WHEAT DISEASE MANAGEMENT WITH FUNGICIDES: QOI-RESISTANT \u3ci\u3e PARASTAGONOSPORA NODORUM \u3c/i\u3e AND \u3ci\u3e ZYMOSEPTORIA TRITICI, \u3c/i\u3e APPLICATION TIMING FOR LEAF DISEASE MANAGEMENT, AND SPRAYER CONFIGURATIONS FOR FUSARIUM HEAD BLIGHT MANAGEMENT

Disease management in winter wheat can be improved by a properly implemented foliar fungicide program. The fungicide, application time, and application system should be selected based on the host, pathogens present, risk of fungicide resistance, and time of disease onset. These factors vary among environments and require region-specific research to determine appropriate practices. Trials were conducted to evaluate different aspects of fungicide applications for managing Fusarium head blight (FHB), caused by Fusarium graminearum, and the Septoria tritici leaf blotch complex, caused by Zymoseptoria tritici and Parastagonospora nodorum. A survey of P. nodorum isolates from Kentucky and Illinois and Z. tritici isolates from Kentucky showed that both pathogen populations included strains that were resistant to quinone outside inhibitor (QoI) fungicides. Trials were conducted to determine the optimal fungicide application time to manage the Septoria leaf blotch complex, and whether disease management programs benefited from adding a foliar fungicide. The effect that sprayer speed, nozzle type, and configuration had on coverage of wheat heads and FHB management was evaluated. Applying alternative fungicide chemistries to the QoI class at Feekes 9 along with an application at Feekes 10.51 made with an appropriate nozzle and application speed will provide a more effective fungicide program for winter wheat in Kentucky

Composition and Structure of Replacement Forest Stands Following Southern Pine Beetle Infestations as Related to Selected Site Variables in the Great Smoky Mountains

Stand composition and eleven site factors were sampled in 49 stands in the Great Smoky Mountains in which the pine overstory had been killed by the southern pine beetle. Replacement community types were determined using cluster analysis of relative densities for 21 common species. absolute densities for total stems, total pine, total oak, and eight individual species in the overstory, understory, and reproduction strata were related to selected site and vegetation variables by correlation and stepwise multiple regression. Infestations greatly reduced the importance of pine in all replacement stands, converting most pine dominated stands to mixed pine-hardwood. Pine reproduction was minimal in all cases. All stands appeared to be in early stages of recovery, and canopy closure was very low. Six replacement types were derived. The red maple-dogwood type occupied low elevation, lower slope, old field sites. The red maple-sourwood type occurred on mid elevation broad ridgetops and protected upper slopes. The blackgum-mixed pine type occurred on mid elevation, mid to upper slope, exposed sites. The mixed pine-scarlet oak and the Virginia pine-blacgum types occupied exposed ridgetops and upper slopes at mid to low elevations. The table mountain pine-pitch pine type occupied high elevations kills on steep, exposed, upper slope positions. Important environmental factors influencing replacement stand composition and dynamics appeared to be elevation, incident solar radiation, topographic position, and soil nutrient availability. Future composition of replacement types was projected based on present composition and site conditions. The red maple-dogwood type will succeeddd to stands dominated by mixed hardwoods and white pine. In the red maple-sourwood type, the blackgum-mixed pine type, and the Virginia pine-blackgum type, chestnut oak will eventually dominate with scarlet oak and scattered pines in the canopy. The mixed pine-scarlet oak type will succeed to stands dominated by scarlet oak with residual pines as associated. Canopy closure will remain very open in the table mountain pine-pitch pine type due to the suppression of regeneration by dense mountain laurel, and the overstory will consist of widely spaced scarlet oaks and residual pines

Ensemble methods in computational protein and ligand design : applications to the Fc[gamma] immunoglobulin, HIV-1 protease, and ketol-acid reductoisomerase systems

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2012.In title on title-page, "[gamma]" appears as the lower-case Greek letter. Cataloged from PDF version of thesis.Includes bibliographical references (p. 170-192).This thesis explores the use of ensemble, free energy models in the study and design of molecular, biochemical systems. We use physics based computational models to analyze the molecular basis of binding affinity in the context of protein-protein and protein-ligand binding as well as reaction rate enhancement in enzyme catalysis. First, we evaluate the solvent screened energetics of immunoglobulin G (IgG):Fc[gamma] receptor binding using molecular mechanics, Poisson-Boltzmann surface area (MMPBSA) models. We assess the role IgG1 linked glycans play in binding to human Fc[gamma]-III and computationally evaluate experimentally designed Fe mutations that recover binding affinity in the absence of glycosylation. Using the insight gained from this study, we developed novel murine IgG variants with engineered Fc[gamma] receptor binding patterns via the computational design and experimental validation of Fc mutations that are predicted to knock out binding to Fc[gamma]R-IV. Our design and analysis highlight the importance of solvent screened electrostatic interactions and electrostatic complementarity in protein-protein binding. Second, we develop novel, ensemble methods to measure configurational free energy and entropy changes in protein-ligand binding and use it to predict the relative binding affinity of a series of previously designed HIV-1 protease inhibitors. We find that using configurational free energies to evaluate inhibitor efficacy significantly improves relative ranking of inhibitors over traditional, single-point energy metrics, but that only a relatively small number of low energy configurations are necessary to capture the ensemble effect. Finally, we present a joint study of the redesign and dynamic analysis of ketol-acid isomeroreductase (KARI). We first develop and apply a novel, end-point method to rationally design enzyme variants that reduce the free energy of activation, and present the computational and experimental analysis of a series of designed KARI mutants. Our analysis reveals that this transition-state theory based approach is effective at reducing the enthalpy of activation, but also increases entropic activation penalties that ultimately overpower the enthalpic gains. A dynamic analysis of these KARI variants is also presented, in which the transition path ensemble is explored using transition path sampling. We find that this ensemble approach is better able to predict relative enzyme activities and suggests a conserved, dynamic mechanism for catalysis. The results and analysis presented herein demonstrate novel, computational approaches to account for ensemble effects in the study and design of effective biomolecules.by Nathaniel White Silver.Ph.D

The Effects of Poetry in Elderly Populations with Memory Impairment

Introduction. A small body of research on therapeutic use of poetry in individuals with memory impairment demonstrates benefits similar to that of more widely studied music interventions. This project aims to assess the effects of participation in a poetry group on the residents of a memory care floor within the Converse Home, an assisted living facility in Burlington, Vermont. Methods.. We evaluated the effects of twelve group poetry sessions on residents\u27 well-being in several domains. Each session included a reading and writing portion, which were evaluated separately to assess differences in measures of communication, interest, and enjoyment. These measures, along with negative responses, were recorded on Likert scales. T-tests, ANOVA, and post-hoc comparisons were used to compare behavioral and affective observations in the reading versus writing sessions. Results.. Positive responses were significantly higher in reading sessions (p Conclusion.. Although the limitations of this project preclude us from drawing individual conclusions regarding the therapeutic efficacy of poetry in individuals with memory impairment, we demonstrate that poetry sessions have a positive impact on global quality of life outcomes and introduction of poetry sessions in this population has a beneficial effect.https://scholarworks.uvm.edu/comphp_gallery/1242/thumbnail.jp

Synergistic cross-scale coupling of turbulence in a tokamak plasma

For the first time, nonlinear gyrokinetic simulations spanning both the ion and electron spatio-temporal scales have been performed with realistic electron mass ratio ((m[subscript D] [over m [subscript e])[superscript 1 over 2] = 60.0), realistic geometry, and all experimental inputs, demonstrating the coexistence and synergy of ion (k[subscript θρs] ~O(1.0)) and electron-scale (k[subscript θρe] ~O(1.0)) turbulence in the core of a tokamak plasma. All multi-scale simulations utilized the GYRO code [J. Candy and R. E. Waltz, J. Comput. Phys. 186, 545 (2003)] to study the coupling of ion and electron-scale turbulence in the core (r/a = 0.6) of an Alcator C-Mod L-mode discharge shown previously to exhibit an under-prediction of the electron heat flux when using simulations only including ion-scale turbulence. Electron-scale turbulence is found to play a dominant role in setting the electron heat flux level and radially elongated (k[subscript r] ≪ k[subscript θ]) “streamers” are found to coexist with ion-scale eddies in experimental plasma conditions. Inclusion of electron-scale turbulence in these simulations is found to increase both ion and electron heat flux levels by enhancing the transport at the ion-scale while also driving electron heat flux at sub-ρ[subscript i] scales. The combined increases in the low and high-k driven electron heat flux may explain previously observed discrepancies between simulated and experimental electron heat fluxes and indicates a complex interaction of short and long wavelength turbulence.United States. Dept. of Energy. Office of Science (Contract DE-AC02-05CH11231)United States. Dept. of Energy (Contract DE-FC02-99ER54512-CMOD)United States. Dept. of Energy. Fusion Energy Postdoctoral Research Program (Oak Ridge Institute for Science and Education

Multi-scale gyrokinetic simulations: Comparison with experiment and implications for predicting turbulence and transport

To better understand the role of cross-scale coupling in experimental conditions, a series of multi-scale gyrokinetic simulations were performed on Alcator C-Mod, L-mode plasmas. These simulations, performed using all experimental inputs and realistic ion to electron mass ratio ((mi/me)1∕2 = 60.0), simultaneously capture turbulence at the ion (kθρs∼(1.0)) and electron-scales (kθρe∼(1.0)). Direct comparison with experimental heat fluxes and electron profile stiffness indicates that Electron Temperature Gradient (ETG) streamers and strong cross-scale turbulence coupling likely exist in both of the experimental conditions studied. The coupling between ion and electron-scales exists in the form of energy cascades, modification of zonal flow dynamics, and the effective shearing of ETG turbulence by long wavelength, Ion Temperature Gradient (ITG) turbulence. The tightly coupled nature of ITG and ETG turbulence in these realistic plasma conditions is shown to have significant implications for the interpretation of experimental transport and fluctuations. Initial attempts are made to develop a “rule of thumb” based on linear physics, to help predict when cross-scale coupling plays an important role and to inform future modeling of experimental discharges. The details of the simulations, comparisons with experimental measurements, and implications for both modeling and experimental interpretation are discussed.United States. Department of Energy (DE-AC02-05CH11231)United States. Department of Energy (DE-FC02-99ER54512-CMOD)United States. Department of Energy (DE-SC0006957)United States. Department of Energy (DE-FG02-06ER54871

Junior Recital, Nathaniel Frost, clarinet

The presentation of this junior recital will fulfill in part the requirements for the Bachelor of Music degree in Music Education. Nathaniel Frost studies clarinet with Dr. Charles West

Performance of downscaled regional climate simulations using a variable-resolution regional climate model : Tasmania as a test case

In this study we develop methods for dynamically downscaling output from six general circulation models (GCMs) for two emissions scenarios using a variable-resolution atmospheric climate model. The use of multiple GCMs and emissions scenarios gives an estimate of model range in projected changes to the mean climate across the region. By modeling the atmosphere at a very fine scale, the simulations capture processes that are important to regional weather and climate at length scales that are subgrid scale for the host GCM. We find that with a multistaged process of increased resolution and the application of bias adjustment methods, the ability of the simulation to reproduce observed conditions improves, with greater than 95% of the spatial variance explained for temperature and about 90% for rainfall. Furthermore, downscaling leads to a significant improvement for the temporal distribution of variables commonly used in applied analyses, reproducing seasonal variability in line with observations. This seasonal signal is not evident in the GCMs. This multistaged approach allows progressive improvement in the skill of the simulations in order to resolve key processes over the region with quantifiable improvements in the correlations with observations

Sustainable Sourcing of Global Agricultural Raw Materials: Assessing Gaps in Key Impact and Vulnerability Issues and Indicators.

Understanding how to source agricultural raw materials sustainably is challenging in today's globalized food system given the variety of issues to be considered and the multitude of suggested indicators for representing these issues. Furthermore, stakeholders in the global food system both impact these issues and are themselves vulnerable to these issues, an important duality that is often implied but not explicitly described. The attention given to these issues and conceptual frameworks varies greatly--depending largely on the stakeholder perspective--as does the set of indicators developed to measure them. To better structure these complex relationships and assess any gaps, we collate a comprehensive list of sustainability issues and a database of sustainability indicators to represent them. To assure a breadth of inclusion, the issues are pulled from the following three perspectives: major global sustainability assessments, sustainability communications from global food companies, and conceptual frameworks of sustainable livelihoods from academic publications. These terms are integrated across perspectives using a common vocabulary, classified by their relevance to impacts and vulnerabilities, and categorized into groups by economic, environmental, physical, human, social, and political characteristics. These issues are then associated with over 2,000 sustainability indicators gathered from existing sources. A gap analysis is then performed to determine if particular issues and issue groups are over or underrepresented. This process results in 44 "integrated" issues--24 impact issues and 36 vulnerability issues--that are composed of 318 "component" issues. The gap analysis shows that although every integrated issue is mentioned at least 40% of the time across perspectives, no issue is mentioned more than 70% of the time. A few issues infrequently mentioned across perspectives also have relatively few indicators available to fully represent them. Issues in the impact framework generally have fewer gaps than those in the vulnerability framework