A Kinetic Vlasov Model for Plasma Simulation Using Discontinuous Galerkin Method on Many-Core Architectures

Thesis (Ph.D.)--University of Washington, 2016-03

Interactions between ecology, demography, capture stress, and profiles of corticosterone and glucose in a free-living population of Australian freshwater crocodiles

In this study we examined three aspects pertaining to adrenocortical responsiveness in free-ranging Australian freshwater crocodiles (Crocodylus johnstoni). First, we examined the ability of freshwater crocodiles to produce corticosterone in response to a typical capture-stress protocol. A second objective addressed the relationship between capture stress, plasma glucose and corticosterone. Next we examined if variation in basal and capture-stress-induced levels of plasma corticosterone was linked to ecological or demographic factors for individuals in this free-ranging population. Blood samples obtained on three field trips were taken from a cross-sectional sample of the population. Crocodiles were bled once during four time categories at 0, 0. 5, 6, and 10 h post-capture. Plasma corticosterone increased significantly with time post-capture. Plasma glucose also significantly increased with duration of capture-stress and exhibited a positive and significant relationship with plasma corticosterone. Significant variation in basal or stress induced levels of corticosterone in crocodiles was not associated with any ecological or demographic factors including sex, age class or the year of capture that the crocodiles were sampled from. However, three immature males had basal levels of plasma corticosterone greater than 2 standard deviations above the mean. While crocodiles exhibited a pronounced, adrenocortical and hyperglycaemic response to capture stress, limited variation in adrenocortical responsiveness due to ecological and demographic factors was not evident. This feature could arise in part because this population was sampled during a period of environmental benigness. (C) 2003 Elsevier Science (USA). All rights reserved.

Dissecting the EphA3/ephrin-A5 interactions using a novel functional mutagenesis screen

The EphA3 receptor tyrosine kinase preferentially binds ephrin-A5, a member of the corresponding subfamily of membrane-associated ligands. Their interaction regulates critical cell communication functions in normal development and may play a role in neoplasia. Here we describe a random mutagenesis approach, which we employed to study the molecular determinants of the EphA3/ephrin-A5 recognition. Selection and functional characterization of EphA3 point mutants with impaired ephrin-A5 binding from a yeast expression library defined three EphA3 surface areas that are essential for the EphA3/ephrin-A5 interaction. Two of these map to regions identified previously in the crystal structure of the homologous EphB2-ephrin-B2 complex as potential ligand/receptor interfaces. In addition, we identify a third EphA3/ephrin-A5 interface that falls outside the structurally characterized interaction domains. Functional analysis of EphA3 mutants reveals that all three Eph/ephrin contact areas are essential for the assembly of signaling-competent, oligomeric receptor-ligand complexes.

Thermosetting Blends of Polybenzoxazine and Poly(ε-caprolactone): Phase Behavior and Intermolecular Specific Interactions

Polybenzoxazine (PBA-a)/poly(epsilon-caprolactone) (PCL) blends were prepared by an in situ curing reaction of benzoxazine (BA-a) in the presence of PCL. Before curing, the benzoxazine (BA-a)/PCL blends are miscible, which was evidenced by the behaviors of single and composition-dependant glass transition temperature and equilibrium melting point depression. However, the phase separation induced by polymerization was observed after curing at elevated temperature. It was expected that after curing, the PBA-a/PCL blends would be miscible since the phenolic hydroxyls in the PBA-a molecular backbone have the potential to form inter- molecular hydrogen-bonding interactions with the carbonyls of PCL and thus would fulfil the miscibility of the blends. The resulting morphology of the blends prompted an investigation of the status of association between PBA-a and PCL under the curing conditions. Although Fourier-transform infrared spectroscopy (FT-IR) showed that there were intermolecular hydrogen-bonding interactions between PBA-a and PCL at room temperature, especially for the PCL-rich blends, the results of variable temperature FT-IR spectroscopy by the model compound indicate that the phenolic hydroxyl groups could not form efficient intermolecular hydrogen-bonding interactions at elevated temperatures, i.e., the phenolic hydroxyl groups existed mainly in the non-associated form in the system during curing. The results are valuable to understand the effect of curing temperature on the resulting morphology of the thermosetting blends. SEM micrograph of the dichloromethane-etched fracture surface of a 90:10 PBA-a PCL blend showing a heterogeneous morphology.

Sorting nexin 5 is localized to a subdomain of the early endosomes and is recruited to the plasma imembrane following EGF stimulation

Sorting nexins are a large family of proteins that contain the phosphoinositide-binding Phox homology (PX) domain. A number of sorting nexins are known to bind to PtdIns(3)P, which mediates their localization to membranes of the endocytic pathway. We show here that sorting nexin 5 (SNX5) can be recruited to two distinct membrane compartments. In non-stimulated cells, the PX domain was independently targeted to endosomal structures and colocalized with full-length SNX5. The membrane binding of the PX domain was inhibited by the PI 3-kinase inhibitor, wortmannin. Although SNX5 colocalized with a fluid-phase marker and was found predominantly within a PtdIns(3)P-rich endosomal domain, very little colocalization was observed between SNX5 and the PtdIns(3)P-binding protein, EEA1. Using liposome-based binding assays, we have shown that the PX domain of SNX5 interacts not only with PtdIns(3)P but also with PtdIns(3,4)P-2. In response to EGF stimulation, either the SNX5-PX domain or full-length SNX5 was rapidly recruited to the plasma membrane. The localization of SNX1, which does not bind PtdIns(3,4)P-2, was unaffected by EGF signalling. Therefore, SNX5 is localized to a subdomain of the early endosome distinct from EEA1 and, following EGF stimulation and elevation of PtdIns(3,4)P-2, is also transiently recruited to the plasma membrane. These results indicate that SNX5 may have functions not only associated with endosomal sorting but also with the phosphoinositide-signalling pathway.

Lipid rafts and plasma membrane microorganization: insights from Ras

The spatial organization of plasma membrane components in discrete microdomains is thought to be a key factor in the generation of distinct signal outputs. A detailed characterization of plasma membrane microdomains, including descriptions of their size, dynamics and abundance, has proved to be a taxing problem for cell biologists and biophysicists. The use of novel techniques is providing exciting new insights into the challenging problem of plasma membrane microstructure and has allowed the visualization of domains with the characteristics expected of lipid rafts - microdomains of the plasma membrane enriched in cholesterol and sphingolipids. This review focuses on some of these recent advances and uses Ras signaling as a paradigm for understanding inner plasma membrane organization and the role of lipid rafts in cellular function.

Classical cadherin adhesion molecules: coordinating cell adhesion, signaling and the cytoskeleton

Classical cadherin adhesion molecules are fundamental determinants of tissue organization in both health and disease. Recent advances in understanding the molecular and cellular basis of cadherin function have revealed that these adhesion molecules serve as molecular couplers, linking cell surface adhesion and recognition to both the actin cytoskeleton and cell signalling pathways. We will review some of these developments. to provide an overview of progress in this rapidly-developing area of cell and developmental biology.

Sea surface temperature variations recorded on coralline Sr/Ca ratios during Mid-Late Holocene in Leizhou Peninsula

High-resolution Sr/Ca ratios of two Porites corals from Leizhou Peninsula were measured using inductively coupled plasma atomic spectrometry (ICP-AES). TIMS U-Th dating reveals that the life-spans of the two corals are 489500 AD and 539-530 BC, respectively. Monthly sea surface temperatures (SSTs) during these two periods can be reconstructed from their skeletal Sr/Ca ratios. The results reveal that SSTs during 539-530 BC were roughly the same as those during 1990-2000 AD in this area, indicating a relative warm climate period. However, the period of 489-500 AD was significantly cooler, with annual mean SST, the 10-a average of minimum monthly winter SSTs and the 10-a average of maximum monthly summer SSTs being about 2, 2.9 and 1degreesC lower than that in the 1990s, respectively. Such climate patterns agree well with the phenological results recorded in the historic documents in other areas of China.

Diving behaviour of a reptile (Crocodylus johnstoni) in the wild: Interactions with heart rate and body temperature

The differences in physical properties of air and water pose unique behavioural and physiological demands on semiaquatic animals. The aim of this study was to describe the diving behaviour of the freshwater crocodile Crocodylus johnstoni in the wild and to assess the relationships between diving, body temperature, and heart rate. Time-depth recorders, temperature-sensitive radio transmitters, and heart rate transmitters were deployed on each of six C. johnstoni (4.0-26.5 kg), and data were obtained from five animals. Crocodiles showed the greatest diving activity in the morning (0600-1200 hours) and were least active at night, remaining at the water surface. Surprisingly, activity pattern was asynchronous with thermoregulation, and activity was correlated to light rather than to body temperature. Nonetheless, crocodiles thermoregulated and showed a typical heart rate hysteresis pattern (heart rate during heating greater than heart rate during cooling) in response to heating and cooling. Additionally, dive length decreased with increasing body temperature. Maximum diving length was 119.6 min, but the greatest proportion of diving time was spent on relatively short (

Application of density functional theory to equilibrium adsorption of argon and nitrogen on amorphous silica surface

We present a new version of non-local density functional theory (NL-DFT) adapted to description of vapor adsorption isotherms on amorphous materials like non-porous silica. The novel feature of this approach is that it accounts for the roughness of adsorbent surface. The solid–fluid interaction is described in the same framework as in the case of fluid–fluid interactions, using the Weeks–Chandler–Andersen (WCA) scheme and the Carnahan–Starling (CS) equation for attractive and repulsive parts of the Helmholtz free energy, respectively. Application to nitrogen and argon adsorption isotherms on non-porous silica LiChrospher Si-1000 at their boiling points, recently published by Jaroniec and co-workers, has shown an excellent correlative ability of our approach over the complete range of pressures, which suggests that the surface roughness is mostly the reason for the observed behavior of adsorption isotherms. From the analysis of these data, we found that in the case of nitrogen adsorption short-range interactions between oxygen atoms on the silica surface and quadrupole of nitrogen molecules play an important role. The approach presented in this paper may be further used in quantitative analysis of adsorption and desorption isotherms in cylindrical pores such as MCM-41 and carbon nanotubes.

Van der Waals-corrected density functional theory: benchmarking for hydrogen-nanotube and nanotube-nanotube interactions

Density functional theory (DFT) is a powerful approach to electronic structure calculations in extended systems, but suffers currently from inadequate incorporation of long-range dispersion, or Van der Waals (VdW) interactions. VdW-corrected DFT is tested for interactions involving molecular hydrogen, graphite, single-walled carbon nanotubes (SWCNTs), and SWCNT bundles. The energy correction, based on an empirical London dispersion term with a damping function at short range, allows a reasonable physisorption energy and equilibrium distance to be obtained for H-2 on a model graphite surface. The VdW-corrected DFT calculation for an (8, 8) nanotube bundle reproduces accurately the experimental lattice constant. For H-2 inside or outside an (8, 8) SWCNT, we find the binding energies are respectively higher and lower than that on a graphite surface, correctly predicting the well known curvature effect. We conclude that the VdW correction is a very effective method for implementing DFT calculations, allowing a reliable description of both short-range chemical bonding and long-range dispersive interactions. The method will find powerful applications in areas of SWCNT research where empirical potential functions either have not been developed, or do not capture the necessary range of both dispersion and bonding interactions.

H-ras, K-ras, and inner plasma membrane raft proteins operate in nanoclusters with differential dependence on the actin cytoskeleton

Plasma membrane compartmentalization imposes lateral segregation on membrane proteins that is important for regulating signal transduction. We use computational modeling of immunogold spatial point patterns on intact plasma membrane sheets to test different models of inner plasma membrane organization. We find compartmentalization at the nanoscale level but show that a classical raft model of preexisting stable domains into which lipid raft proteins partition is incompatible with the spatial point patterns generated by the immunogold labeling of a palmitoylated raft marker protein. Rather, approximate to 30% of the raft protein exists in cholesterol-dependent nanoclusters, with approximate to 70% distributed as monomers. The cluster/monomer ratio (number of proteins in clusters/number of proteins outside clusters) is independent of expression level. H-rasG12V and K-rasG12V proteins also operate in nanoclusters with fixed cluster/monomer ratios that are independent of expression level. Detailed calibration of the immunogold imaging protocol suggests that radii of raft and RasG12V protein nanoclusters may be as small as 11 and 6 nm, respectively, and shows that the nanoclusters contain small numbers (6.0-7.7) of proteins. Raft nanoclusters do not form if the actin cytoskeleton is disassembled. The formation of K-rasG12V but not H-rasG12V nanoclusters also is actin-dependent. K-rasG12V but not H-rasG12V signaling is abrogated by actin cytoskeleton disassembly, which shows that nanoclustering is critical for Ras function. These findings argue against stable preexisting domains on the inner plasma membrane in favor of dynamic actively regulated nanoclusters similar to those proposed for the outer plasma membrane. RasG12V nanoclusters may facilitate the assembly of essential signal transduction complexes.