairs of sibling males monthly. I found that focal males in silver social environments grew the longest, while the focal males in mottled social environments were shorter. Juvenile male weight was only significantly affected by age. However, trends for weight mirrored those for length. For instance, in the length experiment, mottled focal males in a silver context grew the longest. In the weight experiment, we also saw that mottled focal males in a silver context grew the biggest. Based on these results, I concluded that the growth of juvenile mosquitofish depends upon the genetic composition of their social environment, independent of the genotype of the focal male. This suggests that scientists should take IGEs into consideration when measuring the effects of genotype and environment on traits such as growth, and that IGEs may be an important factor contributing to the rapid evolution of growth in some species.
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Date Issued: 2015
Identifier: FSU_migr_uhm-0529
Format: Thesis

Title: Ecology of an Invasive Lupine.
Creator: Luscuskie, Lauren P., Department of Biological Science
Abstract/Description: Since humans began settling in Iceland, the native vegetation has been slowly degrading. Today, Iceland is one of the most heavily environmentally damaged countries due to human impacts. When Iceland was settled, approximately 60% of the land area was vegetated (Arnalds, 2001). Even as recently as two centuries ago, the plant cover of Iceland was far more extensive than it is at the present. Today, vegetation cover is estimated at 25% of the land area, with trees occupying only 1% (Arnalds,...
Show moreSince humans began settling in Iceland, the native vegetation has been slowly degrading. Today, Iceland is one of the most heavily environmentally damaged countries due to human impacts. When Iceland was settled, approximately 60% of the land area was vegetated (Arnalds, 2001). Even as recently as two centuries ago, the plant cover of Iceland was far more extensive than it is at the present. Today, vegetation cover is estimated at 25% of the land area, with trees occupying only 1% (Arnalds, Aradóttir and Thorsteinsson, 1987; Arnalds, 2004). There are many factors that combine to affect the degradation of Iceland’s vegetated areas. The soils are derived from volcanic activity, are mostly classified as andisols, and are very inclined to erosion (Arnalds, 2004; Ólafsdóttir, Schlyter and Haraldsson, 2001). The cold, windy conditions accelerate soil erosion when plant cover is initially removed by human activity, decreasing the likelihood that vegetative cover can be re-established. The cold, wet soils experience regular frosts that further inhibit the ability of plants to colonize and re-establish themselves. Lupinus nootkatensis, the Nootka Lupine, is native to Western North America. This species of lupine has been shown to ameliorate soil characteristics in other locations due to its ability to fix nitrogen and grow in dense monocultures, subsequently influencing successional dynamics. A legume, the Nootka Lupine fixes nitrogen by a symbiosis with a rhizobium bacteria. This facilitates lupine growth in nitrogen-deficient and highly disturbed soils, such as those of volcanic origin present in Iceland (Riege and Sigurgeirsson, 2009; Myrold and Huss-Danell, 2003). In fixing nitrogen, lupine also supplements the surrounding soil with excess nitrogen. Dense monocultures of lupine, as tall as 120cm, increase litter production and decomposition as well as the trapping of detritus, increasing soil organic matter content (Myrold and Huss-Danell, 2003). Both of these methods allow lupine to improve soil characteristics in unvegetated areas, over time increasing nitrogen and organic matter content in the soils to allow for growth of native successional plant species.--Introduction.
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Date Issued: 2015
Identifier: FSU_migr_uhm-0481
Format: Thesis

Title: Exploring Cis Elements and Trans-Acting Factors Involved in the Human Inactive X Chromosome Organization and Compaction.
Creator: Sun, Zhuo, Chadwick, Brian P., Gunjan, Akash, Dennis, Jonathan Hancock, Yu, Hong-Guo, Deng, Wu-Min, Florida State University, College of Arts and Sciences, Department of...
Show moreSun, Zhuo, Chadwick, Brian P., Gunjan, Akash, Dennis, Jonathan Hancock, Yu, Hong-Guo, Deng, Wu-Min, Florida State University, College of Arts and Sciences, Department of Biological Science
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Abstract/Description: In this dissertation, I have explored cis and trans factors involved in the organization and compaction of the human inactive X chromosome (Xi). I describe here three trans factors (SMCHD1, LRIF1 and SETDB1) that were found to have important roles in Xi chromatin compaction, as demonstrated by a doubling of the Xi volume in their absence. I also report a novel enhancer element on the Xi that is reactivated in SETDB1 mutants and is in part responsible for the Xi decompaction phenotype, and...
Show moreIn this dissertation, I have explored cis and trans factors involved in the organization and compaction of the human inactive X chromosome (Xi). I describe here three trans factors (SMCHD1, LRIF1 and SETDB1) that were found to have important roles in Xi chromatin compaction, as demonstrated by a doubling of the Xi volume in their absence. I also report a novel enhancer element on the Xi that is reactivated in SETDB1 mutants and is in part responsible for the Xi decompaction phenotype, and displays complex cis and trans communication between the active X chromosome and Xi. We have generated SMCHD1 and LRIF1 mutants using both TALENs and CRISPR-Cas9 genome engineering platforms. Loss of either protein results in Xi decompaction and reactivation of some Xi genes. Using the X-linked choroideremia locus (CHM) as an example of a reactivated gene, we show that reactivation is coupled with a reduction in the repressive heterochromatin markers histone H3 trimethylated at lysine 9 (H3K9me3) and 27 (H3K27me3) and an increase in the euchromatin marker histone H3 trimethylated at lysine 4 (H3K4me3) in the promoter region. Alongside these chromatin changes, we observed movement of the CHM locus away from the H3K9me3 territory towards the H3K27me3 territory. Previous data from our lab showed that loss of the macrosatellite repeats DXZ4 from the Xi resulted in large-scale changes in cis to the three-dimensional organization of the Xi, including fragmentation of the chromosome territory as observed by light microscopy. Intriguingly, deletion of SMCHD1 in DXZ4 Xi mutants results in a more pronounced Xi decompaction phenotype than that of SMCHD1 loss alone, suggesting that both perform complementary roles to compact the Xi. In the effort to determine which histone lysine methyl-transferase is responsible for H3K9me3 at the Xi, we isolated SETDB1 TALEN mutant clones and discovered that like SMCHD1 and LRIF1, loss of SETDB1 leads to decompaction of the Xi territory. Furthermore, in the SETDB1 mutants, we observed drastic chromatin changes within the 3’ third of the 1.4 megabase Interleukin 1 Receptor Accessory Protein-Like 1 (IL1RAPL1) gene. In this genomic interval, there is localized loss of repressive chromatin defined by H3K9me3 coupled with a gain of the active makers defined by histone H3 di-methylated at lysine-4 (H3K4me2) and acetylated at lysine 27 (H3K27Ac). The DNA underlying the major peak of H3K27Ac possesses very powerful enhancer activity in vitro and is located immediately adjacent to the long terminal repeat of an endogenous retrovirus element ERVL-MaLR that is reactivated from the Xi in the SETDB1 mutants. Reactivation of the ERVL-MaLR results in a significant increase in the transcription of novel bi-directional transcripts originating from the 3’ region, coupled with a significant reduction in full-length IL1RAPL1 transcripts originating from the endogenous 5’ promoter. To determine if this enhancer element contributes to decompaction of the Xi, clones were isolated in which it had been deleted from either the Xa or Xi using CRISPR-Cas9 system. We found that deletion of the enhancer from the Xi increased detection of full-length IL1RAPL1 transcript in trans, but did not result in Xi decompaction. In contrast, deletion of the enhancer from the Xa decompacted the Xi territory and resulted in a total loss of transcript originating from the 5’ promoter on the Xa. These data revealed complex cis and trans effects that affects IL1RAPL1 gene expression and Xi chromatin compaction. Importantly, this same interval is centrally located in a known fragile site on the X chromosome that is frequently lost in patients with intellectual disability. Portions of this dissertation have been published or are being prepared for publication. Parts of Chapter 1 has been published as a book chapter in Epigenetics: Current Research and Emerging Trends, Caister Academic Press (Chadwick, 2015). The data presented in Chapter 3 has been published in Epigenetics & Chromatin (Sun and Chadwick, 2018). Data presented in Chapter 2 are in the process of being prepared as manuscripts for publication.
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Date Issued: 2019
Identifier: 2019_Spring_Sun_fsu_0071E_15036
Format: Thesis

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