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- Genre: Doctoral Dissertation
- Member of: Theses and Dissertations
Description
This dissertation research investigates both spatial and temporal aspects of Bronze Age land use and land cover in the Eastern Mediterranean using botanical macrofossils of charcoal and charred seeds as sources of proxy data. Comparisons through time and over space using seed and charcoal densities, seed to charcoal ratios, and seed and charcoal identifications provide a comprehensive view of island vs. mainland vegetative trajectories through the critical 1000 year time period from 2500 BC to 1500 BC of both climatic fluctuation and significant anthropogenic forces. This research focuses particularly on the Mediterranean island of Cyprus during this crucial interface of climatic and human impacts on the landscape. Macrobotanical data often are interpreted locally in reference to a specific site, whereas this research draws spatial comparisons between contemporaneous archaeological sites as well as temporal comparisons between non-contemporaneous sites. This larger perspective is particularly crucial on Cyprus, where field scientists commonly assume that botanical macrofossils are poorly preserved, thus unnecessarily limiting their use as an interpretive proxy. These data reveal very minor anthropogenic landscape changes on the island of Cyprus compared to those associated with contemporaneous mainland sites. These data also reveal that climatic forces influenced land use decisions on the mainland sites, and provides crucial evidence pertaining to the rise of early anthropogenic landscapes and urbanized civilization.
ContributorsKlinge, JoAnna M (Author) / Fall, Patricia L. (Thesis advisor) / Falconer, Steven E. (Committee member) / Brazel, Anthony J. (Committee member) / Pigg, Kathleen B (Committee member) / Arizona State University (Publisher)
Created2013
Description
This dissertation investigates spatial and temporal changes in land cover and plant species distributions on Cyprus in the past, present and future (1973-2070). Landsat image analysis supports inference of land cover changes following the political division of the island of Cyprus in 1974. Urban growth in Nicosia, Larnaka and Limasol, as well as increased development along the southern coastline, is clearly evident between 1973 and 2011. Forests of the Troodos and Kyrenia Ranges remain relatively stable, with transitions occurring most frequently between agricultural land covers and shrub/herbaceous land covers. Vegetation models were constructed for twenty-two plant species of Cyprus using Maxent to predict potentially suitable areas of occurrence. Modern vegetation models were constructed from presence-only data collected by field surveys conducted between 2008 and 2011. These models provide a baseline for the assessment of potential species distributions under two climate change scenarios (A1b and A2) for the years 2030, 2050, and 2070. Climate change in Cyprus is likely to influence habitat availability, particularly for high elevation species as the relatively low elevation mountain ranges and small latitudinal range prevent species from shifting to areas of suitable environmental conditions. The loss of suitable habitat for some species may allow the introduction of non-native plant species or the expansion of generalists currently excluded from these areas. Results from future projections indicate the loss of suitable areas for most species by the year 2030 under both climate regimes and all four endemic species (Cedrus brevifolia, Helianthemum obtusifolium, Pterocephalus multiflorus, and Quercus alnifolia) are predicted to lose all suitable environments as soon as 2030. As striking exceptions Prunus dulcis (almond), Ficus carica (fig), Punica granatum (pomegranate) and Olea europaea (olive), which occur as both wild varieties and orchard cultigens, will expand under both scenarios. Land cover and species distribution maps are evaluated in concert to create a more detailed interpretation of the Cypriot landscape and to discuss the potential implications of climate change for land cover and plant species distributions.
ContributorsRidder, Elizabeth (Author) / Fall, Patricia L. (Thesis advisor) / Myint, Soe W (Committee member) / Hirt, Paul W (Committee member) / Arizona State University (Publisher)
Created2013
Description
The remarkable conservation of molecular and intra-/inter-cellular pathways underpinning the fundamental aspects of sugar partitioning in two evolutionarily divergent organisms – a non-vascular moss Physcomitrella patens and a vascular cereal crop Oryza sativa (rice) – forms the basis of this manuscript. Much of our current knowledge pertaining to sugar partitioning in plants mainly comes from studies in thale cress, Arabidopsis thaliana, but how photosynthetic sugar is loaded into the phloem in a crop as important as rice is still debated. Even less is known about the mechanistic aspects of sugar movement in mosses. In plants, sugar either moves passively via intercellular channels called plasmodesmata, or through the cell wall spaces in an energy-consuming process. As such, I first investigated the structure of plasmodesmata in rice leaf minor vein using electron tomography to create as of yet unreported 3D models of these channels in both simple and branched conformations. Contrary to generally held belief, I report two different 3D morphotypes of simple plasmodesmata in rice. Furthermore, the complementary body of evidence in arabidopsis implicates plasma membrane localized Proton Pyrophosphatase (H+-PPase) in the energy-dependent movement of sugar. Within this wider purview, I studied the in situ ultrastructural localization patterns of H+-PPase orthologs in high-pressure frozen tissues of rice and physcomitrella. Were H+-PPases neo-functionalized in the vascular tissues of higher plants? Or are there evolutionarily conserved roles of this protein that transcend the phylogenetic diversity of land plants? I show that H+-PPases are distinctly expressed in the actively growing regions of both rice and physcomitrella. As expected, H+-PPases were also localized in the vascular tissues of rice. But surprisingly, H+-PPase orthologs were also prominently expressed at the gametophyte-sporophyte junction of physcomitrella. Upon immunogold labeling, H+-PPases were found to be predominantly localized at the plasma membrane of the phloem complexes of rice source leaves, and both the vacuoles and plasma membrane of the transfer cells in the physcomitrella haustorium, linking H+-PPases in active sucrose loading in both plants. As such, these findings suggest that the localization and presumably the function of H+-PPases are conserved throughout the evolutionary history of land plants.
ContributorsRegmi, Kamesh Chandra (Author) / Gaxiola, Roberto A (Thesis advisor) / Wojciechowski, Martin F (Committee member) / Pigg, Kathleen B (Committee member) / Roberson, Robert W. (Committee member) / Arizona State University (Publisher)
Created2016
Description
In the face of the sixth mass extinction on Earth, with the flowering plant family Cactaceae assessed as the fifth most endangered plant or animal family by the International Union for the Conservation of Nature (IUCN), it is imperative that all available tools be used to understand the biodiversity, habitat suitability, climate change impacts and population viability of cacti. Within the Cactaceae, Mammillaria Haw and the closely related genus Cochemiea (K. Brandegee) Walton of Baja California, Mexico, are species-rich, with 46 regionally endemic taxa, 12 of which have been assessed as threatened or endangered by the IUCN. This study clarifies the evolutionary relationships in the Mammilloid clade, a complex and species-rich clade in tribe Cacteae, and generic circumscription of the genera Mammillaria Haw. and Cochemiea (K. Brandegee) Walton, estimates divergence times, diversification rates and ancestral ranges and explores habitat suitability and the risk of extinction of a representative species within these genera. The r species, Cochemiea halei (K. Brandegee) Walton, a narrowly distributed island endemic, is assessed using species distribution modeling (SDM) and population viability analysis (PVA). SDM in this study includes projections to two climate change scenarios over the next century, using four representative particle concentration pathways, and the PVA uses habitat-specific deterministic and stochastic models. The results of molecular phylogenetic analyses of the Mammilloid cladde restore the genus Mammillaria to monophyly via new combinations in the genus Cochemiea. The taxa in this study are shown to be of recent origin resulting from rapid diversification and radiation. Geological and climatic forces at multiple scales appear to be responsible for the high degree of biodiversity and endemism of these cacti. SDM shows that C. halei is likely to be stranded in its fragmented island habitat, has a facultative adaptation to ultramafic soils, and faces a 21%–53% contraction of its range on the islands under climate change scenarios. PVA suggests that C. halei is at increased risk of extinction in response to slight decreases in fecundity and persistence. In general, the perspectives in this dissertation fill several gaps in our prior knowledge of the evolution, biogeography, and conservation pressures of an important, species-rich group of cacti, occurring in a region of high biodiversity and endemism.
ContributorsBreslin, Peter (Author) / Wojciechowski, Martin F (Thesis advisor) / Albuquerque, Fabio (Committee member) / Fehlberg, Shannon (Committee member) / Majure, Lucas (Committee member) / Rebman, Jon (Committee member) / Arizona State University (Publisher)
Created2020
Description
Drylands cover over 40% of the Earth’s surface, account for one third of global carbon cycling, and are hotspots for climate change, with more frequent and severe droughts coupled with deluges of novel magnitude and frequency. Because of their large terrestrial extent, elucidating dryland ecosystem responses to changes in water availability is critical for a comprehensive understanding of controls on global aboveground net primary productivity (ANPP), an important ecosystem service. The focus of this dissertation is to investigate cause-effect mechanisms between altered water availability and ecosystem processes in dryland ecosystems. Across a network of experimental rainfall manipulations within a semiarid Chihuahuan Desert grassland, I examined short- and long-term dynamics of multiple ecosystem processes—from plant phenology to nitrogen cycling—in response to directional precipitation extremes. Aboveground, I found herbaceous plant phenology to be more sensitive in greenup timing compared to deep-rooted, woody shrubs, implying that precipitation extremes will disproportionately affect grass-dominated compared to woody ecosystems. Surprisingly, after 14 years of experimentally adding water and N, I observed no effect on ANPP. Belowground, bulk soil N dynamics remained stable with differing precipitation amounts. However, mineral associated organic N (MAOM-N) significantly increased under chronic N inputs, indicating potential for dryland soil N sequestration. Conversely, the difference between low- and high-N soil N content may increase a drawdown of N from all soil N pools under low-N conditions whereas plants source N from fertilizer input under high-N conditions. Finally, I considered ecosystem-level acclimation to climate change. I found that N availability decreased with annual precipitation in space across continents, but it posed initially increasing trends in response to rainfall extremes at the Jornada that decreased after 14 years. Mechanisms for the acclimation process are thus likely associated with differential lags to changes in precipitation between plants and microorganisms. Overall, my dissertation demonstrates that examining linkages between multiple ecosystem processes, from aboveground phenological cycles to belowground N cycling dynamics, can provide a more integrative understanding of dryland response to climate change. Because dryland range is potentially expanding globally, water limited systems provide a unique and critical focus area for future research that revisit and revise current ecological paradigms.
ContributorsCurrier, Courtney (Author) / Sala, Osvaldo (Thesis advisor) / Collins, Scott (Committee member) / Reed, Sasha (Committee member) / Throop, Heather (Committee member) / Arizona State University (Publisher)
Created2023
Description
Climate change is making the arid southwestern U.S. (“Southwest”) warmer and drier. Decreases in water availability coupled with increases in episodic heat waves can pose extraordinary challenges for native riparian tree species to persist in their current ranges. However, the morpho-physiological mechanisms that these species deploy to cope with extreme temperature events are not well understood. Specifically, how do these species maintain leaf temperatures within a safe operational threshold in the extreme conditions found across the region? Morpho-physiological mechanisms influencing intraspecific local adaptation to thermal stress were assessed in Populus fremontii using two experimental common gardens. In a common garden located near the mid-point of this species’ thermal distribution, I studied coordinated traits that reflect selection for leaf thermal regulation through the measurement of 28 traits encompassing four different trait spectra: phenology, whole-tree architecture, and the leaf and wood economic spectrum. Also, I assessed how these syndromes resulted in more acquisitive and riskier water-use strategies that explained how warm-adapted populations exhibited lower leaves temperatures than cool-adapted populations. Then, I investigated if different water-use strategies are detectable at inter-annual temporal scales by comparing tree-ring growth, carbon, and oxygen isotopic measurements of cool- versus warm-adapted populations in a common garden located at the extreme hottest edge of P. fremontii’s thermal distribution. I found that P. fremontii’s adaptation to the extreme temperatures is explained by a highly intraspecific specialized trait coordination across multiple trait scales. Furthermore, I found that warmer-adapted populations displayed 39% smaller leaves, 38% higher midday stomatal conductance, reflecting 3.8 °C cooler mean leaf temperature than cool-adapted populations, but with the tradeoff of having 14% lower minimum leaf water potentials. In addition, warm-adapted genotypes at the hot edge of P. fremontii’s distribution had 20% higher radial growth rates, although no differences were detected in either carbon or oxygen isotope ratios indicating that differences in growth may not have reflected seasonal differences in photosynthetic gas exchange. These studies describe the potential effect that extreme climate might have on P. fremontii’s survival, its intraspecific responses to those events, and which traits will be advantageous to cope with those extreme environmental conditions.
ContributorsBlasini, Davis E (Author) / Hultine, Kevin R (Thesis advisor) / Day, Thomas A (Thesis advisor) / Ogle, Kiona (Committee member) / Throop, Heather (Committee member) / Gaxiola, Roberto (Committee member) / Arizona State University (Publisher)
Created2022
Description
Flaviviruses (FVs) are among the most medically important arboviruses of the world with the Dengue virus (DENV) accounting for a large percentage of infections observed in tropical and subtropical regions of the world. Globalization, travel, and the expanding range of mosquito vectors, such as Aedes aegypti, have increased the potential of infection rates and illnesses associated with FVs.
The DENV and the Zika (ZIKV) FVs frequently co-circulate and generally cause mild self-liming febrile illnesses. However, a secondary infection with a heterologous DENV serotype may lead to life threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). DHF/DSS have been linked to antibody dependent enhancement of infection (ADE), a phenomenon that occurs when antibodies (Abs) formed against an initial infection with one serotype of DENV cross-reacts but does not neutralize a heterologous DENV serotype in a secondary infection. Furthermore, Abs raised against the ZIKV have been observed to cross-react with the DENV and vice versa, which can potentially cause ADE and lead to severe DENV disease. The ZIKV can be transmitted vertically and has been linked to devastating congenital defects such as microcephaly in newborns. FDA approved treatments do not exist for DENV and ZIKV illnesses. Thus, there is a need for safe and effective treatments for these co-circulating viruses. Here, a tetravalent bispecific antibody (bsAb) targeting the ZIKV and all four serotypes of the DENV was expressed in the Nicotiana benthamiana (N. benthamiana) plant. Functional assays of the DENV/ZIKV bsAb demonstrated binding, neutralization, and a significant reduction in ADE activity against both the DENV and the ZIKV.
A single chain variable fragment (scFv) and a diabody based on an antibody directed against the immune checkpoint inhibitor PD-L1, were also expressed in N. benthamiana leaves. The smaller sizes of the scFv and diabody confers them with the ability to penetrate deeper tissues making them beneficial in diagnostics, imaging, and possibly cancer therapy. The past few decades has seen long strives in recombinant protein production in plants with significant improvements in production, safety, and efficacy. These characteristics make plants an attractive platform for the production of recombinant proteins, biologics, and therapeutics.
The DENV and the Zika (ZIKV) FVs frequently co-circulate and generally cause mild self-liming febrile illnesses. However, a secondary infection with a heterologous DENV serotype may lead to life threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). DHF/DSS have been linked to antibody dependent enhancement of infection (ADE), a phenomenon that occurs when antibodies (Abs) formed against an initial infection with one serotype of DENV cross-reacts but does not neutralize a heterologous DENV serotype in a secondary infection. Furthermore, Abs raised against the ZIKV have been observed to cross-react with the DENV and vice versa, which can potentially cause ADE and lead to severe DENV disease. The ZIKV can be transmitted vertically and has been linked to devastating congenital defects such as microcephaly in newborns. FDA approved treatments do not exist for DENV and ZIKV illnesses. Thus, there is a need for safe and effective treatments for these co-circulating viruses. Here, a tetravalent bispecific antibody (bsAb) targeting the ZIKV and all four serotypes of the DENV was expressed in the Nicotiana benthamiana (N. benthamiana) plant. Functional assays of the DENV/ZIKV bsAb demonstrated binding, neutralization, and a significant reduction in ADE activity against both the DENV and the ZIKV.
A single chain variable fragment (scFv) and a diabody based on an antibody directed against the immune checkpoint inhibitor PD-L1, were also expressed in N. benthamiana leaves. The smaller sizes of the scFv and diabody confers them with the ability to penetrate deeper tissues making them beneficial in diagnostics, imaging, and possibly cancer therapy. The past few decades has seen long strives in recombinant protein production in plants with significant improvements in production, safety, and efficacy. These characteristics make plants an attractive platform for the production of recombinant proteins, biologics, and therapeutics.
ContributorsEsqueda, Adrian (Author) / Chen, Qiang (Thesis advisor) / Arntzen, Charles (Committee member) / Lake, Douglas (Committee member) / Mason, Hugh (Committee member) / Arizona State University (Publisher)
Created2019
Description
The partitioning of photosynthates between their sites of production (source) and their sites of utilization (sink) is a major determinant of crop yield and the potential of regulating this translocation promises substantial opportunities for yield increases. Ubiquitous overexpression of the plant type I proton pyrophosphatase (H+-PPase) in crops improves several valuable traits including salt tolerance and drought resistance, nutrient and water use efficiencies, and increased root biomass and yield. Originally, type I H+-PPases were described as pyrophosphate (PPi)-dependent proton pumps localized exclusively in vacuoles of mesophyll and meristematic tissues. It has been proposed that in the meristematic tissues, the role of this enzyme would be hydrolyzing PPi originated in biosynthetic reactions and favoring sink strength. Interestingly, this enzyme has been also localized at the plasma membrane of companion cells in the phloem which load and transport photosynthates from source leaves to sinks. Of note, the plasma membrane-localized H+-PPase could only function as a PPi-synthase in these cells due to the steep proton gradient between the apoplast and cytosol. The generated PPi would favor active sucrose loading through the sucrose/proton symporter in the phloem by promoting sucrose hydrolysis through the Sucrose Synthase pathway and providing the ATP required to maintain the proton gradient. To better understand these two different roles of type I H+-PPases, a series of Arabidopsis thaliana transgenic plants were generated. By expressing soluble pyrophosphatases in companion cells of Col-0 ecotype and H+-PPase mutants, impaired photosynthates partitioning was observed, suggesting phloem-localized H+-PPase could generate the PPi required for sucrose loading. Col-0 plants expressed with either phloem- or meristem-specific AVP1 overexpression cassette and the cross between the two tissue specific lines (Cross) were generated. The results showed that the phloem-specific AVP1-overexpressing plants had increased root hair elongation under limited nutrient conditions and both phloem- and meristem-overexpression of AVP1 contributed to improved rhizosphere acidification and drought resistance. It was concluded that H+-PPases localized in both sink and source tissues regulate plant growth and performance under stress through its versatile enzymatic functions (PPi hydrolase and synthase).
ContributorsLi, Lin (Author) / Park, Yujin (Thesis advisor) / Mangone, Marco (Committee member) / Roberson, Robert (Committee member) / Vermaas, Willem (Committee member) / Arizona State University (Publisher)
Created2022
Description
The mineralogy of the deep mantle is one of the key factors for the chemical evolution of the Earth. The constituent minerals of the mantle rock control the physical properties of the mantle, which have significant impacts on the large-scale processes occurring in the Earth's interior. In my PhD research, I adopted experimental approaches to investigate the mineralogy and the physical properties of the Earth's materials in the deep mantle by using the diamond anvil cells (DACs) combined with in-situ X-ray diffraction techniques.
First, I found that Ca-bearing bridgmanite can be stable in the deeper part of the Earth's lower mantle where temperature is sufficiently high. The dissolution of calcium into bridgmanite can change the physical properties of the mantle, such as compressibility and viscosity. This study suggests a new mineralogical model for the lower mantle, which is composed of the two layers depending on whether calcium dissolves in bridgmanite or forms CaSiO3 perovskite as a separate phase.
Second, I investigated the mineralogy and density of the subducting materials in the Archean at the P-T conditions near 670 km-depth. The experiments suggest that the major phases of Archean volcanic crust is majoritic garnet and ringwoodite in the P-T conditions of the deep transition zone, which become bridgmanite with increasing pressure. The density model showed that Archean volcanic crust would have been denser than the surrounding mantle, promoting sinking into the lower mantle regardless of the style of the transportation in the Archean.
Lastly, I further investigated the mineralogies and densities of the ancient volcanic crusts for the Archean and Proterozoic at the P-T conditions of the lower mantle. The experiments suggest that the mineralogy of the ancient volcanic crusts is composed mostly of bridgmanite, which is systemically denser than the surrounding lower mantle. This implies that the ancient volcanic crusts would have accumulated at the base of the mantle because of their large density and thickness. Therefore, the distinctive chemistry of the ancient volcanic crusts from the surrounding mantle would have given a rise to the chemical heterogeneities in the region for billions of years.
First, I found that Ca-bearing bridgmanite can be stable in the deeper part of the Earth's lower mantle where temperature is sufficiently high. The dissolution of calcium into bridgmanite can change the physical properties of the mantle, such as compressibility and viscosity. This study suggests a new mineralogical model for the lower mantle, which is composed of the two layers depending on whether calcium dissolves in bridgmanite or forms CaSiO3 perovskite as a separate phase.
Second, I investigated the mineralogy and density of the subducting materials in the Archean at the P-T conditions near 670 km-depth. The experiments suggest that the major phases of Archean volcanic crust is majoritic garnet and ringwoodite in the P-T conditions of the deep transition zone, which become bridgmanite with increasing pressure. The density model showed that Archean volcanic crust would have been denser than the surrounding mantle, promoting sinking into the lower mantle regardless of the style of the transportation in the Archean.
Lastly, I further investigated the mineralogies and densities of the ancient volcanic crusts for the Archean and Proterozoic at the P-T conditions of the lower mantle. The experiments suggest that the mineralogy of the ancient volcanic crusts is composed mostly of bridgmanite, which is systemically denser than the surrounding lower mantle. This implies that the ancient volcanic crusts would have accumulated at the base of the mantle because of their large density and thickness. Therefore, the distinctive chemistry of the ancient volcanic crusts from the surrounding mantle would have given a rise to the chemical heterogeneities in the region for billions of years.
ContributorsKo, Byeongkwan (Author) / Shim, Sang-Heon (Thesis advisor) / Garnero, Edward (Committee member) / Leinenweber, Kurt (Committee member) / Li, Mingming (Committee member) / Desch, Steven (Committee member) / Arizona State University (Publisher)
Created2020