Faculty Scholarship
Showing 321 - 330 of 733 Items
Is variation in susceptibility to Phytophthora ramorum correlated with population genetic structure in coast live oak (Quercus agrifolia)?
Date: 2005-01-01
Creator: Richard S. Dodd, Daniel Hüberli, Vlad Douhovnikoff, Tamar Y. Harnik, Zara, Afzal-Rafii, Matteo Garbelotto
Access: Open access
- California coastal woodlands are suffering severe disease and mortality as a result of infection from Phytophthora ramorum. Quercus agrifolia is one of the major woodland species at risk. This study investigated within- and among-population variation in host susceptibility to inoculation with P. ramorum and compared this with population genetic structure using molecular markers. Susceptibility was assessed using a branch-cutting inoculation test. Trees were selected from seven natural populations in California. Amplified fragment length polymorphism molecular markers were analysed for all trees used in the trials. Lesion sizes varied quantitatively among individuals within populations, with up to an eightfold difference. There was little support for population differences in susceptibility. Molecular structure also showed a strong within-population, and weaker among-population, pattern of variation. Our data suggest that susceptibility of Q. agrifolia to P. ramorum is variable and is under the control of several gene loci. This variation exists within populations, so that less susceptible local genotypes may provide the gene pool for regeneration of woodlands where mortality is high. © New Phytologist (2004).
The role of adjuvant in mediating antigen structure and stability
Date: 2012-01-01
Creator: Latoya Jones Braun, Aimee M. Eldridge, Jessica Cummiskey, Kelly K. Arthur, Deborah S., Wuttke
Access: Open access
- The purpose of this study was to probe the fate of a model antigen, a cysteine-free mutant of bacteriophage T4 lysozyme, to the level of fine structural detail, as a consequence of its interaction with an aluminum (Al)-containing adjuvant. Fluorescence spectroscopy and differential scanning calorimetry were used to compare the thermal stability of the protein in solution versus adsorbed onto an Al-containing adjuvant. Differences in accessible hydrophobic surface areas were investigated using an extrinsic fluorescence probe, 8-Anilino-1-naphthalenesulfonic acid (ANS). As has been observed with other model antigens, the apparent thermal stability of the protein decreased following adsorption onto the adjuvant. ANS spectra suggested that adsorption onto the adjuvant caused an increase in exposure of hydrophobic regions of the protein. Electrostatic interactions drove the adsorption, and disruption of these interactions with high ionic strength buffers facilitated the collection of two-dimensional 15N heteronuclear single quantum coherence nuclear magnetic resonance data of protein released from the adjuvant. Although the altered stability of the adsorbed protein suggested changes to the protein's structure, the fine structure of the desorbed protein was nearly identical to the protein's structure in the adjuvant-free formulation. Thus, the adjuvant-induced changes to the protein that were responsible for the reduced thermal stability were not observed upon desorption. © 2011 Wiley Periodicals, Inc.
Non-intrusive load identification for smart outlets
Date: 2015-01-12
Creator: Sean Barker, Mohamed Musthag, David Irwin, Prashant Shenoy
Access: Open access
- An increasing interest in energy-efficiency combined with the decreasing cost of embedded networked sensors is lowering the cost of outlet-level metering. If these trends continue, new buildings in the near future will be able to install 'smart' outlets, which monitor and transmit an outlets power usage in real time, for nearly the same cost as conventional outlets. One problem with the pervasive deployment of smart outlets is that users must currently identify the specific device plugged into each meter, and then manually update the outlets meta-data in software whenever a new device is plugged into the outlet. Correct meta-data is important in both interpreting historical outlet energy data and using the data for building management. To address this problem, we propose Non-Intrusive Load Identification (NILI), which automatically identifies the device attached to a smart outlet without any human intervention. In particular, in our approach to NILI, we identify an intuitive and simple-to-compute set of features from time-series energy data and then employ well-known classifiers. Our results achieve accuracy of over 90% across 15 device types on outlet-level energy traces collected from multiple real homes.
Using landscape metrics to characterize towns along an urban-rural gradient
Date: 2021-10-01
Creator: Abigail Kaminski, Dana Marie Bauer, Kathleen P. Bell, Cynthia S. Loftin, Erik J., Nelson
Access: Open access
- Context: Urban-rural gradients are useful tools when examining the influence of human disturbances on ecological, social and coupled systems, yet the most commonly used gradient definitions are based on single broad measures such as housing density or percent forest cover that fail to capture landscape patterns important for conservation. Objectives: We present an approach to defining urban–rural gradients that integrates multiple landscape pattern metrics related to ecosystem processes important for natural resources and wildlife sustainability. Methods: We develop a set of land cover composition and configuration metrics and then use them as inputs to a cluster analysis process that, in addition to grouping towns with similar attributes, identifies exemplar towns for each group. We compare the outcome of the cluster-based urban-rural gradient typology to outcomes for four commonly-used rule-based typologies and discuss implications for resource management and conservation. Results: The resulting cluster-based typology defines five town types (urban, suburban, exurban, rural, and agricultural) and notably identifies a bifurcation along the gradient distinguishing among rural forested and agricultural towns. Landscape patterns (e.g., core and islet forests) influence where individual towns fall along the gradient. Designations of town type differ substantially among the five different typologies, particularly along the middle of the gradient. Conclusions: Understanding where a town occurs along the urban-rural gradient could aid local decision-makers in prioritizing and balancing between development and conservation scenarios. Variations in outcomes among the different urban-rural gradient typologies raise concerns that broad-measure classifications do not adequately account for important landscape patterns. We suggest future urban-rural gradient studies utilize more robust classification approaches.
A strategy for the selective imaging of glycans using caged metabolic precursors
Date: 2010-07-21
Creator: Pamela V. Chang, Danielle H. Dube, Ellen M. Sletten, Carolyn R. Bertozzi
Access: Open access
- Glycans can be imaged by metabolic labeling with azidosugars followed by chemical reaction with imaging probes; however, tissue-specific labeling is difficult to achieve. Here we describe a strategy for the use of a caged metabolic precursor that is activated for cellular metabolism by enzymatic cleavage. An N-azidoacetylmannosamine derivative caged with a peptide substrate for the prostate-specific antigen (PSA) protease was converted to cell-surface azido sialic acids in a PSA-dependent manner. The approach has applications in tissue-selective imaging of glycans for clinical and basic research purposes. © 2010 American Chemical Society.
Arginine methylation of yeast mRNA-binding protein Npl3 directly affects its function, nuclear export, and intranuclear protein interactions
Date: 2005-09-02
Creator: Anne E. McBride, Jeffrey T. Cook, Elizabeth A. Stemmler, Kate L. Rutledge, Kelly A., McGrath, Jeffrey A. Rubens
Access: Open access
- Arginine methylation can affect both nucleocytoplasmic transport and protein-protein interactions of RNA-binding proteins. These effects are seen in cells that lack the yeast hnRNP methyltransferase (HMT1), raising the question of whether effects on specific proteins are direct or indirect. The presence of multiple arginines in individual methylated proteins also raises the question of whether overall methylation or methylation of a subset of arginines affects protein function. We have used the yeast mRNA-binding protein Npl3 to address these questions in vivo. Matrix-assisted laser desorption/ionization Fourier transform mass spectrometry was used to identify 17 methylated arginines in Npl3 purified from yeast: whereas 10 Arg-Gly-Gly (RGG) tripeptides were exclusively dimethylated, variable levels off methylation were found for 5 RGG and 2 RG motif arginines. We constructed a set of Npl3 proteins in which subsets of the RGG arginines were mutated to lysine. Expression of these mutant proteins as the sole form of Npl3 specifically affected growth of a strain that requires Hmtl. Although decreased growth generally correlated with increased numbers of Arg-to-Lys mutations, lysine substitutions in the N terminus of the RGG domain showed more severe effects. Npl3 with all 15 RGG arginines mutated to lysine exited the nucleus independent of Hmtl, indicating a direct effect of methylation on Npl3 transport. These mutations also resulted in a decreased, methylation-independent interaction of Npl3 with transcription elongation factor Tho2 and inhibited Npl3 self-association. These results support a model in which arginine methylation facilitates Npl3 export directly by weakening contacts with nuclear proteins. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.
CO2 induced phase transitions in diamine-appended metal-organic frameworks
Date: 2015-06-15
Creator: Bess Vlaisavljevich, Samuel O. Odoh, Sondre K. Schnell, Allison L. Dzubak, Kyuho, Lee, Nora Planas, Jeffrey B. Neaton, Laura Gagliardi, Berend Smit
Access: Open access
- Using a combination of density functional theory and lattice models, we study the effect of CO2 adsorption in an amine functionalized metal-organic framework. These materials exhibit a step in the adsorption isotherm indicative of a phase change. The pressure at which this step occurs is not only temperature dependent but is also metal center dependent. Likewise, the heats of adsorption vary depending on the metal center. Herein we demonstrate via quantum chemical calculations that the amines should not be considered firmly anchored to the framework and we explore the mechanism for CO2 adsorption. An ammonium carbamate species is formed via the insertion of CO2 into the M-Namine bonds. Furthermore, we translate the quantum chemical results into isotherms using a coarse grained Monte Carlo simulation technique and show that this adsorption mechanism can explain the characteristic step observed in the experimental isotherm while a previously proposed mechanism cannot. Furthermore, metal analogues have been explored and the CO2 binding energies show a strong metal dependence corresponding to the M-Namine bond strength. We show that this difference can be exploited to tune the pressure at which the step in the isotherm occurs. Additionally, the mmen-Ni2(dobpdc) framework shows Langmuir like behavior, and our simulations show how this can be explained by competitive adsorption between the new model and a previously proposed model.
Third-generation effects on fermion mass predictions in supersymmetric grand unified theories
Date: 1993-01-01
Creator: Stephen G. Naculich
Access: Open access
- Relations among fermion masses and mixing angles at the scale of grand unification are modified at lower energies by renormalization group running induced by gauge and Yukawa couplings. In super-symmetric theories, the b quark and lepton Yukawa couplings, as well as the t quark coupling, may cause significant running if tan, the ratio of Higgs field expectation values, is large. We present approximate analytic expressions for the scaling factors for fermion masses and CKM matrix elements induced by all three third generation Yukawa couplings. We then determine how running caused by the third generation of fermions affects the predictions arising from three possible forms for the Yukawa coupling matrices at the GUT scale: the Georgi-Jarlskog, Giudice, and Fritzsch textures. © 1993 The American Physical Society.
Quantum kinks: Solitons at strong coupling
Date: 1992-01-01
Creator: Stephen G. Naculich
Access: Open access
- We examine solitons in theories with heavy fermions. These "quantum" solitons differ dramatically from semiclassical (perturbative) solitons because fermion loop effects are important when the Yukawa coupling is strong. We focus on kinks in a (1 + 1)-dimensional 4 theory coupled to fermions; a large-N expansion is employed to treat the Yukawa coupling g nonperturbatively. A local expression for the fermion vacuum energy is derived using the WKB approximation for the Dirac eigenvalues. We find that fermion loop corrections increase the energy of the kink and (for large g) decrease its size. For large g, the energy of the quantum kink is proportional to g, and its size scales as 1g, unlike the classical kink; we argue that these features are generic to quantum solitons in theories with strong Yukawa couplings. We also discuss the possible instability of fermions to solitons. © 1992 The American Physical Society.