Current Search: Parker, Joseph (x)
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(1 - 9 of 9)
- Title
- BladeFoil - Evidence for a Common Ancestor Between the Beta-Trefoil and Beta-Propeller Protein Architectures.
- Creator
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Parker, Joseph Brandon
- Abstract/Description
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Proteins belong to different architectures (or “folds”) by the way they fold into their tertiary structure. Two common protein architectures are the beta-trefoil fold and the beta-propeller fold. The designed protein “Symfoil-4P” is an example of the beta-trefoil fold and exhibits symmetry in it’s three domains down to the primary level. When a single domain was isolated from Symfoil-4P and studied computationally, it was predicted to fold as a “blade” motif belonging to the beta-propeller...
Show moreProteins belong to different architectures (or “folds”) by the way they fold into their tertiary structure. Two common protein architectures are the beta-trefoil fold and the beta-propeller fold. The designed protein “Symfoil-4P” is an example of the beta-trefoil fold and exhibits symmetry in it’s three domains down to the primary level. When a single domain was isolated from Symfoil-4P and studied computationally, it was predicted to fold as a “blade” motif belonging to the beta-propeller protein methylamine dehydrogenase heavy chain (1MDA). This finding gave rise to the idea that there could be a common ancestor between these two protein architectures. The purpose of this study was to see if evidence could be provided for this common ancestor. To test this a blade sequence substitution was made in Symfoil-4P in two locations. Along with two blade insertions, 3 leucine point mutations in two of the mutants were made, creating four mutants in total. The goal of this study was to see if any of these four mutants fold. All four mutants were resolved using size exclusion chromatography (SEC) in both the presence and absence of guanidine hydrochloride (GuHCl), a chaotropic agent. Two of the mutants were characterized using differential scanning calorimetry (DSC) to test for thermostability and folding. SEC GuHCl experiments all showed significant unfolding events. DSC experiments showed evidence of unfolding events and high thermostability. The outcome from these experiments offers evidence for a possible common ancestor between these two protein architectures.
Show less - Date Issued
- 2018-04-22
- Identifier
- FSU_libsubv1_scholarship_submission_1524438081_15d64dbc
- Format
- Thesis
- Title
- Ab initio Folding of a Trefoil-fold Motif Reveals Structural similarity with a β-propeller Blade Motif.
- Creator
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Tenorio, Connie, Longo, Liam, Parker, Joseph, Lee, Jihun, Blaber, Michael
- Abstract/Description
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Many protein architectures exhibit evidence of internal rotational symmetry postulated to be the result of gene duplication/fusion events involving a primordial polypeptide motif. A common feature of such structures is a domain-swapped arrangement at the interface of the N- and C-termini motifs and postulated to provide cooperative interactions that promote folding and stability. De novo designed symmetric protein architectures have demonstrated an ability to accommodate circular permutation...
Show moreMany protein architectures exhibit evidence of internal rotational symmetry postulated to be the result of gene duplication/fusion events involving a primordial polypeptide motif. A common feature of such structures is a domain-swapped arrangement at the interface of the N- and C-termini motifs and postulated to provide cooperative interactions that promote folding and stability. De novo designed symmetric protein architectures have demonstrated an ability to accommodate circular permutation of the N- and C-termini in the overall architecture; however, the folding requirement of the primordial motif are poorly understood, and tolerance to circular permutation is essentially unknown. The β-trefoil protein fold is a threefold symmetric architecture where the repeating ~42-mer “trefoil-fold” motif assembles via a domain-swapped arrangement. The trefoil-fold structure in isolation exposes considerable hydrophobic area that is otherwise buried in the intact β-trefoil trimeric assembly. The trefoil-fold sequence is not predicted to adopt the trefoil-fold architecture in ab initio folding studies; rather, the predicted fold is closely related to a compact “blade” motif from the β-propeller architecture. Expression of a trefoil-fold sequence and circular permutants shows that only the wild-type N-terminal motif definition yields an intact β-trefoil trimeric assembly, while permutants yield monomers. The results elucidate the folding requirements of the primordial trefoil-fold motif, and also suggest that this motif may sample a compact conformation that limits hydrophobic residue exposure, contains key trefoil-fold structural features, but is more structurally homologous to a β-propeller blade motif.
Show less - Date Issued
- 2020-03-03
- Identifier
- FSU_libsubv1_scholarship_submission_1583283654_54e07068, 10.1002/pro.3850
- Format
- Citation
- Title
- Patterns and Processes of Diversification in Salamanders of the Subfamily Spelerpinae (Caudata: Plethodontidae).
- Creator
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Wray, Kenneth Paul, Steppan, Scott J., Parker, William C., Travis, Joseph, Mast, Austin R., Beerli, Peter, Means, D. Bruce, Department of Biological Science, Florida State...
Show moreWray, Kenneth Paul, Steppan, Scott J., Parker, William C., Travis, Joseph, Mast, Austin R., Beerli, Peter, Means, D. Bruce, Department of Biological Science, Florida State University
Show less - Abstract/Description
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Biologists have long been interested in the diversity of organisms on earth. With their joint presentation to the Linnean Society of London in 1858, Darwin and Wallace proposed natural selection as a clear mechanism to explain the diversity of life. In the 155 years since this seminal presentation, evolutionary biologists have explored the patterns and processes of diversification in a vast number of taxonomic groups, including proposing additional mechanisms and confirming the dominant...
Show moreBiologists have long been interested in the diversity of organisms on earth. With their joint presentation to the Linnean Society of London in 1858, Darwin and Wallace proposed natural selection as a clear mechanism to explain the diversity of life. In the 155 years since this seminal presentation, evolutionary biologists have explored the patterns and processes of diversification in a vast number of taxonomic groups, including proposing additional mechanisms and confirming the dominant presence of natural selection in the role of diversification. The last few decades have seen rigorous debates on the study of these patterns and processes (e.g. adaptive radiation, species concepts) and advances in theory, data acquisition, and analytical methods to address a number of questions associated with diversification. Yet, much of the attention has been on model systems, resulting in deficiencies in our knowledge of how widespread certain phenomena are (e.g. adaptive radiation) or how general certain modes of speciation may be. In the present study, I explore various patterns and processes responsible for the diversification of salamanders in the Spelerpinae (Caudata: Plethodontidae). I examine the role of adaptive radiation in the subfamily, using a completely sampled phylogeny based on multiple loci, by testing a number of predictions based on general theory of the process. I also test a number of hypotheses to explain the diversification patterns observed in a range-wide phylogeographic analysis of the Eurycea quadridigitata species complex. Finally, I use a multilocus nuclear phylogeny and a relatively new species delimitation method to test whether genetic lineages are linked to breeding habitats represent distinct species. Using the species delimitation results, I look for congruence in a number of morphologic traits. I find that adaptive radiation is not a good model for the diversification of the Spelerpinae. In addition, I show strong molecular evidence that habitat isolation has likely lead to ecological speciation in at least three lineages of the complex, with moderate support from the morphology.
Show less - Date Issued
- 2013
- Identifier
- FSU_migr_etd-8085
- Format
- Thesis
- Title
- Dune and Shoreline Evolution of Western Santa Rosa Isand, Florida, 1973-2013.
- Creator
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Bambach, Philip W., Kish, Stephen A., Donoghue, Joseph F., Parker, William C., Wang, Yang, Department of Earth, Ocean and Atmospheric Sciences, Florida State University
- Abstract/Description
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The foredunes at twenty locations on Santa Rosa Island, Florida have been eroded to varying degree in response to Hurricanes Opal (1995), Ivan (2004) and Dennis (2005). At locations where pre-storm foredunes were high and the island was relatively wide, less coastal erosion occurred as a result of storm surge and high winds. For the western portions of Santa Rosa Island Hurricane Ivan had a greater effect on the volume of foredunes and backshore sand than did Hurricane Opal. More erosion is...
Show moreThe foredunes at twenty locations on Santa Rosa Island, Florida have been eroded to varying degree in response to Hurricanes Opal (1995), Ivan (2004) and Dennis (2005). At locations where pre-storm foredunes were high and the island was relatively wide, less coastal erosion occurred as a result of storm surge and high winds. For the western portions of Santa Rosa Island Hurricane Ivan had a greater effect on the volume of foredunes and backshore sand than did Hurricane Opal. More erosion is believed to have occurred during Hurricane Ivan because precursor erosion associated with Hurricane Opal, creating a more vulnerable setting for intense erosion during Hurricane Ivan. During calm conditions, foredunes accrete and migrate inland or prograde depending on shoreline position. In locations where a dune was not completely destroyed by storm surge from a hurricane event, the recovery rate was initially rapid, on the order of 1 ft of dune aggradation per year. In locations where the dunes were completely destroyed due to storm-surge, the recovery rate was much slower, on the order of 0.33 ft of dune aggradation per year. During the time period covered by this study (1973-2013), the foredunes migrated inland seemingly in step with the retreating shoreline. Santa Rosa Island experienced net volume loss of foredune and backshore sediment as well as a net shoreline retreat. Net volume loss of the foredunes and backshore was calculated at seventeen of the twenty locations where profiles were quantified. The greatest volume loss was approximately 58 ft3/ yr per lateral meter. The western portion of the island was the exception where net volume gain occurred at a rate of approximately 104 ft3/ yr per lateral meter. The shoreline retreated at varying degrees at all twenty locations. The most rapid shoreline retreat was approximately 8 ft/yr and the slowest rate was approximately 0.75ft/yr. During the 40-year time period covered in this study, central and western Santa Rosa Island experienced net shoreline retreat and a moderate net volume loss of sand on the backshore and foredunes, similar to results found in previous studies in the Northeast Gulf of Mexico. The retreat is associated with hurricane events that are followed by a limited recovery of the shoreline.
Show less - Date Issued
- 2013
- Identifier
- FSU_migr_etd-8526
- Format
- Thesis
- Title
- Adaptation, Diversification, and Desert Ecology of the Most Diverse Order of Mammals (Mammalia, Rodentia).
- Creator
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Alhajeri, Bader H., Steppan, Scott J., Parker, William C., Erickson, Gregory M., Travis, Joseph, Miller, Thomas E., Department of Biological Science, Florida State University
- Abstract/Description
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Globally, species diversity is regulated by speciation and extinction, and regionally it is regulated by competition, niche, colonization, emigration, and extinction, and more locally, by environmental tolerance and species interactions which filter out non-adapted species based on intrinsic characteristics, or their Hutchinsonian niche. In this dissertation, I examined some of the mechanisms that govern biodiversity patterns in order to determine the main causes of uneven diversity in muroid...
Show moreGlobally, species diversity is regulated by speciation and extinction, and regionally it is regulated by competition, niche, colonization, emigration, and extinction, and more locally, by environmental tolerance and species interactions which filter out non-adapted species based on intrinsic characteristics, or their Hutchinsonian niche. In this dissertation, I examined some of the mechanisms that govern biodiversity patterns in order to determine the main causes of uneven diversity in muroid rodent clades, the most diverse superfamily of mammals, comprising 28% of all mammal species. This extensive diversity, in addition to the remarkable eco-morphological adaptability which facilitated their colonization of all terrestrial biomes make muroids an ideal system to study this fundamental question in evolutionary ecology. In addition, the use of robust phylogenies that have recently been developed in muroids and non-muroid rodents makes the order an especially attractive model system to understand the process of mammalian adaptation to arid environments and the ecological interactions that shaped patterns of coexistence within desert communities, the second main goal of the dissertation. The use of a combination of molecular phylogenetics and geometric morphometrics allows for a robust investigation of general patterns that shape the ecological evolution of this group within and without desert habitats, warranting a reinterpretation of classical studies in evolutionary biology, desert ecology, and the traditional systematics of desert rodent clades.
Show less - Date Issued
- 2014
- Identifier
- FSU_migr_etd-8930
- Format
- Thesis
- Title
- Design and Analysis of Response Surface Designs with Restricted Randomization.
- Creator
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Wesley, Wayne R., Simpson, James R., Srivastava, Anuj, Parker, Peter A., Pignatiello, Joseph J., Department of Industrial and Manufacturing Engineering, Florida State University
- Abstract/Description
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Many industrial experiments are conducted under various conditions which do not facilitate complete randomization of all the experimental factors. In response surface methodology whenever there are restrictions on randomization the experimental procedure usually follows the split plot design approach. Split plot designs are used when there are factors which are difficult or costly to change or adjust during an experiment. Split plot designs are currently generating renewed interest because of...
Show moreMany industrial experiments are conducted under various conditions which do not facilitate complete randomization of all the experimental factors. In response surface methodology whenever there are restrictions on randomization the experimental procedure usually follows the split plot design approach. Split plot designs are used when there are factors which are difficult or costly to change or adjust during an experiment. Split plot designs are currently generating renewed interest because of their usefulness and practical application in industrial settings. Despite the work accomplished through various research efforts, there is still a need to understand the optimality properties of these designs for second-order response surface models. This dissertation provides the development of an analytical approach for the computation of various optimality properties for the assessment of second-order split plot designs. The approach involves a thorough investigation of the impact of restricted randomization on the information matrix, which characterizes much of the relationship between the design points and the proposed response surface model for split plot designs. Several important insights are presented for the construction of second-order split plot designs. In addition, the analytical equations reported compute exact design optimality values and are more efficient than currently available methods. A particular feature of these analytical equations is that they are functions of the design parameters, radius and variance ratio. Further, a significant result is the ability to efficiently compute the exact value of the integrated prediction variance for both split plot designs and completely randomized designs. The functionality of the computational procedures presented provides easy evaluation of the impact of changes in the design structure and variance ratio on the optimality properties of second-order split plot designs.
Show less - Date Issued
- 2006
- Identifier
- FSU_migr_etd-1180
- Format
- Thesis
- Title
- Phylogeny and Character Change in the Feloid Carnivora.
- Creator
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Holliday, Jill A. (Jill Alexandra), Steppan, Scott, Parker, William, Erickson, Gregory, Travis, Joseph, Swofford, David, Department of Biological Science, Florida State University
- Abstract/Description
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This study presents the results of dissertation research performed by Jill Holliday, and includes a study of the effects of specialization to a dental/dietary morphotype, that of the hypercarnivore, on subsequent morphological and taxonomic diversification. This work demonstrates that morphological specialization to hypercarnivory does limit subsequent morphological diversity (disparity) and also reduces frequency of morphological change over the course of a lineage, but has no effect on...
Show moreThis study presents the results of dissertation research performed by Jill Holliday, and includes a study of the effects of specialization to a dental/dietary morphotype, that of the hypercarnivore, on subsequent morphological and taxonomic diversification. This work demonstrates that morphological specialization to hypercarnivory does limit subsequent morphological diversity (disparity) and also reduces frequency of morphological change over the course of a lineage, but has no effect on subsequent taxonomic diversity. Additionally a test of the possibility of biased morphological character evolution as taxa evolve a more hypercarnivorous phenotype indicates that specialists are not subject to strong directional selection, but are instead unable to reverse to a more generalized condition or even move into alternative open niche space, which strongly implies the effects of a functional constraint. To provide a more robust and detailed phylogeny than is currently available, a molecular and morphological dataset was compiled for the feloid Carnivora, a group in which hypercarnivory has evolved at least three times. The molecular dataset is composed of three nuclear and one mitochondrial gene and represents over 5000 base pairs of data for 39 ingroup taxa. This dataset was analyzed under maximum likelihood and Bayesian models, and represents the most robust, thoroughly sampled phylogeny yet available for the feloid Carnivora. However, since the focus of this research is to evaluate character evolution, 103 morphological characters were added to the dataset so that fossil material, particularly ancestral feloids, could also be placed in a phylogenetic context. This combined evidence phylogeny was analyzed using Bayesian inference and with parsimony using a backbone constraint tree based on the previously obtained molecular phylogeny. Both the molecular-only and the combined evidence phylogenies significantly clarify relationships among the feloid families, and also establish the early pattern of divergences within this group. This study establishes that the monotypic family Nandiinidae is the sister to all other extant feloids, while the family Viverridae is the sister to a clade comprised of (Felidae)((Hyaenidae)(Herpestidae/Eupleridae))). The combined evidence tree also allows placement of a number of feloid fossils that occupy key positions at the base of the radiation of extant families. Thus, the genus Herpestides is an early member of Hyaenidae(Herpestidae/Eupleridae), while Plioviverrops is an early herpestid. Finally, the primitive feloids Stenoplesictis, Paleoprionodon, and Haplogale do not position within any of any of the extant families, and instead comprise a paraphyletic grouping at the base of the feloid tree. With these results, the combined evidence phylogeny will enable a more accurate designation of character polarities and estimation of ancestral conditions, which will in turn facilitate additional research in these groups. These phylogenies are the best supported, most thoroughly sampled trees yet produced for the feloid Carnivora, and represent a significant contribution to feloid phylogenetics.
Show less - Date Issued
- 2007
- Identifier
- FSU_migr_etd-3972
- Format
- Thesis
- Title
- Quantifying the Effects of Increased Storminess and Sea-Level Change on the Morphology of Sandy Barrier Islands along the Northwestern and Atlantic Coasts of Florida.
- Creator
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Sankar, Ravi Darwin, Kish, Stephen A., Donoghue, Joseph F. (Joseph Francis), Elsner, James B., Parker, William C., Wang, Yang, Florida State University, College of Arts and...
Show moreSankar, Ravi Darwin, Kish, Stephen A., Donoghue, Joseph F. (Joseph Francis), Elsner, James B., Parker, William C., Wang, Yang, Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
Show less - Abstract/Description
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The ability to accurately quantify shoreline variability along sandy beaches is essential in order to establish aggressive mitigation strategies, based on recent global climate change projections. This investigation employed a suite of coastal data -- topographic maps, aerial photography, high-resolution satellite imagery, and Lidar survey data-- to establish decadal trends of shoreline movement along sandy barrier islands on the northwest and southeast coasts of Florida. An extensive...
Show moreThe ability to accurately quantify shoreline variability along sandy beaches is essential in order to establish aggressive mitigation strategies, based on recent global climate change projections. This investigation employed a suite of coastal data -- topographic maps, aerial photography, high-resolution satellite imagery, and Lidar survey data-- to establish decadal trends of shoreline movement along sandy barrier islands on the northwest and southeast coasts of Florida. An extensive collection of data was assembled for the project, comprising nearly two dozen historic shoreline positions dating from the mid-19th century to the present. The techniques used to detect morphologic change with time were the Digital Shoreline Analysis System (DSAS) and a modernized analytical approach, Analyzing Moving Boundaries Using R (AMBUR). The latter approach was modified with a storm function to provide a forecast of the shoreline under predictions of more intense storminess. Results reveal that severe storms produce dramatic morphological alterations of the coast and in some cases, can result in shoreline retreat in excess of 50 meters during a single event. Special emphasis was placed on rates of change during the past decade and a half period (1995-2013) of active storm conditions. Of the three study areas analyzed, Little St. George Island returned the highest average rate of change of -4.33 m/yr in response to increased storminess. The average rate of change along Perdido Key in response to storms was -0.57 m/yr. Northern Merritt Island however, demonstrated the most stable shoreline of the three study sites and returned an overall mean rate of change of 0.41 m/yr. The results reveal that shoreline orientation, along with engineering projects, act over a variety of spatial and temporal scales to influence shoreline evolution. The trends of shoreline movement also indicate that nearshore bathymetry wields some influence on the behavior of local segments of a barrier island's shoreline. Tidal inlet dynamics were found to cause increased shoreline fluctuations and more notably, accelerated rates of erosion, especially immediately downdrift from the inlets. This project also enumerated volumetric and morphologic change in coastal dunes along a low-profile barrier island. The investigation established that natural dune recovery is directly related to the duration and frequency of storms. Further, the intensity of individual storms was found to be strongly correlated to trends in dune stability and shoreline evolution. Results show that the maintenance of viable dune fields is dependent on several ancillary factors. Such factors include: sediment supply via longshore drift or artificial nourishment, island width, dune field width, continuity of the dune complex, inner-shelf bathymetry and dune re-vegetation. In many cases, dune re-vegetation after storm passage delayed volumetric loss, favoring dune growth and reducing erosion. The analyses indicated that beach and dune recovery was initiated approximately six years following a major storm event. The results demonstrate that the most stable dunes were located along undeveloped and un-nourished segments of the island. In areas where nourishment had taken place however, foredune volumetric loss was significantly less pronounced. The results of this project provide a better and more detailed understanding of the vulnerability of coastal environments to the effects of climate change.
Show less - Date Issued
- 2015
- Identifier
- FSU_migr_etd-9445
- Format
- Thesis
- Title
- Causes of Shoreline Recession in the Chao Phraya Delta.
- Creator
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Bidorn, Butsawan, Kish, Stephen A., Donoghue, Joseph F. (Joseph Francis), Elsner, James B., Burnett, William C., Parker, William C., Florida State University, College of Arts...
Show moreBidorn, Butsawan, Kish, Stephen A., Donoghue, Joseph F. (Joseph Francis), Elsner, James B., Burnett, William C., Parker, William C., Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
Show less - Abstract/Description
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As low-lying areas, deltas are sensitive to changes associated with advance taking place on the land and in the ocean. The pattern of change in shoreline positions over time can be used as an indicator of changes in land and/or ocean environments. Land development and rapid population and economic growth can cause subsidence due to excess groundwater extraction, reduction of river sediment supply by dams, and floodplain engineering. Global eustatic and local relative sea-level changes can...
Show moreAs low-lying areas, deltas are sensitive to changes associated with advance taking place on the land and in the ocean. The pattern of change in shoreline positions over time can be used as an indicator of changes in land and/or ocean environments. Land development and rapid population and economic growth can cause subsidence due to excess groundwater extraction, reduction of river sediment supply by dams, and floodplain engineering. Global eustatic and local relative sea-level changes can also significantly affect the coastline of the lowland area. The main purpose of this study is to investigate the causes of shoreline change in the Chao Phraya (CPY) River delta in Thailand, which is a coastal region dominated by intertidal mudflats. This study focuses on river sediment supply, relative sea level change, and mangrove deforestation. Long-term historical data coupled with field observation were used to determine how these factors are related to shoreline retreat of the delta coastline. Shoreline change evaluation for the Upper Gulf of Thailand, including the Chao Phraya estuary between 1954 and 2013, are based on a series of aerial photographs and satellite imagery. This data set represents historical shoreline positions with time intervals ranging from 2 years to 24 years. The shoreline data were converted into vectorized ArcGIS shapefiles and analyzed using the USGS Digital Shoreline Analysis System ArcGIS extension. River survey data collected during the period 2011-2013 were used for studying the characteristics of river flow and sediment transport in the river system. During the period 2011-2013, the flow and sediment characteristics of rivers were measured 9 times at 8 stations in the Ping, Wang, Yom, Nan, and Chao Phraya rivers. The data cover wet season and dry season flow conditions, including the extreme flood event during 2011. Additionally, sediment deposition rates at the Chao Phraya River mouth were estimated from two sediment cores taken from the Chao Phraya River mouth using 210Pb radiometric dating. The results of this study indicate that relative sea-level rise due to the extremely high rate of land subsidence is the major cause of rapid shoreline change in the CPY Delta, and is responsible for 56 and 63 percent of shoreline retreat in the western and eastern portions of the Chao Phraya Delta, respectively. Unlike other major deltas in the southeast and east Asia, the severe shoreline recession during the period 1954-2013 is not strongly related to sediment supply reduction associated with large dam impoundments. Conversely, sediment deposition rates at the CPY Delta tended to increase after 1994 (30 and 22 years after construction of the Bhumibol and Sirikit Dams, respectively). However, the observed average rate of sediment deposition (8-10 mm/year) is less than the average rate of relative sea-level rise (17 mm/year), and the sediment supply from the CPY is not sufficient to balance land loss due to the rise of sea-level during the past six decades. For land-use changes, most of the vegetation areas, especially mangrove forest bounding along the edge of the shoreline, have been converted into aquacultural farmland by 1994. Results from mangrove area analysis over the period 1954-2013 reveal that the reduction of shoreline retreat rates in the eastern CPY was not directly associated with an increase in mangrove areas undergoing reforestation, and mangrove reforestation could not be cited as a shoreline builder or effective measure for coastal protection for coastlines that are rapidly retreating due to land subsidence. However, conversion of mangrove areas into aquaculture farmland can magnify shoreline retreat caused by relative sea-level rise. Results of this study may provide a useful analog for other coastal regimes of the Earth that may experience the effect of the predicted 1-2 meter rise over the next century associated with global warming.
Show less - Date Issued
- 2016
- Identifier
- FSU_2016SU_Bidorn_fsu_0071E_13407
- Format
- Thesis
