Comparative DNA sequencing of matK, a maturase-encoding gene located within the intron of the chloroplast trnK gene, was evaluated for phylogenetic utility above the family level and within the grass family (Poaceae). There are three major objectives in the research. The first one is to study the utility of the matK gene in plant evolution. The second objective is to characterize the matK gene in the grass family. The last major goal is to address the phylogenetic questions in the Poaceae using the matK sequences from representatives of different grass groups. In order to study the potential application of matK to plant systematics above the family level, eleven complete sequences from GenBank representing seed plants and liverworts and nine partial sequences generated for genera representing the monocot families Poaceae, Joinvilleaceae, Cyperaceae, and Smilacaceae were analyzed. The study underscored the following useful properties of the matK gene for phylogenetic reconstruction: reasonable size (1500 bp), high rate of substitution, large proportion of variation at the first and the second codon positions, low transition-transversion ratio, and the presence of mutationally-conserved sectors. The use of different sectors of the gene and the cumulative inclusion of informative sites showed that the 3' region was the most useful in resolving phylogeny, and that the topology and robustness of the tree reached a plateau after the inclusion of 100 informative sites. The presence of a relatively conserved 3' region and the less conserved 5' region provides two sets of characters that can be used at different taxonomic levels from the tribal to the division levels. It also has demonstrated the potential of partial sequencing in resolving systematic relationships from the tribe to the division level. The matK gene in the Poaceae was characterized with complete sequences from 11 grass genera, representing 7 subfamilies and 11 tribes, and one outgroup (Joinvillea plicata, Joinvillaceae). The alignment of 1632 base pairs from 14 species yielded a data set of 601 (36.8)% variable sites and 246 (15.1%) informative sites. The variations at nucleic and amino acid levels evenly distributed throughout the entire gene, and the 5' region appears to have more variation than the 3' region. The changes at the third codon position are very low as compared to the total of the first and second positions. This has led to a similar variation pattern at nucleic and at amino acid levels. The average tr/tv ratio generated from 14 entire matK sequences is 1.29. It is intriguing to find that the tr/tv ratios were regionally related. RASA analysis of the alignment data indicated a relatively high phylogenetic signal in the data set of 14 taxa. In the two half analyses, while the tRASA of the 5' half of the matK gene (0.43) is not significant, the 3' of the matK gene showed a significant phylogenetic signal. Among the 5 sections of the 14 entire matK sequences, only the fourth sector contains a statistically significant phylogenetic signal. These results indicate that matK is a phylogenetically valuable gene and that the 3' region of the matK gene contains strong phylogenetic information. A single most parsimonious tree was obtained from the 246 informative sites of the 14 entire matK sequences. Seven major groups were well resolved on the most parsimonious tree, corresponding to the seven commonly recognized subfamilies: Aruninoideae, Bambusoideae, Centothecoideae, Chloridoideae, Panicoideae, Pooideae and Oryzoideae. Approximately 960 base pairs of the matK gene were sequenced from grass species representing 48 genera, 21 tribes, and seven subfamilies to reconstruct a phylogeny for the Poaceae. Joinvillea plicata (Joinvilleaceae) was used as an outgroup species. The aligned sequences showed that 495 nucleotides (51%) were variable and 390 (36%) were phylogenetically informative. RASA indicated that very significant phylogenetic signals exist in this data set. The cumulative addition of informative sites starting at the internal end of the sequences revealed that at 300 sites, tree topology and bootstrap values matched those of the consensus tree based on the entire sequence. Parsimony analyses using PAUP resulted in six most parsimonious trees and a strict consensus tree showing major lineages supported by high bootstrap values. These lineages corresponded to six subfamilies: Bambusoideae, Oryzoideae, Pooideae, Chloridoideae, Panicoideae, and Arundinoideae. The Bambusoideae, including woody and herbaceous taxa, diverged as the most basal lineage, and the monophyletic oryzoid species formed a sister group. The Chloridoideae, Panicoideae, Arundinoideae, and the centothecoid Zeugitis (PACC group) emerged as a monophyletic assemblage with 95% bootstrap support. The Aristideae branched off as a monophyletic line basal to the chloridoid clade. Stipeae appeared as a sister taxon to the Pooideae. The matK-based phylogeny did not reveal a major dichotomy in the family. The matK gene has provided sequence information sufficient for good resolution of the major grass lineages. / Ph. D.

Platanthera is one of the largest genera of temperate orchids and exemplifies a lineage that has adaptively radiated into diverse habitats within North America, Asia, Europe, North Africa, Borneo, and Sarawak. Major centers of diversity in this genus are western North America and eastern Asia. The diversity in floral morphological traits such as floral color, shape and the length of nectar spur is associated with numerous pollination syndromes, making Platanthera an ideal system to study the evolution of floral traits and pollination biology. Despite its diversity, a thorough phylogenetic hypothesis for the genus is lacking because no studies have yet sampled taxa exhaustively or developed a robust molecular toolkit. Nevertheless, in past phylogenetic studies some intrageneric groups of species appear to be monophyletic. One of these groups is subgenus Limnorchis, but the majority of taxa in this group have not been included in a phylogenetic analysis. In this study, I developed a new toolkit for Platanthera consisting of genomic information from 617 low-copy nuclear loci. Using a targeted enrichment approach, I collected high-throughput sequence data from these loci in 23 accessions, including nine of the 12 diploids of subgenus Limnorchis and nine outgroup Platanthera species. A maximum likelihood search was performed on a 570,818 nucleotide supermatrix to generate a phylogeny. This analysis resolved a strongly supported monophyletic clade for subgenus Limnorchis. This phylogeny was then used to test hypotheses of biogeographic diversification and floral trait evolution of subgenus Limnorchis. Ancestral biogeographic reconstruction indicated that subgenus Limnorchis originated in western North America ca. 3 – 4.5 Mya from an ancestor that was widespread in western North America and eastern Asia and subsequently diversified in western North America, followed by dispersal of some species to eastern North America. Floral macro and micro-morphological traits were characterized across the subgenus. Ancestral character reconstruction suggests convergent evolution of spur length, spur shape and viscidium shape, possibly in response to selection by similar pollinators. Understanding the biogeographic history and morphological diversification of subgenus Limnorchis within a phylogenetic context will contribute to an updated taxonomy for the subgenus.

The advent of large-scale genomic sequencing is providing researchers with an unparalleled wealth of information which can be used to elucidate the evolutionary relationships of living organisms. The newly available genome sequence data have enabled the use of comparative genomic techniques for the identification of novel molecular signatures, shared uniquely by evolutionarily related groups of organisms: conserved signature indels (CSIs) and conserved signature proteins (CSPs). These signatures allow for the unambiguous delineation of the prokaryotic taxa, independent of gene and genome based phylogenetic trees, and provide insights into novel aspects of their evolutionary relationships. The phylum Spirochaetes and the class Betaproteobacteria are large, diverse groups of bacteria, containing many important pathogenic and environmental organisms, which are classified primarily on the basis of 16S rRNA gene analysis. Here, I describe phylogenetic analyses of the phylum Spirochaetes based on genome derived molecular signatures. These analyses have yielded substantial evidence for differentiation between the three main sequenced groups of organisms within the phylum Spirochaetes and between the genus Borrelia from other closely related Spirochaetes. These findings have prompted a proposal to create three new orders and a new family within the phylum. These analyses have also supported the differentiation of two clinically distinct groups within the genus Borrelia and a proposal to divide the genus Borrelia into two genera. The use of molecular signatures and phylogenetic analysis of major groups within the class Betaproteobacteria are also described. The analyses of the order Neisseriales within this class resulted in a division of the order into two families, while the analyses of the genus Burkholderia supported the differentiation of the clinically relevant members of the genus Burkholderia from the plant-beneficial and environmental Burkholderia and a proposal to divide the genus into two genera. I also describe the use of phylogenomic techniques and molecular signatures to differentiate the seven main groups within the order Enterobacteriales and the integrated software pipeline used to produce the supermatrix based phylogenomic tree and genome distance calculations in the analysis of the order Enterobacteriales. The molecular signatures described in this thesis represent powerful new tools for evolutionary and systematic studies. Additionally, due to their taxon specificity, these molecular signatures are novel diagnostic markers for their specified group. Further analyses of these molecular signatures should lead to the discovery of novel functions and biological characteristics, mediated by CSIs and CSPs, which will provide important insights into the physiology, evolution, and adaptations of these groups. / Thesis / Doctor of Philosophy (PhD)

This dissertation is composed of four different studies focused on using Human Factors Engineering (HFE) assessment tools traditionally used in industrial settings to evaluate personal protective equipment (PPE) footwear of basketball athletes and assessment of compressible soft robotic sensors to evaluate pressures. The first study developed a Basketball Shoe Taxonomy (BST) designed to categorize shoes using a combination of design factors and effects on performance. The second study investigated the influence of basketball shoe design on jumping performance. Using four jumping patterns, six male and ten female basketball National Collegiate Athletic Association (NCAA) Division I student-athletes completed 16 trials wearing two different Adidas basketball shoe designs. There was no significant difference in effect of shoe type on jumping performance (p > 0.05). The third study examined each athlete’s perception of comfort and quality of fit of the shoes used in the second study using a visual analog scale (VAS) and Likert scale survey. One student-athlete out of 16 reported that one of the shoes tested was their favorite and the most comfortable basketball shoe they had ever worn. Results indicated an average overall comfort rating below 60% for both shoes and there was not a significant difference in perception of comfort or quality of fit between the shoes (p > 0.05). The final study was designed to validate the use of compressible Stretchsense™ sensors (CSSs) to ground reaction pressures. Participants performed three repetitions of squatting, shifting center of pressure between the right foot and left foot, and shifting center of pressure forward and back between the toes and heels. Performance was evaluated using CSSs, BodiTrak Vector Plater™ (BVP), and Kistler Force Plates™ (KFPs). The results indicate that CSSs are an acceptable replacement to ground reaction pressure mats. In addition, the use of an Autoregressive Integrated Moving Average (ARIMA) model resulted in average R2 values greater than 90%. High R2 values in the ARIMA modeling indicates that the software accurately models the human 3D foot-shoe interaction pressures used in the development of the ground reaction pressure socks (GRPS) for sport applications and for fall detection in elderly and balance impaired individuals.

No description available.

No description available.

No description available.

Pistacia is an economically important genus because it contains the pistachio crop, P. vera, which has edible seeds of considerable commercial importance. The evolutionary history of the genus and the taxonomic relationships among the species are controversial and not well understood. This study that has been conducted on this genus to refine taxonomic and evolutionary relationship utilizing different types of data (including morphology, anatomy and molecular) The studied species were the following: Pistacia aethiopica J. O. Kokwaro, P. atlantica Desf., P. chinensis Bunge, P. eurycarpa Yaltirik, P. falcata Becc. ex Martelli, P. integerrima Stew. ex Brand., P. khinjuk Stocks, P. lentiscus L., P. mexicana HBK, P. mutica Fisch. & Mey., P. palaestina Boiss., P. terebinthus L., P. texana Swingle, P. vera L., and P. weinmannifolia Poiss. ex Franch. Phylogenetic analysis based on morphological data strongly supported the monophyly of Pistacia. The genus divided into two monophyletic groups. One group (Section Pistacia) contains P. atlantica, P. chinensis, P. eurycarpa, P. falcata, P. integerrima, P. khinjuk, P. mutica, P. palaestina, P. terebinthus, and P. vera while the other group (Section Lentiscus) contains P. aethiopica, P. lentiscus, P. mexicana, P. texana, and P. weinmannifolia. In anatomical analysis, all species had anomocytic stomata. In most species, the stomata density was higher on the abaxial surface than the adaxial. The ratio of abaxial to adaxial stomatal density varied from 0.0 to 1.7. Stomatal distribution may provide insights into how Pistacia species evolve in terms of leaf anatomy and respond to different climatic changes. Stomatal distribution changed (losing stomata on either surface) as the genus moved into regions of higher rainfall. This study revealed leaflets of P. vera, which have random orientation, were isobilateral, while leaflets of the other species were dorsiventral and were oriented horizontally. RAPD analysis showed that P. khinjuk and P. vera are very close species. This study provides more insights into understanding the evolution, taxonomy and genetics of this economically important genus. / Ph. D.

Astilbe (Saxifragaceae) is a genus of herbaceous perennials widely cultivated for their ornamental value. The genus is considered taxonomically complex because of its geographic distribution, variation within species, and the lack of adequate morphological characters to delineate taxa. To date, an inclusive investigation of the genus has not been conducted. This study was undertaken to (a) develop a well-resolved phylogeny of the genus Astilbe using an expanded morphological data set and sequences from the plastid gene matK, (b) use single nucleotide polymorphisms to determine the lineages of cultivated varieties, and (c) successfully culture Astilbe in vitro and evaluate potential somaclonal variation of resulting Astilbe microshoots. Phylogenetic trees generated from a morphological character matrix of 28 character states divided Astilbe into three distinct clades. Relationships were well resolved among the taxa, though only a few branches had greater than 50% bootstrap support. There is evidence from the phylogeny that some described species may actually represent variation within populations of species. From our analysis I propose an Astilbe genus with 13 to 15 species and offer a key for distinguishing species and varieties. There was little matK sequence variation among taxa of Astilbe. Phylogeny of Astilbe generated from the maximum parsimony and maximum likelihood analysis of matK sequences resulted in a polytomy of seven Astilbe species, with relationships within the genus poorly resolved. A second phylogeny of 21 taxa of Astilbe was more informative, aligning cultivated varieties near species from which they were derived. The matK sequence variation for Astilbe taxa was aligned to reveal DNA polymorphisms. Closely related taxa retained polymorphisms at the same sites within the gene sequence. These polymorphic sites could potentially be utilized to confirm the lineage of popular cultivated Astilbe varieties. Propagation of Astilbe seedlings in tissue culture gave rise to various numbers of microshoots from each of 15 seedlings. Multivariate and cluster analysis of morphological characters from 138 plants derived from 15 seedlings revealed potential somaclonal variants. These variants were characterized by one or more of the following traits: dwarf habit, dark green leaves (high chlorophyll content), increased flowering, or larger plant size. Somaclonal variants with desirable phenotypes may be valuable for cultivar development. / Ph. D.

Since its release in 1999, Bluetooth has become a commonly used technology available on billions of devices through the world. Bluetooth is a wireless technology used for information transfer by devices such as Smartphones, headsets, keyboard/mice, laptops/desktops, video game systems, automobiles, printers, heart monitors, and surveillance cameras. Dozens of threats have been developed by researchers and hackers which targets these Bluetooth enabled devices. The work in this thesis provides insight into past and current Bluetooth threats along with methods of threat mitigation. The main focus of this thesis is the Bluetooth Threat Taxonomy (BTT); it is designed for classifying threats against Bluetooth enabled technology. The BTT incorporates nine distinct classifications to categorize Bluetooth attack tools and methods and a discussion on 42 threats. In addition, several new threats developed by the author will be discussed. This research also provides means to secure Bluetooth enabled devices. The Bluetooth Attack Detection Engine (BLADE) is as a host-based Intrusion Detection System (IDS) presented to detect threats targeted toward a host system. Finally, a threat mitigation schema is provided to act as a guideline for securing Bluetooth enabled devices. / Master of Science