ASU Scholarship Showcase

Fine particulate matter (PM_2.5) was collected in Shiprock, New Mexico, a small community located near two coal–fired power plants and numerous abandoned uranium mine tailing sites. Eleven PM_2.5 samples were collected for 96 h over three sampling periods (April/May 2009, November 2009, and October/November, 2010). Nine samples were analyzed for 64 elements using inductively coupled plasma–mass spectrometry. B, Bi, Cu, Pb, Sb, Sn, and Zn were observed in at least eight samples at levels indicative of anthropogenic enrichment (enrichment factors between 30 and 650). All the seven elements could be explained by coal–combustion processes. B, Bi, and Sb are enriched in coals; Cu, Pb, Sn, and Zn are chalcophile–lithophile or chalcophile elements, all with appreciable affinity for sulfur, a component of coal. Principal component analysis also supported these findings. Four major sources (percent variance) were identified: soil (61%), coal combustion (17%), industrial (11%), and sea salt (5%). Concentrations of elements associated with coal combustion in Shiprock were lower than levels observed in other industrially influenced cities. This was explained by Shiprock’s location west of the power plants. Back trajectories indicated that winds arrive to Shiprock from the W, SW, and NW, but the power plants are located to the east (upwind) of the city. Samples were also analyzed for uranium (0.002–0.02 ng/m³) and other metals associated with mine tailings (Sr, Mo). All metals were detected but at low levels, and concentrations did not vary predictably with wind direction. Hence, the tailings sites could not be attributed as the source.

Solutions to meet growing food requirements in a world of limited suitable land and degrading environment focus mainly on increasing crop yields, particularly in poorly performing regions, and reducing animal product consumption. Increasing yields could alleviate land requirements, but imposing higher soil nutrient withdrawals and in most cases larger fertilizer inputs. Lowering animal product consumption favors a more efficient use of land as well as soil and fertilizer nutrients; yet actual saving may largely depend on which crops and how much fertilizer are used to feed livestock versus people. We show, with a global analysis, how the choice of cultivated plant species used to feed people and livestock influences global food production as well as soil nutrient withdrawals and fertilizer additions. The 3 to 15-fold differences in soil nutrient withdrawals per unit of energy or protein produced that we report across major crops explain how composition shifts over the last 20 years have reduced N, maintained P and increased K harvest withdrawals from soils while contributing to increasing dietary energy, protein and, particularly, vegetable fat outputs. Being highly variable across crops, global fertilization rates do not relate to actual soil nutrient withdrawals, but to monetary values of harvested products. Future changes in crop composition could contribute to achieve more sustainable food systems, optimizing land and fertilizer use.

We present results from experiments at the Linac Coherent Light Source (LCLS) demonstrating that serial femtosecond crystallography (SFX) can be performed to high resolution (~2.5 Å) using protein microcrystals deposited on an ultra-thin silicon nitride membrane and embedded in a preservation medium at room temperature. Data can be acquired at a high acquisition rate using x-ray free electron laser sources to overcome radiation damage, while sample consumption is dramatically reduced compared to flowing jet methods. We achieved a peak data acquisition rate of 10 Hz with a hit rate of ~38%, indicating that a complete data set could be acquired in about one 12-hour LCLS shift using the setup described here, or in even less time using hardware optimized for fixed target SFX. This demonstration opens the door to ultra low sample consumption SFX using the technique of diffraction-before-destruction on proteins that exist in only small quantities and/or do not produce the copious quantities of microcrystals required for flowing jet methods.

Climate change will result in reduced soil water availability in much of the world either due to changes in precipitation or increased temperature and evapotranspiration. How communities of mites and nematodes may respond to changes in moisture availability is not well known, yet these organisms play important roles in decomposition and nutrient cycling processes. We determined how communities of these organisms respond to changes in moisture availability and whether common patterns occur along fine-scale gradients of soil moisture within four individual ecosystem types (mesic, xeric and arid grasslands and a polar desert) located in the western United States and Antarctica, as well as across a cross-ecosystem moisture gradient (CEMG) of all four ecosystems considered together.

An elevation transect of three sampling plots was monitored within each ecosystem and soil samples were collected from these plots and from existing experimental precipitation manipulations within each ecosystem once in fall of 2009 and three times each in 2010 and 2011. Mites and nematodes were sorted to trophic groups and analyzed to determine community responses to changes in soil moisture availability. We found that while both mites and nematodes increased with available soil moisture across the CEMG, within individual ecosystems, increases in soil moisture resulted in decreases to nematode communities at all but the arid grassland ecosystem; mites showed no responses at any ecosystem. In addition, we found changes in proportional abundances of mite and nematode trophic groups as soil moisture increased within individual ecosystems, which may result in shifts within soil food webs with important consequences for ecosystem functioning. We suggest that communities of soil animals at local scales may respond predictably to changes in moisture availability regardless of ecosystem type but that additional factors, such as climate variability, vegetation composition, and soil properties may influence this relationship over larger scales.

The emergence of the disease chytridiomycosis caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd) has been implicated in dramatic global amphibian declines. Although many species have undergone catastrophic declines and/or extinctions, others appear to be unaffected or persist at reduced frequencies after Bd outbreaks. The reasons behind this variance in disease outcomes are poorly understood: differences in host immune responses have been proposed, yet previous studies suggest a lack of robust immune responses to Bd in susceptible species. Here, we sequenced transcriptomes from clutch-mates of a highly susceptible amphibian, Atelopus zeteki, with different infection histories. We found significant changes in expression of numerous genes involved in innate and inflammatory responses in infected frogs despite high susceptibility to chytridiomycosis.

We show evidence of acquired immune responses generated against Bd, including increased expression of immunoglobulins and major histocompatibility complex genes. In addition, fungal-killing genes had significantly greater expression in frogs previously exposed to Bd compared with Bd-naïve frogs, including chitinase and serine-type proteases. However, our results appear to confirm recent in vitro evidence of immune suppression by Bd, demonstrated by decreased expression of lymphocyte genes in the spleen of infected compared with control frogs. We propose susceptibility to chytridiomycosis is not due to lack of Bd-specific immune responses but instead is caused by failure of those responses to be effective. Ineffective immune pathway activation and timing of antibody production are discussed as potential mechanisms. However, in light of our findings, suppression of key immune responses by Bd is likely an important factor in the lethality of this fungus.

Fungal hyphae are among the most highly polarized cells. Hyphal polarized growth is supported by tip-directed transport of secretory vesicles, which accumulate temporarily in a stratified manner in an apical vesicle cluster, the Spitzenkörper. The exocyst complex is required for tethering of secretory vesicles to the apical plasma membrane. We determined that the presence of an octameric exocyst complex is required for the formation of a functional Spitzenkörper and maintenance of regular hyphal growth in Neurospora crassa. Two distinct localization patterns of exocyst subunits at the hyphal tip suggest the dynamic formation of two assemblies. The EXO-70/EXO-84 subunits are found at the peripheral part of the Spitzenkörper, which partially coincides with the outer macrovesicular layer, whereas exocyst components SEC-5, -6, -8, and -15 form a delimited crescent at the apical plasma membrane. Localization of SEC-6 and EXO-70 to the plasma membrane and the Spitzenkörper, respectively, depends on actin and microtubule cytoskeletons. The apical region of exocyst-mediated vesicle fusion, elucidated by the plasma membrane–associated exocyst subunits, indicates the presence of an exocytotic gradient with a tip-high maximum that dissipates gradually toward the subapex, confirming the earlier predictions of the vesicle supply center model for hyphal morphogenesis.

Collective cell migration plays a substantial role in maintaining the cohesion of epithelial cell layers and in wound healing. A number of mathematical models of this process have been developed, all of which reduce to essentially a reaction-diffusion equation with diffusion and proliferation terms that depend on material assumptions about the cell layer. In this paper we extend a one-dimensional mathematical model of cell layer migration of Mi et al. [Biophys. J., 93 (2007), pp. 3745–3752] to incorporate stretch-dependent proliferation, and show that this formulation reduces to a generalized Stefan problem for the density of the layer. We solve numerically the resulting partial differential equation system using an adaptive finite difference method and show that the solutions converge to self-similar or traveling wave solutions. We analyze self-similar solutions for cases with no prolifera- tion, and necessary and sufficient conditions for existence and uniqueness of traveling solutions for a wide range of material assumptions about the cell layer.

Background: An accurate method that can diagnose and predict lupus and its neuropsychiatric manifestations is essential since currently there are no reliable methods. Autoantibodies to a varied panel of antigens in the body are characteristic of lupus. In this study we investigated whether serum autoantibody binding patterns on random-sequence peptide microarrays (immunosignaturing) can be used for diagnosing and predicting the onset of lupus and its central nervous system (CNS) manifestations. We also tested the techniques for identifying potentially pathogenic autoantibodies in CNS-Lupus. We used the well-characterized MRL/lpr lupus animal model in two studies as a first step to develop and evaluate future studies in humans.

Results: In study one we identified possible diagnostic peptides for both lupus and altered behavior in the forced swim test. When comparing the results of study one to that of study two (carried out in a similar manner), we further identified potential peptides that may be diagnostic and predictive of both lupus and altered behavior in the forced swim test. We also characterized five potentially pathogenic brain-reactive autoantibodies, as well as suggested possible brain targets.

Conclusions: These results indicate that immunosignaturing could predict and diagnose lupus and its CNS manifestations. It can also be used to characterize pathogenic autoantibodies, which may help to better understand the underlying mechanisms of CNS-Lupus.

Background: The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity.

Results: By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition.

Conclusions: Clustering based on the frequency in which orthologous proteins occur among metagenomes facilitated accurate prediction of the ordering of community functional composition along geochemical gradients, despite a lack of geochemical input. The consistency in the results obtained from the application of Markov clustering and multivariate methods to distinct natural systems underscore their utility in predicting the functional potential of microbial communities within a natural system based on system geochemistry alone, allowing geochemical measurements to be used to predict purely biological metrics such as microbial community composition and metabolism.

High-statistics measurements of differential cross sections and spin density matrix elements for the reaction γp → ϕp have been made using the CLAS detector at Jefferson Lab. We cover center-of-mass energies (√s) from 1.97 to 2.84 GeV, with an extensive coverage in the ϕ production angle. The high statistics of the data sample made it necessary to carefully account for the interplay between the ϕ natural lineshape and effects of the detector resolution, that are found to be comparable in magnitude. We study both the charged- (ϕ → K⁺K^-) and neutral- (ϕ → K[0 over S]K[0 over L]) K[⎯⎯⎯ over K] decay modes of the ϕ. Further, for the charged mode, we differentiate between the cases where the final K^- track is directly detected or its momentum reconstructed as the total missing momentum in the event. The two charged-mode topologies and the neutral-mode have different resolutions and are calibrated against each other. Extensive usage is made of kinematic fitting to improve the reconstructed ϕ mass resolution. Our final results are reported in 10- and mostly 30-MeV-wide √s bins for the charged- and the neutral-modes, respectively. Possible effects from K⁺Λ^* channels with pK[⎯⎯⎯ over K] final states are discussed. These present results constitute the most precise and extensive ϕ photoproduction measurements to date and in conjunction with the ω photoproduction results recently published by CLAS, will greatly improve our understanding of low energy vector meson photoproduction.