Now showing items 41-60 of 134

    • An experiment in directed study

      Pierce, Lucia M. (2013-01-17)
      Not available.
    • Applying Geophysics and Geochemistry to Understand Middle Woodland Site Spatial Organization At the Northwood Site, Vigo County, Indiana

      Grossman, Tiffany (2012-10-22)
      The Northwood site (12Vi194) in northern Vigo County is attributed to the Late Middle Woodland culture known as Allison-LaMotte. Previous studies at other Allison-LaMotte sites are inconclusive regarding the village structure of this culture. While some studies identify a habitation zone surrounding a circular plaza, other Allison-LaMotte sites lack an observable spatial layout to the site. Magnetometry studies completed at the Northwood site in 2005 reveal a possible semi-circular community pattern with a central plaza. This study employed the 2005 magnetometer survey data, magnetic susceptibility, ground penetrating radar (GPR), and geochemical analyses to confirm the hypothesized site organization. Magnetic data from the magnetometer survey and magnetic susceptibility of artifact classes were compared to identify sources of magnetic anomalies. The map produced by magnetometry was compared with the GPR map to identify overlaps in possible pit features and the plaza zone. Excavating in locations identified as magnetic anomalies allowed for ground truthing survey results and collecting magnetic susceptibility measurements and soil samples for geochemical analysis. Geochemical analyses included detailed phosphorus geochemistry, total organic matter content, and organic carbon enhancement of soils collected from the site. Finally, determination of the source and strength of feature magnetic signals were analyzed using magnetic susceptibility and magnetometer data. These investigations provide better estimates of site spatial structure at the Northwood Site.
    • Tree-Ring Analysis of Outbreak Dynamics across an Insect’s Entire Range: The Pandora Moth System

      de Graauw, Kristen (2012-10-22)
      In montane forests of the western United States, pandora moth (Coloradia pandora Blake) defoliates local pines, primarily ponderosa pine (Pinus ponderosa Dougl. Ex Laws.) and Jeffrey pine (Pinus jeffreyi Grev. & Balf.). This defoliation stresses the tree, leaving a distinct outbreak signature in the tree-rings. The occurrence of pandora moth outbreaks has been recorded in ponderosa pine tree rings in Oregon as far back as 1500 years, however little is known of the outbreak history throughout the rest of the pandora moth range. To gain a better understanding of the spatiotemporal dynamics of pandora moth I have reconstructed outbreaks across the entire range of the insect using 121 tree-ring chronologies from the International Tree-Ring Databank (ITRDB) and 19 chronologies from sites sampled for this study using dendrochronological techniques. I then created a fine resolution habitat model for pandora moth and a gridded tree-ring network of non-host chronologies, which was used to validate statistically confirmed outbreak events across the entire range of the insect. Sites with confirmed outbreaks were then tested against the habitat model for accuracy of model parameters. ArcMap 10 was used to create an animated map of the spatial and temporal distribution of pandora moth across its range. One of my most notable findings is the record of outbreak events further north than previously documented, and the agreement between those northern sites with my habitat model. In my research I have demonstrated the use of dendrochronology to study outbreaks across an insect’s range. The methods I have used here can be applied to other range-wide analyses.
    • Holocene Landscape Evolution of the Ohio River Valley from Knob Creek to Rosewood Bottom

      De Rego, Kathryn G. (2012-10-19)
      Rivers and floodplain environments have provided human settlements with resources for thousands of years. By understanding how rivers shape the land around them, we can use landforms to reconstruct ancient fluvial processes and to examine how they have conditioned the way humans interact with their environment. This study investigates the Lower Ohio River during the Holocene. During this period, Midwestern landscapes were adjusting to a variety of processes, including millennial-scale climate change involving the transition from a glacial to an interglacial environment. At the same time, Archaic hunter-gatherers adopted a settlement strategy that favored large river valleys. The cause of this shift has not been resolved. This study examined floodplain sedimentation and change along the Lower Ohio from Knob Creek to Rosewood Bottom through two different scales of analysis: the regional (geologic) scale and within local bottoms. A model of floodplain structure from Madison to Tell City, Indiana was created using a GIS and used to examine differences between geologic regions and Early and Late Holocene sediment. Swales were identified using a DEM, and depth, area, and perimeter-area ratio were used as proxies of their characteristics, which are correlated with backwater environments. Subsurface soil and sediment data were collected from a transect across Rosewood Bottom and within a paleochannel common to the study reach and used to reconstruct floodplain production within an individual bottom. Radiocarbon dates from geologic and archaeological contexts were used to examine Early and Late Holocene sedimentation rates. The Ohio River was active during the Early Holocene. It migrated rapidly and constructed most of the modern floodplain. In some areas, it was anabranching because resistant Pleistocene braid bars formed obstructions to flow that became islands. During the Late Holocene, deposition has been mainly characterized by overbank backwater/slackwater deposition in swales. There is not enough evidence to assign an exogenic cause to this phenomenon. Significant differences in floodplain structure between individual bottoms and regions, the influence of underlying Pleistocene gravels on river migration, and different dates for paleochannel abandonment are indicators of autogenic controls on the Ohio’s behavior and show that bottoms have independent histories. This study complements current models of environmental change for river basins in the Midwest, but it suggests that the stability of the floodplain be given more consideration when analyzing Archaic settlement strategy.
    • Phylogenomics: Molecular Evolution in the Genomics Era

      Seetharam, Arun Somwarpet (2012-10-19)
      Evolutionary studies in recent years have been transformed by the development of new, powerful techniques for investigating many mechanisms and events of molecular evolution. Large collections of many different complete genomes now available in the public domain offer great advantages to genomic scale evolutionary studies. Phylogenomics, a term often used to describe the use of genomic scale data to infer species phylogeny or to predict protein function through evolutionary history, is greatly benefitted by the revolutionary progress in DNA sequencing technology. In the present study we developed and utilized various phylogenomic methods on large genome-scale data. In the first study, we applied Singular Value Decomposition (SVD) analysis to reexamine current evolutionary relationships for 12 Drosophila species using the predicted proteins from whole genomes. An SVD analysis on unfiltered whole genomes (193,622 predicted proteins) produced the currently accepted Drosophila phylogeny at higher dimensions, except for the generally accepted, but difficult to discern, sister relationship between D. erecta and D. yakuba. Also, in accordance with previous studies, many sequences appear to support alternative phylogenies. In this case, we observed grouping of D. erecta with D. sechellia when approximately 55% to 95% of the proteins were removed using a filter based on projection values or by reducing resolution by using fewer dimensions. In the second study, we simulated restriction enzyme digestions on 21 sequenced genomes of various Drosophila species. Using the fragments generated by simulated digestion from the predicted targets of 16 Type IIB restriction enzymes, we sampled a large and effectively arbitrary selection of loci from these genomes. The resulting fragments were then used to compare organisms and to calculate the distance between genomes in pair-wise combination by counting the number of shared fragments between the two genomes. Phylogenetic trees were then generated for each enzyme using this distance measure, and the consensus was calculated. The consensus tree obtained agrees well with the currently accepted tree for these Drosophila species. We conclude that multi-locus sub-genomic representation combined with next generation sequencing, especially for individuals and species without previous genome characterization, can improve studies of comparative genomics and the building of accurate phylogenetic trees. The third study utilized the relatively new Daphnia genome in an attempt to identify 40 orthologous groups of C2H2 Zinc-finger proteins that were previously determined to be well conserved in bilaterians. We identified 58 C2H2 ZFP genes in Daphnia that belong to these 40 distinct families. The Daphnia genome appears to be relatively efficient with respect to these well-conserved C2H2 ZFP, since only 7 of the 40 gene families have more than one identified member. Worms have a comparable number of 6. In flies and humans, C2H2 ZFP gene expansions are more common, since these organisms display 15 and 24 multi-member families respectively. In contrast, only three of the well-conserved C2H2 ZFP families have expanded in Daphnia relative to Drosophila, and in two of these cases, just one additional gene was found. The KLF/SP family in Daphnia, however, is significantly larger than that of Drosophila, and many of the additional members found in Daphnia appear to correspond to KLF 1/2/4 homologs, which are absent in Drosophila, but present in vertebrates. The last study was conducted to investigate the conservation and distribution of 38 C2H2 ZNF gene families in Eukaryotes. We combined two popular approaches for homolog detection, Reciprocal Best Hit (RBH) and Hidden–Markov model (HMM) profile search, on a diverse set of complete genomes of 124 eukaryotic species ranging from excavates to humans. We succeeded in identifying 3,675 genes as distinct members of the 38 C2H2 gene families. This largely automated technique is much faster than manual methods and is able to detect homologs accurately and efficiently among a diverse set of organisms. Our analysis of the 38 evolutionarily conserved C2H2 ZNF gene families revealed a stepwise appearance of ZNF families, agreeing well with the phylogenetic relationship of the organisms compared and their presumed stepwise increase in complexity.
    • Under the Influence of Large Woody Debris: A Survey of the La Crosse River In the Upper Midwest Driftless Area

      Prise, Adam (2012-10-19)
      Streams are dynamic environments driven by the force of gravity and shaped by local climate, geology, and vegetation. Large woody debris (LWD) can have important influences on stream processes. The main influence of LWD on these systems is a resistance to flow; this added roughness induces a multitude of channel adjustments. Despite the importance of LWD, streams have been heavily managed by humankind, often involving the removal of debris to improve flow. Recent studies have highlighted the significance of large woody debris in mountain streams, particularly in the Pacific Northwest of the United States and Canada. However, there has been little research on the influence of LWD on streams in the Upper Midwest. This study will specifically investigate a stream (the La Crosse River) in southwestern Wisconsin’s Driftless Area. This area remained untouched by glaciers during the Last Glacial Maximum, but outwash from melting glaciers was deposited here, making the main bed material coarse sand. Combining stream survey methods (channel cross-sections) and a wood census, the influence of LWD was determined through statistical analysis of measurements of stream (velocity, depth, and width) and LWD (total counts, length, DBH, and volume) characteristics, in conjunction with qualitative analysis of detailed cross-sections. LWD are present in the study reach, but few relationships proved statistically significant, while local influences (initiation of scour and deposition) are clearly seen. Explanations of human, regional, historical, and bed form influences are explored.
    • Manipulation of Angiogenesis by Cyclosporine-A and Extracellular Matrix Molecules

      Pandey, Raghav (2012-10-19)
      Angiogenesis is the formation of new capillaries from pre-existing capillaries. Angiogenesis plays an important role in the blood vessel formation required during embryonic development, tissue injury, wound healing, and menstruation. It also plays a major role in tumor progression. We propose a mechanism that links the developmental pathways to a therapeutic pathway. Moreover, we show anti-angiogenic nature of an FDA approved immunosuppressant. Extra cellular matrix (ECM) has an important role in maintaining the shape and structure of organisms and in signaling mechanisms. Two major components of ECM are lumican and Magp2. Investigating their role might help us further link angiogenesis to tumor progression in cancer. We show the pro-angiogenic nature of Magp2 in an in-vivo model. Although this project is in early stages, it would provide a good foundation for future study. The aim of this thesis was to check the effect of blocking angiogenesis on tumor growth through different ECM proteins (Lumican and Magp2) and therapeutics (cyclosporine-A). Studying the progression of tumor links the chapters together.
    • Some recent investigations in the teaching of mathematics

      Strong, Orvel E. (2012-08-20)
      Not Available.