Matching Items (87)
Description
This dissertation creates models of past potential vegetation in the Southern Levant during most of the Holocene, from the beginnings of farming through the rise of urbanized civilization (12 to 2.5 ka BP). The time scale encompasses the rise and collapse of the earliest agrarian civilizations in this region. The archaeological record suggests that increases in social complexity were linked to climatic episodes (e.g., favorable climatic conditions coincide with intervals of prosperity or marked social development such as the Neolithic Revolution ca. 11.5 ka BP, the Secondary Products Revolution ca. 6 ka BP, and the Middle Bronze Age ca. 4 ka BP). The opposite can be said about periods of climatic deterioration, when settled villages were abandoned as the inhabitants returned to nomadic or semi nomadic lifestyles (e.g., abandonment of the largest Neolithic farming towns after 8 ka BP and collapse of Bronze Age towns and cities after 3.5 ka BP during the Late Bronze Age). This study develops chronologically refined models of past vegetation from 12 to 2.5 ka BP, at 500 year intervals, using GIS, remote sensing and statistical modeling tools (MAXENT) that derive from species distribution modeling. Plants are sensitive to alterations in their environment and respond accordingly. Because of this, they are valuable indicators of landscape change. An extensive database of historical and field gathered observations was created. Using this database as well as environmental variables that include temperature and precipitation surfaces for the whole study period (also at 500 year intervals), the potential vegetation of the region was modeled. Through this means, a continuous chronology of potential vegetation of the Southern Levantwas built. The produced paleo-vegetation models generally agree with the proxy records. They indicate a gradual decline of forests and expansion of steppe and desert throughout the Holocene, interrupted briefly during the Mid Holocene (ca. 4 ka BP, Middle Bronze Age). They also suggest that during the Early Holocene, forest areas were extensive, spreading into the Northern Negev. The two remaining forested areas in the Northern and Southern Plateau Region in Jordan were also connected during this time. The models also show general agreement with the major cultural developments, with forested areas either expanding or remaining stable during prosperous periods (e.g., Pre Pottery Neolithic and Middle Bronze Age), and significantly contracting during moments of instability (e.g., Late Bronze Age).
ContributorsSoto-Berelov, Mariela (Author) / Fall, Patricia L. (Thesis advisor) / Myint, Soe (Committee member) / Turner, Billie L (Committee member) / Falconer, Steven (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
Pathogenic Gram-negative bacteria employ a variety of molecular mechanisms to combat host defenses. Two-component regulatory systems (TCR systems) are the most ubiquitous signal transduction systems which regulate many genes required for virulence and survival of bacteria. In this study, I analyzed different TCR systems in two clinically-relevant Gram-negative bacteria, i.e., oral pathogen Porphyromonas gingivalis and enterobacterial Escherichia coli. P. gingivalis is a major causative agent of periodontal disease as well as systemic illnesses, like cardiovascular disease. A microarray study found that the putative PorY-PorX TCR system controls the secretion and maturation of virulence factors, as well as loci involved in the PorSS secretion system, which secretes proteinases, i.e., gingipains, responsible for periodontal disease. Proteomic analysis (SILAC) was used to improve the microarray data, reverse-transcription PCR to verify the proteomic data, and primer extension assay to determine the promoter regions of specific PorX regulated loci. I was able to characterize multiple genetic loci regulated by this TCR system, many of which play an essential role in hemagglutination and host-cell adhesion, and likely contribute to virulence in this bacterium. Enteric Gram-negative bacteria must withstand many host defenses such as digestive enzymes, low pH, and antimicrobial peptides (AMPs). The CpxR-CpxA TCR system of E. coli has been extensively characterized and shown to be required for protection against AMPs. Most recently, this TCR system has been shown to up-regulate the rfe-rff operon which encodes genes involved in the production of enterobacterial common antigen (ECA), and confers protection against a variety of AMPs. In this study, I utilized primer extension and DNase I footprinting to determine how CpxR regulates the ECA operon. My findings suggest that CpxR modulates transcription by directly binding to the rfe promoter. Multiple genetic and biochemical approaches were used to demonstrate that specific TCR systems contribute to regulation of virulence factors and resistance to host defenses in P. gingivalis and E. coli, respectively. Understanding these genetic circuits provides insight into strategies for pathogenesis and resistance to host defenses in Gram negative bacterial pathogens. Finally, these data provide compelling potential molecular targets for therapeutics to treat P. gingivalis and E. coli infections.
ContributorsLeonetti, Cori (Author) / Shi, Yixin (Thesis advisor) / Stout, Valerie (Committee member) / Nickerson, Cheryl (Committee member) / Sandrin, Todd (Committee member) / Arizona State University (Publisher)
Created2013
Description
The study of bacterial resistance to antimicrobial peptides (AMPs) is a significant area of interest as these peptides have the potential to be developed into alternative drug therapies to combat microbial pathogens. AMPs represent a class of host-mediated factors that function to prevent microbial infection of their host and serve as a first line of defense. To date, over 1,000 AMPs of various natures have been predicted or experimentally characterized. Their potent bactericidal activities and broad-based target repertoire make them a promising next-generation pharmaceutical therapy to combat bacterial pathogens. It is important to understand the molecular mechanisms, both genetic and physiological, that bacteria employ to circumvent the bactericidal activities of AMPs. These understandings will allow researchers to overcome challenges posed with the development of new drug therapies; as well as identify, at a fundamental level, how bacteria are able to adapt and survive within varied host environments. Here, results are presented from the first reported large scale, systematic screen in which the Keio collection of ~4,000 Escherichia coli deletion mutants were challenged against physiologically significant AMPs to identify genes required for resistance. Less than 3% of the total number of genes on the E. coli chromosome was determined to contribute to bacterial resistance to at least one AMP analyzed in the screen. Further, the screen implicated a single cellular component (enterobacterial common antigen, ECA) and a single transporter system (twin-arginine transporter, Tat) as being required for resistance to each AMP class. Using antimicrobial resistance as a tool to identify novel genetic mechanisms, subsequent analyses were able to identify a two-component system, CpxR/CpxA, as a global regulator in bacterial resistance to AMPs. Multiple previously characterized CpxR/A members, as well as members found in this study, were identified in the screen. Notably, CpxR/A was found to transcriptionally regulate the gene cluster responsible for the biosynthesis of the ECA. Thus, a novel genetic mechanism was uncovered that directly correlates with a physiologically significant cellular component that appears to globally contribute to bacterial resistance to AMPs.
ContributorsWeatherspoon-Griffin, Natasha (Author) / Shi, Yixin (Thesis advisor) / Clark-Curtiss, Josephine (Committee member) / Misra, Rajeev (Committee member) / Nickerson, Cheryl (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2013
Description
Two critical limitations for hyperspatial imagery are higher imagery variances and large data sizes. Although object-based analyses with a multi-scale framework for diverse object sizes are the solution, more data sources and large amounts of testing at high costs are required. In this study, I used tree density segmentation as the key element of a three-level hierarchical vegetation framework for reducing those costs, and a three-step procedure was used to evaluate its effects. A two-step procedure, which involved environmental stratifications and the random walker algorithm, was used for tree density segmentation. I determined whether variation in tone and texture could be reduced within environmental strata, and whether tree density segmentations could be labeled by species associations. At the final level, two tree density segmentations were partitioned into smaller subsets using eCognition in order to label individual species or tree stands in two test areas of two tree densities, and the Z values of Moran's I were used to evaluate whether imagery objects have different mean values from near segmentations as a measure of segmentation accuracy. The two-step procedure was able to delineating tree density segments and label species types robustly, compared to previous hierarchical frameworks. However, eCognition was not able to produce detailed, reasonable image objects with optimal scale parameters for species labeling. This hierarchical vegetation framework is applicable for fine-scale, time-series vegetation mapping to develop baseline data for evaluating climate change impacts on vegetation at low cost using widely available data and a personal laptop.
ContributorsLiau, Yan-ting (Author) / Franklin, Janet (Thesis advisor) / Turner, Billie (Committee member) / Myint, Soe (Committee member) / Arizona State University (Publisher)
Created2013
Description
Land transformation under conditions of rapid urbanization has significantly altered the structure and functioning of Earth's systems. Land fragmentation, a characteristic of land transformation, is recognized as a primary driving force in the loss of biological diversity worldwide. However, little is known about its implications in complex urban settings where interaction with social dynamics is intense. This research asks: How do patterns of land cover and land fragmentation vary over time and space, and what are the socio-ecological drivers and consequences of land transformation in a rapidly growing city? Using Metropolitan Phoenix as a case study, the research links pattern and process relationships between land cover, land fragmentation, and socio-ecological systems in the region. It examines population growth, water provision and institutions as major drivers of land transformation, and the changes in bird biodiversity that result from land transformation. How to manage socio-ecological systems is one of the biggest challenges of moving towards sustainability. This research project provides a deeper understanding of how land transformation affects socio-ecological dynamics in an urban setting. It uses a series of indices to evaluate land cover and fragmentation patterns over the past twenty years, including land patch numbers, contagion, shapes, and diversities. It then generates empirical evidence on the linkages between land cover patterns and ecosystem properties by exploring the drivers and impacts of land cover change. An interdisciplinary approach that integrates social, ecological, and spatial analysis is applied in this research. Findings of the research provide a documented dataset that can help researchers study the relationship between human activities and biotic processes in an urban setting, and contribute to sustainable urban development.
ContributorsZhang, Sainan (Author) / Boone, Christopher G. (Thesis advisor) / York, Abigail M. (Committee member) / Myint, Soe (Committee member) / Arizona State University (Publisher)
Created2013
Description
Species distribution modeling is used to study changes in biodiversity and species range shifts, two currently well-known manifestations of climate change. The focus of this study is to explore how distributions of suitable habitat might shift under climate change for shrub communities within the Santa Monica Mountains National Recreation Area (SMMNRA), through a comparison of community level to individual species level distribution modeling. Species level modeling is more commonly utilized, in part because community level modeling requires detailed community composition data that are not always available. However, community level modeling may better detect patterns in biodiversity. To examine the projected impact on suitable habitat in the study area, I used the MaxEnt modeling algorithm to create and evaluate species distribution models with presence only data for two future climate models at community and individual species levels. I contrasted the outcomes as a method to describe uncertainty in projected models. To derive a range of sensitivity outcomes I extracted probability frequency distributions for suitable habitat from raster grids for communities modeled directly as species groups and contrasted those with communities assembled from intersected individual species models. The intersected species models were more sensitive to climate change relative to the grouped community models. Suitable habitat in SMMNRA's bounds was projected to decline from about 30-90% for the intersected models and about 20-80% for the grouped models from its current state. Models generally captured floristic distinction between community types as drought tolerance. Overall the impact on drought tolerant communities, growing in hotter, drier habitat such as Coastal Sage Scrub, was predicted to be less than on communities growing in cooler, moister more interior habitat, such as some chaparral types. Of the two future climate change models, the wetter model projected less impact for most communities. These results help define risk exposure for communities and species in this conservation area and could be used by managers to focus vegetation monitoring tasks to detect early response to climate change. Increasingly hot and dry conditions could motivate opportunistic restoration projects for Coastal Sage Scrub, a threatened vegetation type in Southern California.
ContributorsJames, Jennifer (Author) / Franklin, Janet (Thesis advisor) / Rey, Sergio (Committee member) / Wentz, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2014
Description
Climate and land use change are projected to threaten biodiversity over the coming century. However, the combined effects of these threats on biodiversity and the capacity of current conservation networks to protect species' habitat are not well understood. The goals of this study were to evaluate the effect of climate change and urban development on vegetation distribution in a Mediterranean-type ecosystem; to identify the primary source of uncertainty in suitable habitat predictions; and to evaluate how well conservation areas protect future habitat in the Southwest ecoregion of the California Floristic Province. I used a consensus-based modeling approach combining three different species distribution models to predict current and future suitable habitat for 19 plant species representing different plant functional types (PFT) defined by fire-response (obligate seeders, resprouting shrubs), and life forms (herbs, subshurbs). I also examined the response of species grouped by range sizes (large, small). I used two climate models, two emission scenarios, two thresholds, and high-resolution (90m resolution) environmental data to create a range of potential scenarios. I evaluated the effectiveness of an existing conservation network to protect suitable habitat for rare species in light of climate and land use change. The results indicate that the area of suitable habitat for each species varied depending on the climate model, emission scenario, and threshold combination. The suitable habitat for up to four species could disappear from the ecoregion, while suitable habitat for up to 15 other species could decrease under climate change conditions. The centroid of the species' suitable environmental conditions could shift up to 440 km. Large net gains in suitable habitat were predicted for a few species. The suitable habitat area for herbs has a small response to climate change, while obligate seeders could be the most affected PFT. The results indicate that the other two PFTs gain a considerable amount of suitable habitat area. Several rare species could lose suitable habitat area inside designated conservation areas while gaining suitable habitat area outside. Climate change is predicted to be more important than urban development as a driver of habitat loss for vegetation in this region in the coming century. These results indicate that regional analyses of this type are useful and necessary to understand the dynamics of drivers of change at the regional scale and to inform decision making at this scale.
ContributorsBeltrán Villarreal, Bray de Jesús (Author) / Franklin, Janet (Thesis advisor) / Fenichel, Eli P (Committee member) / Kinzig, Ann P (Committee member) / Collins, James P. (Committee member) / Arizona State University (Publisher)
Created2012
Description
Hepatitis C virus (HCV) is a globally prevalent infection which is a main contributor to the global burden of liver disease. Due to its ability to establish a chronic infection, and the lack of usefulness of traditional neutralizing antibody vaccine design in producing a protective immune response, a preventative vaccine has been notoriously difficult to produce. To overcome this, a vaccine using non-structural protein 3 (NS3) as a target to elicit a T cell specific immune response is thought to be a possible strategy for eliciting a protective immune response against hepatitis C infection. In this paper, a recombinant strain of measles virus (MV) that expresses HCV NS3 protein was analyzed. The replication fitness of this recombinant virus also indicates that this construct replicates at a higher rate than parental measles strain. It is also demonstrated through western blot analysis of protein expression and immunofluorescence that this recombinant virus expresses both the inserted HCV NS3 protein, as well as native measles proteins.
ContributorsWoell, Dana Marie (Author) / Reyes del Valle, Jorge (Thesis director) / Nickerson, Cheryl (Committee member) / Julik, Emily (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2015-05
Description
Clean water for drinking, food preparation, and bathing is essential for astronaut health and safety during long duration habitation of the International Space Station (ISS), including future missions to Mars. Despite stringent water treatment and recycling efforts on the ISS, it is impossible to completely prevent microbial contamination of onboard water supplies. In this work, we used a spaceflight analogue culture system to better understand how the microgravity environment can influence the pathogenesis-related characteristics of Burkholderia cepacia complex (Bcc), an opportunistic pathogen previously recovered from the ISS water system. The results of the present study suggest that there may be important differences in how this pathogen can respond and adapt to spaceflight and other low fluid shear environments encountered during their natural life cycles. Future studies are aimed at understanding the underlying mechanisms responsible for these phenotypes.
ContributorsKang, Bianca Younseon (Author) / Nickerson, Cheryl (Thesis director) / Barrila, Jennifer (Committee member) / Ott, Mark (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05