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- Creators: Arizona State University
- Creators: Chen, Qiang
Description
Acceptance of the plant group Martyniaceae as a distinct family has long been questioned. Previously placed in the family Pedaliaceae, the Martyniaceae have been allied to numerous other families within the order Lamiales. The objectives of this study include the investigation of the placement of the Martyniaceae within the order Lamiales using molecular data (chloroplast DNA sequences), the further examination of the internal relationships of the Martyniaceae using an expanded nuclear and chloroplast sequences data set, and the construction of a taxonomic treatment of the family that includes all published names and taxa in the Martyniaceae. An analysis of the Lamiales using two chloroplast gene regions (ndhF and rps16) reveals that the Martyniaceae should be segregated from the family Pedaliaceae, but is not able to support the placement of any of its putatively-related families as sister to the Martyniaceae. Sequences from 151 taxa of the Lamiales are included in the analysis, including six representatives from the Martyniaceae. An analysis of the Martyniaceae using three chloroplast gene regions (psbA-trnH spacer, trnQ-5'rps16 intergenic spacer, and trnS-trnG-trnG spacer and intron) and the Internal Transcribed Spacer resolves two major clades within the Martyniaceae corresponding to the North American taxa (Martynia and Proboscidea) and the South American taxa (Craniolaria, Holoregmia, and Ibicella). Sequences from all five genera and 15 taxa were included in the analysis. Results from the molecular phylogenetic analyses are incorporated into a revised taxonomic treatment of the family. Five genera and thirteen species are recognized for the family Martyniaceae.
ContributorsGutiérrez, Raúl (Author) / Wojciechowski, Martin F (Thesis advisor) / Pigg, Kathleen B (Committee member) / Landrum, Leslie R (Committee member) / Butterworth, Charlie (Committee member) / Arizona State University (Publisher)
Created2011
Description
This study was designed to produce a comprehensive flora of Usery Mountain Regional Park and Pass Mountain of the Tonto National Forest. A total of 168 vascular plant species representing 46 families and 127 genera were collected or documented at this study area. Sixteen species were not native to the flora of Arizona and represent 9.5% of the flora. Nevertheless, the study area does not appear to be significantly damaged or degraded in spite of its historical and current land use. The location and types of invasive species recorded in this study will assist with implementing preventative measures to prevent further spreading of certain species. The complete list of all vascular species recorded in this study will provide a valuable tool for land management decisions and future restoration projects that may occur at this area or similar sites and invasive species control. The distribution of the saguaro (Carnegiea gigantea) population on Pass Mountain was documented through the measurement of saguaros by random sampling. ArcGIS was used to generate 50 random points for sampling the saguaro population. Analysis to determine saguaro habitat preferences based on the parameters of aspect, slope and elevation was conducted through ArcGIS. The saguaro population of Pass Mountain significantly favored the southern aspects with the highest concentration occurring in the southwest aspects at an average density of 42.66 saguaros per hectare. The large numbers of saguaros recorded in the younger size classes suggests a growing populations.
ContributorsMarshall, Laura Lee (Author) / Steele, Kelly P (Thesis advisor) / Miller, William H. (Committee member) / Alford, Eddie J (Committee member) / Arizona State University (Publisher)
Created2011
Description
The cyanobacterium Synechocystis sp. PCC 6803 performs oxygenic photosynthesis. Light energy conversion in photosynthesis takes place in photosystem I (PSI) and photosystem II (PSII) that contain chlorophyll, which absorbs light energy that is utilized as a driving force for photosynthesis. However, excess light energy may lead to formation of reactive oxygen species that cause damage to photosynthetic complexes, which subsequently need repair or replacement. To gain insight in the degradation/biogenesis dynamics of the photosystems, the lifetimes of photosynthetic proteins and chlorophyll were determined by a combined stable-isotope (15N) and mass spectrometry method. The lifetimes of PSII and PSI proteins ranged from 1-33 and 30-75 hours, respectively. Interestingly, chlorophyll had longer lifetimes than the chlorophyll-binding proteins in these photosystems. Therefore, photosynthetic proteins turn over and are replaced independently from each other, and chlorophyll is recycled from the damaged chlorophyll-binding proteins. In Synechocystis, there are five small Cab-like proteins (SCPs: ScpA-E) that share chlorophyll a/b-binding motifs with LHC proteins in plants. SCPs appear to transiently bind chlorophyll and to regulate chlorophyll biosynthesis. In this study, the association of ScpB, ScpC, and ScpD with damaged and repaired PSII was demonstrated. Moreover, in a mutant lacking SCPs, most PSII protein lifetimes were unaffected but the lifetime of chlorophyll was decreased, and one of the nascent PSII complexes was missing. SCPs appear to bind PSII chlorophyll while PSII is repaired, and SCPs stabilize nascent PSII complexes. Furthermore, aminolevulinic acid biosynthesis, an early step of chlorophyll biosynthesis, was impaired in the absence of SCPs, so that the amount of chlorophyll in the cells was reduced. Finally, a deletion mutation was introduced into the sll1906 gene, encoding a member of the putative bacteriochlorophyll delivery (BCD) protein family. The Sll1906 sequence contains possible chlorophyll-binding sites, and its homolog in purple bacteria functions in proper assembly of light-harvesting complexes. However, the sll1906 deletion did not affect chlorophyll degradation/biosynthesis and photosystem assembly. Other (parallel) pathways may exist that may fully compensate for the lack of Sll1906. This study has highlighted the dynamics of photosynthetic complexes in their biogenesis and turnover and the coordination between synthesis of chlorophyll and photosynthetic proteins.
ContributorsYao, Cheng I Daniel (Author) / Vermaas, Wim (Thesis advisor) / Fromme, Petra (Committee member) / Roberson, Robert (Committee member) / Webber, Andrew (Committee member) / Arizona State University (Publisher)
Created2011
Description
ABSTRACT The Phoenix Four Rivers Flora is an inventory of all the vascular plants growing along the Salt, Gila, New and Agua Fria Rivers, and their tributaries in the Phoenix Metropolitan Area during the years of the study (2009-2011). This floristic inventory documents the plant species and habitats that exist currently in the project area, which has changed dramatically from previous times. The data gathered by the flora project thus not only documents how the current flora has been altered by urbanization, but also will provide a baseline for future ecological studies. The Phoenix Metropolitan Area is a large urbanized region in the Sonoran Desert of Central Arizona, and its rivers are important for the region for many uses including flood control, waste water management, recreation, and gravel mining. The flora of the rivers and tributaries within the project area is extremely diverse; the heterogeneity of the systems being caused by urbanization, stream modification for flood control, gravel mining, and escaped exotic species. Hydrological changes include increased runoff in some areas because of impermeable surfaces (e.g. paved streets) and decreased runoff in other areas due to flood retention basins. The landscaping trade has introduced exotic plant species that have escaped into urban washes and riparian areas. Many of these have established with native species to form novel plant associations.
ContributorsJenke, Darin (Author) / Landrum, Leslie R. (Committee member) / Pigg, Kathleen B. (Committee member) / Makings, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2011
Description
Climate change has the potential to affect vegetation via changes in temperature and precipitation. In the semi-arid southwestern United States, heightened temperatures will likely lead to accelerated groundwater pumping to meet human needs, and altered storm patterns may lead to changes in flood regimes. All of these hydrologic changes have the potential to alter riparian vegetation. This research, consisting of two papers, examines relationships between hydrology and riparian vegetation along the Verde River in central Arizona, from applied and theoretical perspectives. One paper investigates how dominance of tree and shrub species and cover of certain functional groups change along hydrologic gradients. The other paper uses the Verde River flora along with that river's flood and moisture gradients to answer the question of whether functional groups can be defined universally. Drying of the Verde River would lead to a shift from cottonwood-willow streamside forest to more drought adapted desert willow or saltcedar, a decline in streamside marsh species, and decreased species richness. Effects drying will have on one dominant forest tree, velvet ash, is unclear. Increase in the frequency of large floods would potentially increase forest density and decrease average tree age and diameter. Correlations between functional traits of Verde River plants and hydrologic gradients are consistent with "leaf economics," or the axis of resource capture, use, and release, as the primary strategic trade-off for plants. This corresponds to the competitor-stress tolerator gradient in Grime's life history strategy theory. Plant height was also a strong indicator of hydrologic condition, though it is not clear from the literature if plant height is independent enough of leaf characteristics on a global scale to be considered a second axis. Though the ecohydrologic relationships are approached from different perspectives, the results of the two papers are consistent if interpreted together. The species that are currently dominant in the near-channel Verde River floodplain are tall, broad-leaf trees, and the species that are predicted to become more dominant in the case of the river drying are shorter trees or shrubs with smaller leaves. These results have implications for river and water management, as well as theoretical ecology.
ContributorsHazelton, Andrea Florence (Author) / Stromberg, Juliet C. (Thesis advisor) / Schmeeckle, Mark W (Committee member) / Franklin, Janet (Committee member) / Arizona State University (Publisher)
Created2011
Description
Over the past decade, several high-value proteins have been produced using plant-based transient expression systems. However, these studies exposed some limitations that must be overcome to allow plant expression systems to reach their full potential. These limitations are the low level of recombinant protein accumulation achieved in some cases, and lack of efficient co-expression vectors for the production of multi-protein complexes. This study report that tobacco Extensin (Ext) gene 3' untranslated region (UTR) can be broadly used to enhance recombinant protein expression in plants. Extensin is the hydroxyproline-rich glycoprotein that constitutes the major protein component of cell walls. Using transient expression, it was found that the Ext 3' UTR increases recombinant protein expression up to 13.5- and 6-fold in non-replicating and replicating vector systems, respectively, compared to previously established terminators. Enhanced protein accumulation was correlated with increased mRNA levels associated with reduction in read-through transcription. Regions of Ext 3' UTR essential for maximum gene expression included a poly-purine sequence used as a major poly-adenylation site. Furthermore, modified bean yellow dwarf virus (BeYDV)-based vectors designed to allow co-expression of multiple recombinant genes were constructed and tested for their performance in driving transient expression in plants. Robust co-expression and assembly of heavy and light chains of the anti-Ebola virus monoclonal antibody 6D8, as well as E. coli heat-labile toxin (LT) were achieved with the modified vectors. The simultaneous co-expression of three fluoroproteins using the single replicon, triple cassette is demonstrated by confocal microscopy. In conclusion, this study provides an excellent tool for rapid, cost-effective, large-scale manufacturing of recombinant proteins for use in medicine and industry.
ContributorsRosenthal, Sun Hee (Author) / Mason, Hugh (Thesis advisor) / Mor, Tsafrir (Committee member) / Chang, Yung (Committee member) / Arntzen, Charles (Committee member) / Arizona State University (Publisher)
Created2012
Description
The Zingiberales, including the gingers (Zingiber), bananas (Musa) and ornamental flowers (Strelitzia, Canna, and Heliconia) are a diverse group of monocots that occupy the tropics and subtropics worldwide. The monophyly of the order is well supported, although relationships between families are not well resolved. A rapid divergence of the Zingiberales has been proposed to explain the poor resolution of paraphyletic families in the order, and direct fossil evidence shows members of both of these lineages of Zingiberaceae and Musaceae were present by the Late Cretaceous. Comparisons of the fossils with extant relatives and their systematic placement have been limited because variation within modern taxa is not completely known. The current study focuses on describing zingiberalean fossil material from North Dakota that includes seeds, leaves, buds, adventitious roots and rhizomes. A survey of extant zingiberalean seeds was conducted, including descriptions of those for which data were previously unknown, in order to resolve the taxonomic placement of the fossil material. Upon careful examination, anatomical characters of the seed coat in fossil and extant seeds provide the basis for a more accurate taxonomic placement of the fossils and a better understanding of character evolution within the order.
ContributorsBenedict, John C (Author) / Pigg, Kathleen B. (Thesis advisor) / Wojciechowski, Martin F. (Committee member) / Devore, Melanie L. (Committee member) / Fall, Patricia L. (Committee member) / Arizona State University (Publisher)
Created2012
Description
This study identifies the flora of the Eagletail Mountain Region, an area covering approximately 100,600 acres, located in west-central Arizona that includes the Eagletail Mountains, Granite Mountains, portions of the Harquahala Valley, and Cemetery Ridge near Clanton Well. The region is located about 129 km (80 mi) west of Phoenix and 24 km (15 mi) south of Interstate 10. Plants were collected over a six-year period, beginning September, 2004 and ending May, 2010, including two wet winters and two wet summers. A total of 702 collections were made covering 292 species that represented 63 families. Additional information on the region included in the thesis are: 1) an analysis of the climate, based on 20 years of rainfall records; 2) a description of the geology and its influence on plant distribution; 3) a prehistory and history identifying archeological sites; 4) an analysis of food plants used by the Native Americans that suggests how they were able to live in the region; 5)a paleo-botanical history based on an evaluation of pack-rat midden collections from mountain ranges around the region; 6) a comparison of the trees, shrubs, and perennials of the Eagletail Mountain Region with those of the Sierra Estrella and Kofa Mountains; and 7) a survey of non-native species. The habitats that the plants occupied based on climate and soils included were: 1) the bottoms and sides of sandy/ gravelly washes, 2) bajada slopes-volcanic soils, 3) bajada slopes-granitic sandy soils, 4) slot canyons/rock outcrops, 5) desert pavement, and 6) open valleys. Each habitat has its own characteristic species composition and distribution.
ContributorsNewton, Douglas R (Author) / Landrum, Leslie (Thesis advisor) / Alcock, John (Thesis advisor) / Makings, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2012
Description
The Arizona State University Herbarium began in 1896 when Professor Fredrick Irish collected the first recorded Arizona specimen for what was then called the Tempe Normal School - a Parkinsonia microphylla. Since then, the collection has grown to approximately 400,000 specimens of vascular plants and lichens. The most recent project includes the digitization - both the imaging and databasing - of approximately 55,000 vascular plant specimens from Latin America. To accomplish this efficiently, possibilities in non-traditional methods, including both new and existing technologies, were explored. SALIX (semi-automatic label information extraction) was developed as the central tool to handle automatic parsing, along with BarcodeRenamer (BCR) to automate image file renaming by barcode. These two developments, combined with existing technologies, make up the SALIX Method. The SALIX Method provides a way to digitize herbarium specimens more efficiently than the traditional approach of entering data solely through keystroking. Using digital imaging, optical character recognition, and automatic parsing, I found that the SALIX Method processes data at an average rate that is 30% faster than typing. Data entry speed is dependent on user proficiency, label quality, and to a lesser degree, label length. This method is used to capture full specimen records, including close-up images where applicable. Access to biodiversity data is limited by the time and resources required to digitize, but I have found that it is possible to do so at a rate that is faster than typing. Finally, I experiment with the use of digital field guides in advancing access to biodiversity data, to stimulate public engagement in natural history collections.
ContributorsBarber, Anne Christine (Author) / Landrum, Leslie R. (Thesis advisor) / Wojciechowski, Martin F. (Thesis advisor) / Gilbert, Edward (Committee member) / Lafferty, Daryl (Committee member) / Arizona State University (Publisher)
Created2012
Description
Is it possible to treat the mouth as a natural environment, and determine new methods to keep the microbiome in check? The need for biodiversity in health may suggest that every species carries out a specific function that is required to maintain equilibrium and homeostasis within the oral cavity. Furthermore, the relationship between the microbiome and its host is mutually beneficial because the host is providing microbes with an environment in which they can flourish and, in turn, keep their host healthy. Reviewing examples of larger scale environmental shifts could provide a window by which scientists can make hypotheses. Certain medications and healthcare treatments have been proven to cause xerostomia. This disorder is characterized by a dry mouth, and known to be associated with a change in the composition, and reduction, of saliva. Two case studies performed by Bardow et al, and Leal et al, tested and studied the relationships of certain medications and confirmed their side effects on the salivary glands [2,3]. Their results confirmed a relationship between specific medicines, and the correlating complaints of xerostomia. In addition, Vissink et al conducted case studies that helped to further identify how radiotherapy causes hyposalivation of the salivary glands [4]. Specifically patients that have been diagnosed with oral cancer, and are treated by radiotherapy, have been diagnosed with xerostomia. As stated prior, studies have shown that patients having an ecologically balanced and diverse microbiome tend to have healthier mouths. The oral cavity is like any biome, consisting of commensalism within itself and mutualism with its host. Due to the decreased salivary output, caused by xerostomia, increased parasitic bacteria build up within the oral cavity thus causing dental disease. Every human body contains a personalized microbiome that is essential to maintaining health but capable of eliciting disease. The Human Oral Microbiomics Database (HOMD) is a set of reference 16S rRNA gene sequences. These are then used to define individual human oral taxa. By conducting metagenomic experiments at the molecular and cellular level, scientists can identify and label micro species that inhabit the mouth during parasitic outbreaks or a shifting of the microbiome. Because the HOMD is incomplete, so is our ability to cure, or prevent, oral disease. The purpose of the thesis is to research what is known about xerostomia and its effects on the complex microbiome of the oral cavity. It is important that researchers determine whether this particular perspective is worth considering. In addition, the goal is to create novel experiments for treatment and prevention of dental diseases.
ContributorsHalcomb, Michael Jordan (Author) / Chen, Qiang (Thesis director) / Steele, Kelly (Committee member) / Barrett, The Honors College (Contributor) / College of Letters and Sciences (Contributor)
Created2015-05