bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of the hybridization of impurity electron states on the quantum magneto-oscillation phenomena in mercury selenide with iron impurities
Authors: Alshanskiĭ G. A. , Govorkova T. E. , Okulov V. I. , Korolyov A. V. , Paranchich S. Yu.
Published: July 2008

Experimental study of the concentration dependence of the parameters of the Shubnikov–de Haas and de Haas–van Alphen oscillations in mercury selenide crystals containing iron impurities under conditions where the donor resonance energy level of the impurities falls into the conduction band and hybridization of the electronic states occurs. The observed concentration dependence of the Dingle temperature and g factor of the electrons exhibit minima correlated in position with the maximum of the electronic mobility. It is shown that the observed anomalies can be explained on the basis of a previously developed theory of hybridization effects.
Fast calculation of the electrostatic potential in ionic crystals by direct summation method
Authors: Gellé Alain , Lepetit Marie-Bernadette
Published: July 2008

An efficient real space method is derived for the evaluation of the Madelung’s potential of ionic crystals. The proposed method is an extension of Evjen’s method. It takes advantage of a general analysis of the potential convergence in real space. Indeed, we show that the series convergence is exponential as a function of the number of canceled multipolar moments in the unit cell. The method proposed in this work reaches such an exponential convergence rate. Its efficiency is comparable to Ewald’s method. However, unlike the latter, it uses only simple algebraic functions.
Formation of counter rotating vortices for electron acoustic waves
Authors: Haque Q.
Published: July 2008

Electron acoustic waves are discussed for two electron population plasma with shear flow perpendicular to the ambient magnetic field. Stationary solution in the form of counter rotating vortices is found for the particular equilibrium potential profile. It is noticed that these nonlinear structures can travel with the electron acoustic velocity. The speed of these structures is decreased while the amplitude is increased for large ion thermal velocity.
A new instrument for automated microcontact printing with stamp load adjustment
Authors: Bou Chakra Elie , Hannes Benjamin , Dilosquer Gilles , Mansfield Colin D. , Cabrera Michel
Published: July 2008

An instrument for automated microcontact printing (μCP) on microscope slides is described. The movement of the stamp, which is actuated by a computer controlled pneumatic actuator, is precisely guided until it makes contact with the substrate. As a consequence, the absolute position of the microprinted patterns is reproducible over a series of substrates with 1μm standard deviation. Exchange of substrates and stamps is a quick and simple procedure. This makes possible the microprinting of adjacent or superimposable patterns, with different products, in a reproducible manner. Furthermore, a novel approach is described for adjusting the load on the stamp during contact. Two adjustable screws are set up so that their length (with reference to the substrate holder) limits the stamp compression during contact. The load on the stamp is proportional to the stamp compression and from the experimental point of view, this is controlled by the operator adjusting the screws. This makes possible the μCP with stamps incorporating large surface features as well as stamps with isolated features raised on the surface. For proof of concept, automated μCP of a single parallelepiped polydimethylsiloxane feature, with a surface of 2cm×30μm and a height of 25μm, is demonstrated inside a microfluidic channel without roof collapse. A second example is provided with a single cross feature, possessing an overall surface of 140×140μm2 and a height of 14μm. Potential applications of this versatile, inexpensive and compact instrument are discussed. The machine’s potential for high throughput also makes it suitable for mass production applications.
A ceramic radial insulation structure for a relativistic electron beam vacuum diode
Authors: Xun Tao , Yang Hanwu , Zhang Jiande , Liu Zhenxiang , Wang Yong , Zhao Yansong
Published: July 2008

For one kind of a high current diode composed of a small disk-type alumina ceramic insulator water/vacuum interface, the insulation structure was designed and experimentally investigated. According to the theories of vacuum flashover and the rules for radial insulators, a “cone-column” anode outline and the cathode shielding rings were adopted. The electrostatic field along the insulator surface was obtained by finite element analysis simulating. By adjusting the outline of the anode and reshaping the shielding rings, the electric fields were well distributed and the field around the cathode triple junction was effectively controlled. Area weighted statistical method was applied to estimate the surface breakdown field. In addition, the operating process of an accelerator based on a spiral pulse forming line (PFL) was simulated through the PSPICE software to get the waveform of charging and diode voltage. The high voltage test was carried out on a water dielectric spiral PFL accelerator with long pulse duration, and results show that the diode can work stably in 420kV, 200ns conditions. The experimental results agree with the theoretical and simulated results.
Extended x-ray absorption fine structure measurements of quasi-isentropically compressed vanadium targets on the OMEGA laser
Authors: Yaakobi B. , Boehly T. R. , Sangster T. C. , Meyerhofer D. D. , Remington B. A. , Allen P. G. , Pollaine S. M. , Lorenzana H. E. , Lorenz K. T. , Hawreliak J. A.
Published: July 2008

The use of in situ extended x-ray absorption fine structure (EXAFS) for characterizing nanosecond laser-shocked vanadium, titanium, and iron has recently been demonstrated. These measurements are extended to laser-driven, quasi-isentropic compression experiments (ICE). The radiation source (backlighter) for EXAFS in all of these experiments is obtained by imploding a spherical target on the OMEGA laser [T. R. Boehly et al., Rev. Sci. Instrum. 66, 508 (1995)]. Isentropic compression (where the entropy is kept constant) enables to reach high compressions at relatively low temperatures. The absorption spectra are used to determine the temperature and compression in a vanadium sample quasi-isentropically compressed to pressures of up to ∼0.75Mbar. The ability to measure the temperature and compression directly is unique to EXAFS. The drive pressure is calibrated by substituting aluminum for the vanadium and interferometrically measuring the velocity of the back target surface by the velocity interferometer system for any reflector (VISAR). The experimental results obtained by EXAFS and VISAR agree with each other and with the simulations of a hydrodynamic code. The role of a shield to protect the sample from impact heating is studied. It is shown that the shield produces an initial weak shock that is followed by a quasi-isentropic compression at a relatively low temperature. The role of radiation heating from the imploding target as well as from the laser-absorption region is studied. The results show that in laser-driven ICE, as compared with laser-driven shocks, comparable compressions can be achieved at lower temperatures. The EXAFS results show important details not seen in the VISAR results.
Nonlinear transport processes in tokamak plasmas. I. The collisional regimes
Authors: Sonnino Giorgio , Peeters Philippe
Published: July 2008

An application of the thermodynamic field theory (TFT) to transport processes in L-mode tokamak plasmas is presented. The nonlinear corrections to the linear (“Onsager”) transport coefficients in the collisional regimes are derived. A quite encouraging result is the appearance of an asymmetry between the Pfirsch–Schlüter (P-S) ion and electron transport coefficients: the latter presents a nonlinear correction, which is absent for the ions, and makes the radial electron coefficients much larger than the former. Explicit calculations and comparisons between the neoclassical results and the TFT predictions for Joint European Torus (JET) plasmas are also reported. It is found that the nonlinear electron P-S transport coefficients exceed the values provided by neoclassical theory by a factor that may be of the order 102. The nonlinear classical coefficients exceed the neoclassical ones by a factor that may be of order 2. For JET, the discrepancy between experimental and theoretical results for the electron losses is therefore significantly reduced by a factor 102 when the nonlinear contributions are duly taken into account but, there is still a factor of 102 to be explained. This is most likely due to turbulence. The expressions of the ion transport coefficients, determined by the neoclassical theory in these two regimes, remain unaltered. The low-collisional regimes, i.e., the plateau and the banana regimes, are analyzed in the second part of this work.
Synchronization in networks of spatially extended systems
Authors: Filatova Anastasiya E. , Hramov Alexander E. , Koronovskii Alexey A. , Boccaletti Stefano
Published: July 2008

Synchronization processes in networks of spatially extended dynamical systems are analytically and numerically studied. We focus on the relevant case of networks whose elements (or nodes) are spatially extended dynamical systems, with the nodes being connected with each other by scalar signals. The stability of the synchronous spatio-temporal state for a generic network is analytically assessed by means of an extension of the master stability function approach. We find an excellent agreement between the theoretical predictions and the data obtained by means of numerical calculations. The efficiency and reliability of this method is illustrated numerically with networks of beam-plasma chaotic systems (Pierce diodes). We discuss also how the revealed regularities are expected to take place in other relevant physical and biological circumstances.
Short-pulse space-charge-limited electron flows in a drift space
Authors: Zhang P. , Koh W. S. , Ang L. K. , Chen S. H.
Published: July 2008

In this paper, the space-charge-limited (SCL) electron flows in a drift space is studied by including the effect of finite electron pulse length, which is smaller than the gap transit time. Analytical formulas are derived to calculate the maximum SCL current density that can be transported across a drift space under the short-pulse injection condition. For a given voltage or injection energy, the maximum current density that can be transported is enhanced by a large factor (as compared to the long-pulse or steady-state case), and the enhancement is inversely proportional to the electron pulse length. In drift space, the effect of pulse expansion is important at very short-pulse length, and the short-pulse enhancement factor is smaller as compared to a diode. The enhancement factor will be suppressed when the injection energy is larger than the electron rest mass, and effect of pulse expansion is less critical at relativistic energy. The analytical formulas have been verified by performing a particle-in-cell simulation in the electrostatic mode.
Reynolds number dependence of relative dispersion statistics in isotropic turbulence
Authors: Sawford Brian L. , Yeung P. K. , Hackl Jason F.
Published: July 2008

Direct numerical simulation results for a range of relative dispersion statistics over Taylor-scale Reynolds numbers up to 650 are presented in an attempt to observe and quantify inertial subrange scaling and, in particular, Richardson’s t3 law. The analysis includes the mean-square separation and a range of important but less-studied differential statistics for which the motion is defined relative to that at time t=0. It seeks to unambiguously identify and quantify the Richardson scaling by demonstrating convergence with both the Reynolds number and initial separation. According to these criteria, the standard compensated plots for these statistics in inertial subrange scaling show clear evidence of a Richardson range but with an imprecise estimate for the Richardson constant. A modified version of the cube-root plots introduced by Ott and Mann [J. Fluid Mech. 422, 207 (2000)] confirms such convergence. It has been used to yield more precise estimates for Richardson’s constant g which decrease with Taylor-scale Reynolds numbers over the range of 140–650. Extrapolation to the large Reynolds number limit gives an asymptotic value for Richardson’s constant in the range g=0.55–0.57, depending on the functional form used to make the extrapolation.
Effect of substrate temperature and deposition rate on alloyzation for Co or Fe onto Cu(001) substrate
Authors: Hong Zheng-Han , Hwang Shun-Fa , Fang Te-Hua
Published: July 2008

The mixing situation of Fe or Co atoms implanting onto Cu(001) substrate is investigated with regard to substrate temperature and deposition rate by molecular dynamics. The tight-binding-second-momentum-approach many-body potential is used to model the atomic interaction. The results indicate that the morphology of the layer is under epitaxial growth as the substrate temperature is 700 or 1000 K, while it is not epitaxial at the substrate temperature of 300 or 450 K. The quality of epitaxial film is better when the substrate temperature is increased. The intermixing at the deposited layers becomes clear as the substrate temperature increases. It also indicates that there are more Co atoms penetrating into the substrate than the Fe atoms, regardless of the substrate temperature. Hence, one could say that the interface mixing of Co and Cu atoms is better than that of Fe and Cu atoms. When the deposition rate is raised from 5 to 10 atoms/ps, there is no increase in the interface mixing at both systems except for that at low substrate temperature. Furthermore, the first peak of the radial distribution function becomes lower and wider for both the Fe–Cu and Co–Cu systems as the substrate temperature is increasing from 300 to 1000 K.
Dynamic topology in spatiotemporal chaos
Authors: Ouellette Nicholas T. , Gollub J. P.
Published: July 2008

By measuring the tracks of tracer particles in a quasi-two-dimensional spatiotemporally chaotic laboratory flow, we determine the instantaneous curvature along each trajectory and use it to construct the instantaneous curvature field. We show that this field can be used to extract the time-dependent hyperbolic and elliptic points of the flow. These important topological features are created and annihilated in pairs only above a critical Reynolds number that is largest for highly symmetric flows. We also study the statistics of curvature for different driving patterns and show that the curvature probability distribution is insensitive to the details of the flow.
An ab initio multireference perturbation theory study on the manganese dimer
Authors: Angeli Celestino , Cavallini Alex , Cimiraglia Renzo
Published: July 2008

The potential energy curves of the ground state and of some excited states of the manganese dimer have been calculated over a wide range of internuclear distances using the second order n-electron valence state perturbation theory applied to a complete active space self-consistent field reference wave function. The ground state of Mn2, for which also the third order NEVPT has been used, is calculated to be a singlet belonging to the Σg+ symmetry, characterized by a large equilibrium internuclear distance Re of 3.7–3.8 Å, by a low dissociation energy De of 0.07–0.08 eV, and by a small harmonic frequency ωe of 43 cm−1. The experimental evidence that Mn2 is a van der Waals molecule is thus confirmed. Among the excited states, Π11u, which is usually indicated as the ground state by density functional theory studies, appears as a low-lying state with Re=2.50 Å, De=1.35 eV, and ωe=246 cm−1.
Ultrafast nonresonant response of TiO2 nanostructured films
Authors: Portuondo-Campa E. , Tortschanoff A. , van Mourik F. , Chergui M.
Published: July 2008

We present a detailed study of the nonresonant third-order ultrafast response of TiO2 nanostructured films, combining a classical heterodyned optical Kerr effect experiment, with two polarization selective Kerr techniques, based on transient lensing and phase modulation effects. The complementarity of these techniques is highlighted and demonstrated with calculations. Different aspects of the experimental results are addressed in detail and, finally, the possibilities of performing experiments on liquid dynamics in the pores of TiO2 films, are discussed in the light of the present results.
Multiobjective Decision Support for Land-Use Planning
Authors: Janssen Ron , van Herwijnen Marjan , Stewart Theodor J , Aerts Jeroen C J H
Published: July 2008

The overall objective of this paper is to show how a formal decision support method can be used effectively to support a land-use planning problem. Central to our approach is a heuristic algorithm based on a goal-programming/reference-point approach. The algorithm is tested on a small region in the Netherlands. To demonstrate the potential use of the algorithm, a planning problem is defined for this region. An interactive session with a land-use planner is then simulated, to show how feedback from the planner is used to generate a plan in a number of rounds. It is concluded that the approach has potential for the support of land-use problems especially in the first rounds of policy design as long as maps are used to interface between planner and algorithm. It is also shown that computational problems still hinder the achievement of realistic detail in the representation of the plan area.
Genotypic variation for drought stress response traits in soybean. I. Variation in soybean and wild Glycine spp. for epidermal conductance, osmotic potential, and relative water content
Authors: James A. T. , Lawn R. J. , Cooper M.
Published: July 2008

Studies were undertaken to assess genotypic variation in soybean and related wild species for traits with putative effects on leaf turgor maintenance in droughted plants. Traits of interest were (i) epidermal conductance (ge) which influences the rate of water loss from stressed leaves after stomatal closure; (ii) osmotic adjustment (OA) as indicated by tissue osmotic potential (π), which potentially affects the capacity to withdraw water at low soil water potential; and (iii) relative water content (RWC) at incipient leaf death (critical relative water content, RWCC), which is a measure of the dehydration tolerance of leaf tissue. The germplasm comprised a diverse set of 58 soybean genotypes, 2 genotypes of the annual wild species G. soja and 9 genotypes representing 6 perennial wild Glycine spp. indigenous/endemic to Australia. Seedling plants were grown in soil-filled beds in the glasshouse and exposed to terminal water deficit stress from the second trifoliolate leaflet stage (21 days after sowing). Measurements were made on well watered plants, moderately stressed plants, and at incipient plant death, in 2 separate studies. In both studies, there were significant genotypic differences in all 3 traits in the stressed plants. However, across the 3 sample times, ge decreased and the absolute magnitude of π increased, indicating that the expression of these traits changed as the plants acclimated to the stress. RWC was therefore used as a covariate to adjust the genotypic values of π and ge in order to facilitate comparison at a consistent plant water status of 70% RWC. There was statistically significant genotypic variation for the adjusted values, ge70 and π70, in both studies, and genotypic correlations between the 2 studies were significant (P < 0.05) and positive for all 3 traits: ge70 (r = 0.48), π70 (r = 0.50), and RWCC (r = 0.53). Among the soybean genotypes, there was at least a 2-fold range in ge70, a 0.7 MPa range in π70, and a 12 percentage point range in RWCC. Some of the perennial wild genotypes exhibited lower values of ge and RWCC and greater OA than soybean and G. soja, consistent with adaptation to drier environments. While the repeatability of measurement between experiments was variable among genotypes, the studies confirmed the existence of genotypic differences for ge, OA, and RWCC in cultivated soybean, with a wider range among the wild germplasm.
Effects of low temperature on grain filling, amylose content, and activity of starch biosynthesis enzymes in endosperm of basmati rice
Authors: Ahmed Nisar , Maekawa Masahiko , Tetlow Ian J.
Published: July 2008

The effects of low temperature on amylose contents and activities of key enzymes related to starch biosynthesis in basmati rice (Oryza sativa L.) endosperm were investigated. Low temperature treatment prolonged the grain-filling period from 32 days to 53 days, but had no significant effect on the final grain weight. Results showed that low temperature during grain filling had no significant effect on total starch content but increased the amylose content in the mature endosperm of hulled rice by 21%. The measurable activities of sucrose synthase (SuSy), ADP-glucose pyrophosphorylase (AGPase), starch phosphorylase (SPase), starch branching enzyme (SBE), and soluble starch synthase (SS) in endosperms developed at 12°C were lower than those at 22°C when compared at a similar ripening stage on an endosperm basis, but the activity of granule-bound starch synthase (GBSS) was significantly higher than the corresponding activity in endosperms developing at 22°C. These findings suggest that GBSS might play a crucial role in increasing amylose during low-temperature growth conditions.
Rhizosphere processes do not explain variation in P acquisition from sparingly soluble forms among Lupinus albus accessions
Authors: Pearse Stuart J. , Veneklaas Erik J. , Cawthray Greg , Bolland Mike D. A. , Lambers Hans
Published: July 2008

Seven Lupinus albus L. landraces were selected, based on their geographic origin and the soil type and pH at the site of collection of the seeds, and compared with the cv. Kiev mutant. We hypothesised that those landraces collected from red/yellow acidic sands (pH 5–5.7) would be better at acquiring P from FePO4 or AlPO4 than those selected from brown neutral (pH 7) or fine, calcareous, alkaline sands (pH 9), and that those selected from fine calcareous sands would be more effective at acquiring P from Ca5OH(PO4)3. Plants were grown in sand and supplied with 40 mg P/kg as the above sparingly soluble forms, or as soluble KH2PO4; control plants received no P. All genotypes were able to use these P sources. Variation in using poorly soluble P was not due to differences in rhizosphere carboxylate concentration, cluster-root development, or rhizosphere-extract pH. L. albus landraces with a better ability to use P from different sparingly soluble forms could be exploited to develop cultivars that are more P-acquisition efficient on soils that are low in [P] or highly P-sorbing; however, desirable genotypes cannot simply be selected based on soil type of origin.
Measuring molecular rupture forces between single actin filaments and actin-binding proteins
Authors: Ferrer Jorge M. , Lee Hyungsuk , Chen Jiong , Pelz Benjamin , Nakamura Fumihiko , Kamm Roger D. , Lang Matthew J.
Published: July 2008

Actin-binding proteins (ABPs) regulate the assembly of actin filaments (F-actin) into networks and bundles that provide the structural integrity of the cell. Two of these ABPs, filamin and α-actinin, have been extensively used to model the mechanical properties of actin networks grown
in vitro
; however, there is a lack in the understanding of how the molecular interactions between ABPs and F-actin regulate the dynamic properties of the cytoskeleton. Here, we present a native-like assay geometry to test the rupture force of a complex formed by an ABP linking two quasiparallel actin filaments. We readily demonstrate the adaptability of this assay by testing it with two different ABPs: filamin and α-actinin. For filamin/actin and α-actinin/actin, we measured similar rupture forces of 40–80 pN for loading rates between 4 and 50 pN/s. Both ABP unfolding and conformational transition events were observed, demonstrating that both are important and may be a significant mechanism for the temporal regulation of the mechanical properties of the actin cytoskeleton. With this modular, single-molecule assay, a wide range of ABP/actin interactions can be studied to better understand cytoskeletal and cell dynamics.
Corticotropin-releasing factor-1 receptor involvement in behavioral neuroadaptation to ethanol: A urocortin1-independent mechanism
Authors: Pastor Raúl , McKinnon Carrie S. , Scibelli Angela C. , Burkhart-Kasch Sue , Reed Cheryl , Ryabinin Andrey E. , Coste Sarah C. , Stenzel-Poore Mary P. , Phillips Tamara J.
Published: July 2008

A common expression of neuroadaptations induced by repeated exposure to addictive drugs is a persistent sensitized behavioral response to their stimulant properties. Neuroplasticity underlying drug-induced sensitization has been proposed to explain compulsive drug pursuit and consumption characteristic of addiction. The hypothalamic-pituitary-adrenal (HPA) axis-activating neuropeptide, corticotropin-releasing factor (CRF), may be the keystone in drug-induced neuroadaptation. Corticosterone-activated glucocorticoid receptors (GRs) mediate the development of sensitization to ethanol (EtOH), implicating the HPA axis in this process. EtOH-induced increases in corticosterone require CRF activation of CRF1receptors. We posited that CRF1signaling pathways are crucial for EtOH-induced sensitization. We demonstrate that mice lacking CRF1receptors do not show psychomotor sensitization to EtOH, a phenomenon that was also absent in CRF1 + 2receptor double-knockout mice. Deletion of CRF2receptors alone did not prevent sensitization. A blunted endocrine response to EtOH was found only in the genotypes showing no sensitization. The CRF1receptor antagonist CP-154,526 attenuated the acquisition and prevented the expression of EtOH-induced psychomotor sensitization. Because CRF1receptors are also activated by urocortin-1 (Ucn1), we tested Ucn1knockout mice for EtOH sensitization and found normal sensitization in this genotype. Finally, we show that the GR antagonist mifepristone does not block the expression of EtOH sensitization. CRF and CRF1receptors, therefore, are involved in the neurobiological adaptations that underlie the development and expression of psychomotor sensitization to EtOH. A CRF/CRF1-mediated mechanism involving the HPA axis is proposed for acquisition, whereas an extrahypothalamic CRF/CRF1participation is suggested for expression of sensitization to EtOH.
CD73 is required for efficient entry of lymphocytes into the central nervous system during experimental autoimmune encephalomyelitis
Authors: Mills Jeffrey H. , Thompson Linda F. , Mueller Cynthia , Waickman Adam T. , Jalkanen Sirpa , Niemela Jussi , Airas Laura , Bynoe Margaret S.
Published: July 2008

CD73 is a cell surface enzyme of the purine catabolic pathway that catalyzes the breakdown of AMP to adenosine. Because of the strong immunosuppressive and antiinflammatory properties of adenosine, we predicted thatcd73−/−mice would develop severe experimental autoimmune encephalomyelitis (EAE), an animal model for the central nervous system (CNS) inflammatory disease, multiple sclerosis. Surprisingly,cd73−/−mice were resistant to EAE. However, CD4 T cells fromcd73−/−mice secreted more proinflammatory cytokines than wild-type (WT) mice and were able to induce EAE when transferred into naïvecd73+/+T cell-deficient recipients. Therefore, the protection from EAE observed incd73−/−mice was not caused by a deficiency in T cell responsiveness. Immunohistochemistry showed thatcd73−/−mice had fewer infiltrating lymphocytes in their CNS compared with WT mice. Importantly, susceptibility to EAE could be induced incd73−/−mice after the transfer of WT CD73+CD4+T cells, suggesting that CD73 must be expressed either on T cells or in the CNS for disease induction. In the search for the source of CD73 in the CNS that might facilitate lymphocyte migration, immunohistochemistry revealed a lack of CD73 expression on brain endothelial cells and high expression in the choroid plexus epithelium which regulates lymphocyte immunosurveillance between the blood and cerebrospinal fluid. Because blockade of adenosine receptor signaling with the A2aadenosine receptor-specific antagonist SCH58261 protected WT mice from EAE induction, we conclude that CD73 expression and adenosine receptor signaling are required for the efficient entry of lymphocytes into the CNS during EAE development.
Cytoplasmic lipid droplets are translocated into the lumen of the
Chlamydia trachomatis
parasitophorous vacuole
Authors: Cocchiaro Jordan L. , Kumar Yadunanda , Fischer Elizabeth R. , Hackstadt Ted , Valdivia Raphael H.
Published: July 2008

The acquisition of host-derived lipids is essential for the pathogenesis of the obligate intracellular bacteria
Chlamydia trachomatis
. Current models of chlamydial lipid acquisition center on the fusion of Golgi-derived exocytic vesicles and endosomal multivesicular bodies with the bacteria-containing parasitophorous vacuole (“inclusion”). In this study, we describe a mechanism of lipid acquisition and organelle subversion by
C. trachomatis
. We show by live cell fluorescence microscopy and electron microscopy that lipid droplets (LDs), neutral lipid storage organelles, are translocated from the host cytoplasm into the inclusion lumen. LDs dock at the surface of the inclusion, penetrate the inclusion membrane and intimately associate with reticulate Bodies, the replicative form of
Chlamydia
. The inclusion membrane protein IncA, but not other inclusion membrane proteins, cofractionated with LDs and accumulated in the inclusion lumen. Therefore, we postulate that the translocation of LDs may occur at IncA-enriched subdomains of the inclusion membrane. Finally, the chlamydial protein Lda3 may participate in the cooption of these organelles by linking cytoplasmic LDs to inclusion membranes and promoting the removal of the LD protective coat protein, adipocyte differentiation related protein (ADRP). The wholesale transport of LDs into the lumen of a parasitophorous vacuole represents a unique mechanism of organelle sequestration and subversion by a bacterial pathogen.
Syntrophin mutation associated with long QT syndrome through activation of the nNOS–SCN5A macromolecular complex
Authors: Ueda Kazuo , Valdivia Carmen , Medeiros-Domingo Argelia , Tester David J. , Vatta Matteo , Farrugia Gianrico , Ackerman Michael J. , Makielski Jonathan C.
Published: July 2008

Mutations in 11 genes that encode ion channels or their associated proteins cause inherited long QT syndrome (LQTS) and account for ≈75–80% of cases (LQT1–11). Direct sequencing of
SNTA1
, the gene encoding α1-syntrophin, was performed in a cohort of LQTS patients that were negative for mutations in the 11 known LQTS-susceptibility genes. A missense mutation (A390V-SNTA1) was found in a patient with recurrent syncope and markedly prolonged QT interval (QTc, 530 ms). SNTA1 links neuronal nitric oxide synthase (nNOS) to the nNOS inhibitor plasma membrane Ca-ATPase subtype 4b (PMCA4b); SNTA1 also is known to associate with the cardiac sodium channel SCN5A. By using a GST-fusion protein of the C terminus of SCN5A, we showed that WT-SNTA1 interacted with SCN5A, nNOS, and PMCA4b. In contrast, A390V-SNTA1 selectively disrupted association of PMCA4b with this complex and increased direct nitrosylation of SCN5A. A390V-SNTA1 expressed with SCN5A, nNOS, and PMCA4b in heterologous cells increased peak and late sodium current compared with WT-SNTA1, and the increase was partially inhibited by NOS blockers. Expression of A390V-SNTA1 in cardiac myocytes also increased late sodium current. We conclude that the A390V mutation disrupted binding with PMCA4b, released inhibition of nNOS, caused
S
-nitrosylation of SCN5A, and was associated with increased late sodium current, which is the characteristic biophysical dysfunction for sodium-channel-mediated LQTS (LQT3). These results establish an SNTA1-based nNOS complex attached to SCN5A as a key regulator of sodium current and suggest that
SNTA1
be considered a rare LQTS-susceptibility gene.
Functional diversity in coral–dinoflagellate symbiosis
Authors: Stat Michael , Morris Emily , Gates Ruth D.
Published: July 2008

Symbioses are widespread in nature and occur along a continuum from parasitism to mutualism. Coral–dinoflagellate symbioses are defined as mutualistic because both partners receive benefit from the association via the exchange of nutrients. This successful interaction underpins the growth and formation of coral reefs. The symbiotic dinoflagellate genusSymbiodiniumis genetically diverse containing eight divergent lineages (clades A–H). Corals predominantly associate with clade CSymbiodiniumand to a lesser extent with clades A, B, D, F, and G. Variation in the function and interactive physiology of different coral–dinoflagellate assemblages is virtually unexplored but is an important consideration when developing the contextual framework of factors that contribute to coral reef resilience. In this study, we present evidence that clade ASymbiodiniumare functionally less beneficial to corals than the dominant clade CSymbiodiniumand may represent parasitic rather than mutualistic symbionts. Our hypothesis is supported by (i) a significant correlation between the presence ofSymbiodiniumclade A and health-compromised coral; (ii) a phylogeny and genetic diversity withinSymbiodiniumthat suggests a different evolutionary trajectory for clade A compared with the other dominantSymbiodiniumlineages; and (iii) a significantly lower amount of carbon fixed and released by clade A in the presence of a coral synthetic host factor as compared with the dominant coral symbiont lineage, clade C. Collectively, these data suggest that along the symbiotic continuum the interaction between clade ASymbiodiniumand corals may be closer to parasitism than mutualism.
The environmental impact of recombinant bovine somatotropin (rbST) use in dairy production
Authors: Capper Judith L. , Castañeda-Gutiérrez Euridice , Cady Roger A. , Bauman Dale E.
Published: July 2008

The environmental impact of using recombinant bovine somatotropin (rbST) in dairy production was examined on an individual cow, industry-scale adoption, and overall production system basis. An average 2006 U.S. milk yield of 28.9 kg per day was used, with a daily response to rbST supplementation of 4.5 kg per cow. Rations were formulated and both resource inputs (feedstuffs, fertilizers, and fuels) and waste outputs (nutrient excretion and greenhouse gas emissions) calculated. The wider environmental impact of production systems was assessed via acidification (AP), eutrophication (EP), and global warming (GWP) potentials. From a producer perspective, rbST supplementation improved individual cow production, with reductions in nutrient input and waste output per unit of milk produced. From an industry perspective, supplementing one million cows with rbST reduced feedstuff and water use, cropland area, N and P excretion, greenhouse gas emissions, and fossil fuel use compared with an equivalent milk production from unsupplemented cows. Meeting future U.S. milk requirements from cows supplemented with rbST conferred the lowest AP, EP, and GWP, with intermediate values for conventional management and the highest environmental impact resulting from organic production. Overall, rbST appears to represent a valuable management tool for use in dairy production to improve productive efficiency and to have less negative effects on the environment than conventional dairying.
Detrimental effects of
Bartonella henselae
are counteracted by
l
-arginine and nitric oxide in human endothelial progenitor cells
Authors: Salvatore Paola , Casamassimi Amelia , Sommese Linda , Fiorito Carmela , Ciccodicola Alfredo , Rossiello Raffaele , Avallone Bice , Grimaldi Vincenzo , Costa Valerio , Rienzo Monica , Colicchio Roberta , Williams-Ignarro Sharon , Pagliarulo Caterina , Prudente Maria Evelina , Abbondanza Ciro , Lamberti Florentia , Baroni Adone , Buommino Elisabetta , Farzati Bartolomeo , Tufano Maria Antonietta , Ignarro Louis Joseph , Napoli Claudio
Published: July 2008

The recruitment of circulating endothelial progenitor cells (EPCs) might have a beneficial effect on the clinical course of several diseases. Endothelial damage and detachment of endothelial cells are known to occur in infection, tissue ischemia, and sepsis. These detrimental effects in EPCs are unknown. Here we elucidated whether human EPCs internalize
Bartonella henselae
constituting a circulating niche of the pathogen.
B. henselae
invades EPCs as shown by gentamicin protection assays and transmission electron microscopy (TEM). Dil-Ac-LDL/lectin double immunostaining and fluorescence-activated cell sorting (FACS) analysis of EPCs revealed EPC bioactivity after infection with
B. henselae
. Nitric oxide (NO) and its precursor
l
-arginine (
l
-arg) exert a plethora of beneficial effects on vascular function and modulation of immune response. Therefore, we tested also the hypothesis that
l
-arg (1–30 mM) would affect the infection of
B. henselae
or tumor necrosis factor (TNF) in EPCs. Our data provide evidence that
l
-arg counteracts detrimental effects induced by TNF or
Bartonella
infections via NO (confirmed by DETA-NO and L-NMMA experiments) and by modulation of p38 kinase phosphorylation. Microarray analysis indicated several genes involved in immune response were differentially expressed in
Bartonella
-infected EPCs, whereas these genes returned in steady state when cells were exposed to sustained doses of
l
-arg. This mechanism may have broad therapeutic applications in tissue ischemia, angiogenesis, immune response, and sepsis.
Spatiotemporal activation of Rac1 for engulfment of apoptotic cells
Authors: Nakaya Michio , Kitano Masahiro , Matsuda Michiyuki , Nagata Shigekazu
Published: July 2008

The engulfment of apoptotic cells requires phagocytes to coordinately activate Rho family GTPases that regulate actin dynamics. Here, we used a FRET biosensor to visualize the spatiotemporal activation of Rac1 during engulfment of apoptotic cells. We report that apoptotic cells were usually engulfed by the phagocytes' lamellipodia, where Rac1 was activated. Often, apoptotic cells were engulfed successively at the same lamellipodial site, suggesting the presence of portals for apoptotic cells. At this location, the activated Rac1 was recruited to form phagocytic cups that were comprised of actin patches. When the phagocytic cup was closed, Rac1 was down-regulated, and the actin patches were abruptly broken down. The constitutively active Rac1 remained at phagocytic cup for a longer period than the wild-type Rac1, and the closure of the phagocytic cup was significantly delayed in cells expressing a constitutive active form of Rac1, resulting in inefficient engulfment. These results indicate that activated Rac1 is necessary to assemble F-actin, but closing the phagocytic cup requires Rac1 to be deactivated.
Does quality of sleep mediate the effect of depression on hopelessness?
Authors: Mystakidou Kyriaki , Parpa Efi , Tsilika Eleni , Galanos Antonis , Vlahos Lambros
Published: July 2008

The objectives of the study were to evaluate the relationship between sleep quality, depression, and hopelessness in advanced cancer patients and whether sleep quality mediated the effect of depression on hopelessness. The final sample consisted of 102 advanced cancer patients under palliative treatment. Patients completed the Greek Pittsburgh Sleep Quality Index, a sleep quality instrument, the Greek Beck Depression Inventory for measuring depression, and finally the Beck Hopelessness Scale. Patients' performance status was assessed by their overall physical functioning, as defined by the Eastern Cooperative Oncology Group. Depression was highly associated with hopelessness (r = .52, p<.001). Statistically significant associations were found between sleep quality with hopelessness (r = .37, p<.001), as well as with depression (r = .36, p<.001). Mediation analyses indicated that depression influenced hopelessness directly as well as indirectly by its effect on sleep quality. About 14.58% of the variation in hopelessness was explained by depression; 4% of the variance in hopelessness explained by depression was accounted for by the mediation pathway indicating that sleep quality mediated the relationship between depression and hopelessness. Similarly, in the reverse mediation analysis, depression mediated the relationship between sleep quality and hopelessness; 43% of the variation in hopelessness was explained by sleep quality. In conclusion, some of the effect of depression on hopelessness was mediated by sleep quality, but depression had a direct effect on hopelessness as well. Additionally, some of the effect of sleep quality on hopelessness was mediated by depression. The current findings are important because improving sleep quality by treating depression may contribute to decreased hopelessness scores and vice versa: Treating depression by improving sleep quality may also contribute to lower hopelessness scores.
Polymers and inflammation: disease mechanisms of the serpinopathies
Authors: Gooptu Bibek , Lomas David A.
Published: July 2008

Members of the serpin (serine proteinase inhibitor) superfamily play a central role in the control of inflammatory, coagulation, and fibrinolytic cascades. Point mutations that cause abnormal conformational transitions in these proteins can trigger disease. Recent work has defined three pathways by which these conformers cause tissue damage. Here, we describe how these three mechanisms can be integrated into a new model of the pathogenesis of emphysema caused by mutations in the serpin α1-antitrypsin.
Protective influenza-specific CD8 T cell responses require interactions with dendritic cells in the lungs
Authors: McGill Jodi , Van Rooijen Nico , Legge Kevin L.
Published: July 2008

Influenza infections induce a rapid, but transient, dendritic cell (DC) migration from the lungs to the lymph nodes (LNs) that is followed by substantial recruitment of DCs into the lungs without subsequent migration to the LNs. Given that peripheral DCs are primarily thought to be involved in the initiation of adaptive immunity after migration into lymphoid tissues, what role these newly lung-recruited DCs play in influenza virus immunity is unclear. In this study, we demonstrate that loss of non-LN migratory pulmonary DC subsets increases mortality, sustains higher viral titers, and impairs pulmonary CD8 T cell responses. Reconstitution of the lungs with pulmonary plasmacytoid DCs, CD8α+ DCs, or interstitial DCs restores CD8 T cell responses in a cell contact–, major histocompatability complex I–, and influenza peptide–dependent manner. Thus, after their initial activation in the LN, protective influenza-specific CD8 T cell responses require additional antigen-dependent interactions, specifically with DCs in the lungs.
The DHR1 Domain of DOCK180 Binds to SNX5 and Regulates Cation-independent Mannose 6-phosphate Receptor Transport
Authors: Hara Shigeo , Kiyokawa Etsuko , Iemura Shun-ichiro , Natsume Tohru , Wassmer Thomas , Cullen Peter J. , Hiai Hiroshi , Matsuda Michiyuki
Published: July 2008

DOCK180 is the archetype of the DOCK180-family guanine nucleotide exchange factor for small GTPases Rac1 and Cdc42. DOCK180-family proteins share two conserved domains, called DOCK homology region (DHR)-1 and -2. Although the function of DHR2 is to activate Rac1, DHR1 is required for binding to phosphoinositides. To better understand the function of DHR1, we searched for its binding partners by direct nanoflow liquid chromatography/tandem mass spectrometry, and we identified sorting nexins (SNX) 1, 2, 5, and 6, which make up a multimeric protein complex mediating endosome-to-trans-Golgi-network (TGN) retrograde transport of the cation-independent mannose 6-phosphate receptor (CI-MPR). Among these SNX proteins, SNX5 was coimmunoprecipitated with DOCK180 most efficiently. In agreement with this observation, DOCK180 colocalized with SNX5 at endosomes. The RNA interference-mediated knockdowns of SNX5 and DOCK180, but not Rac1, resulted in the redistribution of CI-MPR from TGN to endosomes. Furthermore, expression of the DOCK180 DHR1 domain was sufficient to restore the perturbed CI-MPR distribution in DOCK180 knockdown cells. These data suggest that DOCK180 regulates CI-MPR trafficking via SNX5 and that this function is independent of its guanine nucleotide exchange factor activity toward Rac1.
Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational FFT generating functions
Authors: Ritchie David W. , Kozakov Dima , Vajda Sandor
Published: July 2008

Motivation: Predicting how proteins interact at the molecular level is a computationally intensive task. Many protein docking algorithms begin by using fast Fourier transform (FFT) correlation techniques to find putative rigid body docking orientations. Most such approaches use 3D Cartesian grids and are therefore limited to computing three dimensional (3D) translational correlations. However, translational FFTs can speed up the calculation in only three of the six rigid body degrees of freedom, and they cannot easily incorporate prior knowledge about a complex to focus and hence further accelerate the calculation. Furthemore, several groups have developed multi-term interaction potentials and others use multi-copy approaches to simulate protein flexibility, which both add to the computational cost of FFT-based docking algorithms. Hence there is a need to develop more powerful and more versatile FFT docking techniques.

Results: This article presents a closed-form 6D spherical polar Fourier correlation expression from which arbitrary multi-dimensional multi-property multi-resolution FFT correlations may be generated. The approach is demonstrated by calculating 1D, 3D and 5D rotational correlations of 3D shape and electrostatic expansions up to polynomial order L=30 on a 2 GB personal computer. As expected, 3D correlations are found to be considerably faster than 1D correlations but, surprisingly, 5D correlations are often slower than 3D correlations. Nonetheless, we show that 5D correlations will be advantageous when calculating multi-term knowledge-based interaction potentials. When docking the 84 complexes of the Protein Docking Benchmark, blind 3D shape plus electrostatic correlations take around 30 minutes on a contemporary personal computer and find acceptable solutions within the top 20 in 16 cases. Applying a simple angular constraint to focus the calculation around the receptor binding site produces acceptable solutions within the top 20 in 28 cases. Further constraining the search to the ligand binding site gives up to 48 solutions within the top 20, with calculation times of just a few minutes per complex. Hence the approach described provides a practical and fast tool for rigid body protein-protein docking, especially when prior knowledge about one or both binding sites is available.

Availability:  http://www.csd.abdn.ac.uk/hex/

Contact:  d.w.ritchie@abdn.ac.uk