bluuebunny/crossref_metadata_2025 huggingface dataset:
CO adsorption and CO and O coadsorption on Rh(111) studied by reflection absorption infrared spectroscopy and density functional theory
Authors: Krenn G. , Bako I. , Schennach R.
Published: April 2006

The adsorption of carbon monoxide on Rh(111) and on oxygen modified Rh(111) was investigated using thermal desorption spectroscopy, reflection absorption infrared spectroscopy (RAIRS), and density functional theory. The results show that CO adsorbs on Rh(111) in on top sites at low coverages. With increasing coverage hollow sites and bridge sites get occupied according to the RAIRS results. A new vibrational feature at high wave numbers was found in the on top region of the CO stretching frequency. This feature can be explained by a local high density CO structure where two CO molecules are adsorbed in the (√3×√3)R30° structure. The coadsorption of oxygen and carbon monoxide leads to a shift of the CO stretching frequency to higher wave numbers with increasing O to CO ratio. CO adsorption on a (2×1) oxygen layer is possible and RAIRS shows that the CO adsorbs in on top and most likely in bridge sites in this case.
Quantifying electron transfer during hyperthermal scattering of C60+ from Au(111) and n-alkylthiol self-assembled monolayers
Authors: Jester Stefan-Sven , Weis Patrick , Hillenkamp Matthias , Ehrler Oli T. , Böttcher Artur , Kappes Manfred M.
Published: April 2006

A tandem time-of-flight mass spectrometer with an intermediate surface was used to quantify electron transfer during glancing incidence scattering of hyperthermal C60+ (Ecoll=250–500eV, θin=75°) from (i) self-assembled monolayers of n-alkylthiols on gold (of various chain lengths), (ii) partly fluorinated alkylthiols on gold, as well as (iii) clean gold surfaces. Self-assembled monolayers (SAMs) behave as insulating layers with their thicknesses determining the electron tunneling probability during collision. Correspondingly, a roughly exponential dependence of the neutralization probability on the chain length n was found. A pronounced dependence of the neutral yield on the primary beam kinetic energy indicates that dynamic SAM deformation and associated projectile penetration depth also play a role in determining electron transfer efficiency. Results are consistent with the molecular deformability of SAMs as determined with other experimental methods.
The ionic KAl13 molecule: A stepping stone to cluster-assembled materials
Authors: Zheng W.-J. , Thomas O. C. , Lippa T. P. , Xu S.-J. , Bowen K. H.
Published: April 2006

Theoretical calculations by Khanna and Jena predicted KAl13 to be an ionically bonded, cluster-assembled “diatomic molecule,” i.e., K+Al13−. We have conducted both mass spectral and anion photoelectron spectroscopic studies on KAln−, finding a “dip” at n=13 in both their mass spectrum and in their electron affinity versus n trend. While these largely qualitative results are consistent with KAl13 being a salt, they can also be explained in terms of the shell model and thus, by themselves, are not conclusive. Quantitative comparisons between calculated photodetachment transition energies and the photoelectron spectrum of KAl13−, however, allow a strong case to be made for ionic bonding in KAl13. As a prototype for ionic bonding involving intact Al13− subunits, KAl13 may be a stepping stone toward forming ionic, cluster-assembled materials.
Electric field-induced force between two identical uncharged spheres
Authors: Cox Barry J. , Thamwattana Ngamta , Hill James M.
Published: April 2006

The problem of electric field-induced force between spheres is fundamental to electrorheological fluids. Previously published experimental results indicate that the interaction force between two spheres under an external field is not adequately explained by the existing approximate and numerical methods. The specific models compared were dipole, dipole with local field corrections and a finite-element analysis. This letter employs an exact solution (via the equivalent multipole-moment method) to the electrostatic problem which accurately predicts the low-frequency experimental results at all measured interstices. The solution presented later is self-contained and addresses specifically the geometry of the previously mentioned experimental results. While more general solutions have been published previously, they are more complex than is required by this problem. The solution presented here is accurate for all sphere spacings, but in particular could apply to nano-spheres in close proximity.
Differences in electronic properties of fluorinated and trifluoromethylated fullerenes revealed by their propensity for dianion formation
Authors: Streletskiy Alexey V. , Hvelplund Preben , Nielsen Steen Brøndsted , Liu Bo , Tomita Shigeo , Goryunkov Alexey A. , Boltalina Olga V.
Published: April 2006

The cross sections for electron transfer from sodium to C60Fn− and C60(CF3)n− anions in 50-keV collisions as a function of the number of functional groups n are reported. There are clear differences between derivatives of fluorine and trifluoromethyl due to the different electron withdrawing properties of F and CF3. The role of inductive effects and π electron delocalization on the electron affinity is discussed, assuming a correlation between the cross section and the electron affinity of the anion.
Dynamic interactions between nematic point defects in the spinning extrusion duct of spiders
Authors: De Luca Gino , Rey Alejandro D.
Published: April 2006

Spider silk fibers have remarkable mechanical properties as a result of an ultraoptimized spinning process. Silk fibers are spun from a lyotropic nematic liquid crystalline anisotropic fluid phase which undergoes significant structural changes throughout the spinning pathway. In the silk extrusion duct, those structural changes are expected to be driven by elastic-mediated interactions between point defects. In this work, the interaction between two point defects of opposite topological charges located on the axis of a cylindrical cavity is studied using a tensor order parameter formalism. Distinct regimes leading to defect annihilation and structural transitions are described in detail. The driving force setting the defects into motion is also examined. The different results suggest that the tensorial approach is primordial in describing the complicated physics of the problem. The phenomenon described is important to the understanding of the process-induced structuring of silk fibers and to defect physics in a more general context.
Effects of confinement on the order-disorder transition of diblock copolymer melts
Authors: Miao Bing , Yan Dadong , Han Charles C. , Shi An-Chang
Published: April 2006

The effects of confinement on the order-disorder transition of diblock copolymer melts are studied theoretically. Confinements are realized by restricting diblock copolymers in finite spaces with different geometries (slabs, cylinders, and spheres). Within the random phase approximation, the correlation functions are calculated using the eigenvalues and eigenfunctions of the Laplacian operator ∇2 in the appropriate geometries. This leads to a size-dependent scattering function, and the minimum of the inverse scattering function determines the spinodal point of the homogeneous phase. For diblock copolymers confined in a slab or in a cylindrical nanopore, the spinodal point of the homogeneous phase (χN)s is found to be independent of the confinement. On the other hand, for diblock copolymers confined in a spherical nanopore, (χN)s depends on the confinement and it oscillates as a function of the radius of the sphere. Further understanding of the finite-size effects is provided by examining the fluctuation modes using the Landau-Brazovskii model.
Establishment of the ac electrokinetic elongation mechanism of DNA by three-dimensional fluorescent imaging
Authors: Wälti C. , Tosch P. , Davies A. G. , Germishuizen W. A. , Kaminski C. F.
Published: April 2006

We report three-dimensional imaging measurements using confocal microscopy of fluorescently labelled deoxyribonucleic acid (DNA) strands subjected to strong ac electric fields. The DNA molecules are covalently tethered by one end to gold microelectrodes and the observed elongation patterns are compared with the electric field lines obtained from numerical simulations and with previously determined fluid flow patterns. We demonstrate that the major contribution to the elongation stems from the ac electrokinetic torque, supplemented by a small bias force provided by the electric-field-induced fluid flow, and we provide evidence that the observed restricted elongation owing to the geometries of the electrodes results from a sign change in the bias force.
Electrostatic placement of single ferritin molecules
Authors: Kumagai Shinya , Yoshii Shigeo , Yamada Kiyohito , Matsukawa Nozomu , Fujiwara Isamu , Iwahori Kenji , Yamashita Ichiro
Published: April 2006

We electrostatically placed a single ferritin molecule on a nanometric 3-aminopropyltriethoxysilane (APTES) pattern that was on an oxidized Si substrate. The numerical analysis of the total interaction free energy for ferritin predicted that a quadrilateral array of 15nm diameter APTES nanodisks placed at intervals of 100nm would accommodate a single molecule of ferritin in each disk under a Debye length of 14nm. The experiments we conducted conformed to theoretical predictions and we successfully placed a single ferritin molecule on each ATPES disk without ferritin adsorbing on the SiO2 substrate surface.
Adsorption of platinum on the stoichiometric RuO2(110) surface
Authors: Liu Ping , Muckerman James T. , Adzic Radoslav R.
Published: April 2006

Density functional theory was used to calculate the geometries and electronic structures of Pt adsorption on the stoichiometric RuO2(110) surface at different coverages. The calculated results revealed that the Pt atoms strongly adsorb on RuO2, and two-dimensional growth up to 1.25ML deposition is energetically favorable. At low coverage, the binding between Pt and RuO2 is very strong, accompanied by a significant transfer of electron density from Pt to the support and a large downshift of the d-band compared to that of the unsupported Pt. At high coverage, a weak interaction of RuO2 with the Pt cluster is observed, and the electronic structure of Pt is only slightly modified with respect to that of the unsupported material. Our results suggest that among the systems investigated, the RuO2-supported Pt at a coverage of 1ML may become one of the best alternatives to pure Pt as a catalyst because it combines a high stability and a moderate activity similar to Pt.
Thermionic-tunneling multilayer nanostructures for power generation
Authors: Zeng Taofang
Published: April 2006

A method for power generation based on nanoengineered interface design with partially filled gap is presented. The proposed device allows a substantial temperature difference to exist between heat source and heat sink or two electrodes, thereby maximizing heat source utilization. A unified model and detailed analyses are provided for the solid device operating either as a power generator or as a cooler. Our analyses show that efficiency of about 50% of the corresponding Carnot efficiency can be achieved.
Fabrication of multiferroic epitaxial BiCrO3 thin films
Authors: Murakami M. , Fujino S. , Lim S.-H. , Long C. J. , Salamanca-Riba L. G. , Wuttig M. , Takeuchi I. , Nagarajan V. , Varatharajan A.
Published: April 2006

We report on the growth and multiferroic properties of epitaxial BiCrO3 thin films. Single phase epitaxial thin films were grown on LaAlO3 (001), SrTiO3 (001), and NdGaO3 (110) substrates by pulsed laser deposition. The films display weak ferromagnetism with the Curie temperature of 120K. Piezoelectric response and tunability of the dielectric constant were detected in the films at room temperature.
Photoluminescence of energetic particle-irradiated InxGa1−xN alloys
Authors: Li S. X. , Jones R. E. , Haller E. E. , Yu K. M. , Walukiewicz W. , Ager J. W. , Liliental-Weber Z. , Lu Hai , Schaff William J.
Published: April 2006

A study of the photoluminescence characteristics of InxGa1−xN alloys in which the Fermi level is controlled by energetic particle irradiation is reported. In In-rich InxGa1−xN the photoluminescence intensity initially increases with irradiation dose before falling rapidly at high doses. This unusual trend is attributed to the high location of the average energy of the dangling-bond-type native defects (the Fermi level stabilization energy). Our calculations of the photoluminescence intensity based on the effect of the electron concentration and the minority carrier lifetime show good agreement with the experimental data. Finally the blueshift of the photoluminescence signal with increasing electron concentration is explained by the breakdown of momentum conservation due to the irradiation damage.
Interference between independent fluctuating condensates
Authors: Polkovnikov Anatoli , Altman Ehud , Demler Eugene
Published: April 2006

We consider a problem of interference between two independent condensates that lack true long-range order. We show that their interference pattern contains information about correlation functions within each condensate. As an example, we analyze the interference between a pair of one-dimensional interacting Bose liquids. We find universal scaling of the average fringe contrast with system size and temperature that depends only on the Luttinger parameter. Moreover, the full distribution of the fringe contrast, which is also equivalent to the full counting statistics of the interfering atoms, changes with interaction strength and lends information on high-order correlation functions. We also demonstrate that the interference between two-dimensional condensates at finite temperature can be used as a direct probe of the Kosterlitz–Thouless transition. Finally, we discuss the generalization of our results to describe the interference of a periodic array of independent fluctuating condensates.
Phosphorylation and activation of PINOID by the phospholipid signaling kinase 3-phosphoinositide-dependent protein kinase 1 (PDK1) in
Arabidopsis
Authors: Zegzouti Hicham , Anthony Richard G. , Jahchan Nadine , Bögre László , Christensen Sioux K.
Published: April 2006

Activity of the serine-threonine protein kinase PINOID (PID) has been implicated in the asymmetrical localization of the membrane-associated PINFORMED (PIN) family of auxin transport facilitators. However, the means by which PID regulates PIN protein distribution is unknown. We have used recombinant PID protein to dissect the regulation of PID activity
in vitro
. We demonstrate that intramolecular PID autophosphorylation is required for the ability of PID to phosphorylate an exogenous substrate. PID-like mammalian AGC kinases act in a phosphorylation cascade initiated by the phospholipid-associated kinase, 3-phosphoinositide-dependent protein kinase 1 (PDK1), which binds to the C-terminal hydrophobic PDK1-interacting fragment (PIF) domain found in PDK1 substrates. We find that
Arabidopsis
PDK1 interacts with PID, and that transphosphorylation by PDK1 increases PID autophosphorylation. We show that a PID activation loop serine is required for PDK1-dependent PID phosphorylation. This activation is rapid and requires the PIF domain. Cell extracts from flowers and seedling shoots dramatically increase PID phosphorylation in a tissue-specific manner. A PID protein variant in which the PIF domain was mutated failed to be activated by the seedling shoot extracts. PID immunoprecipitated from
Arabidopsis
cells in which PDK1 expression was inhibited by RNAi showed a dramatic reduction in transphosphorylation of myelin basic protein substrate. These results indicate that AtPDK1 is a potent enhancer of PID activity and provide evidence that phospholipid signaling may play a role in the signaling processes controlling polar auxin transport.
Finite simple groups as expanders
Authors: Kassabov Martin , Lubotzky Alexander , Nikolov Nikolay
Published: April 2006

We prove that there exist
k
∈ ℕ and 0 < ε ∈ ℝ such that every non-abelian finite simple group
G
, which is not a Suzuki group, has a set of
k
generators for which the Cayley graph Cay(
G
;
S
) is an ε-expander.
Reduced Incidence of Slowly Progressive Heymann Nephritis in Rats Immunized With a Modified Vaccination Technique
Authors: Barabas Arpad Z. , Cole Chad D. , Barabas Arpad D. , Barabas Aron N. , Lafreniere Rene
Published: April 2006

A slowly progressive Heymann nephritis (SPHN) was induced in three groups of rats by weekly injections of a chemically modified renal tubular antigen in an aqueous medium. A control group of rats received the chemically unmodified version of the antigen in an aqueous solution. One group of SPHN rats were pre‐ and post‐treated with weekly injections of IC made up of rKF3 and rarKF3 IgM antibody at antigen excess (MIC) (immune complexes [ICs] containing sonicated ultracentrifuged [u/c] rat kidney fraction 3 [rKF3] antigen and IgM antibodies specific against the antigen, at slight antigen excess). One group of SPHN rats were post‐treated with MIC 3 weeks after the induction of the disease and one group of SPHN animals received no treatment. The control group of rats received pre‐ and post‐treatment with sonicated u/c rKF3.

The incidence of immune‐complex glomerulonephritis (ICGN) in the untreated SPHN rats was 87%, in the pre‐ and post‐treated animals 13%, and in the post‐treated‐only rats 20%. Rats receiving sonicated ultracentrifuged rKF3 antigen did not develop ICGN.

The present experiment demonstrates that the development of SPHN can be not only prevented but also effectively terminated by our newly developed modified vaccination
technique.
Rheumatoid Arthritis is an Autoimmune Disease Triggered by Proteus Urinary Tract Infection
Authors: Ebringer Alan , Rashid Taha
Published: April 2006

Rheumatoid arthritis (RA) is a chronic and disabling polyarthritic disease, which affects mainly women in middle and old age.

Extensive evidence based on the results of various microbial, immunological and molecular studies from different parts of the world, shows that a strong link exists between Proteus mirabilis microbes and RA. We propose that sub‐clinical Proteus urinary tract infections are the main triggering factors and that the presence of molecular mimicry and cross‐reactivity between these bacteria and RA‐targeted tissue antigens assists in the perpetuation of the disease process through production of cytopathic auto‐antibodies.

Patients with RA especially during the early stages of the disease could benefit from Proteus anti‐bacterial measures involving the use of antibiotics, vegetarian diets and high intake of water and fruit juices such as cranberry juice in addition to the currently employed treatments.
[Retracted] Cure of Chronic Viral Infection and Virus‐Induced Type 1 Diabetes by Neutralizing Antibodies
Authors: Ejrnaes Mette , von Herrath Matthias G. , Christen Urs
Published: April 2006

The use of neutralizing antibodies is one of the most successful methods to interfere with receptor–ligand interactions in vivo. In particular blockade of soluble inflammatory mediators or their corresponding cellular receptors was proven an effective way to regulate inflammation and/or prevent its negative consequences. However, one problem that comes along with an effective neutralization of inflammatory mediators is the general systemic immunomodulatory effect. It is, therefore, important to design a treatment regimen in a way to strike at the right place and at the right time in order to achieve maximal effects with minimal duration of immunosuppression or hyperactivation. In this review, we reflect on two examples of how short time administration of such neutralizing antibodies can block two distinct inflammatory consequences of viral infection. First, we review recent findings that blockade of IL‐10/IL‐10R interaction can resolve chronic viral infection and second, we reflect on how neutralization of the chemokine CXCL10 can abrogate virus‐induced type 1 diabetes.
Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins
Authors: Pasek Sophie , Risler Jean-Loup , Brézellec Pierre
Published: April 2006

Most proteins comprise one or several domains. New domain architectures can be created by combining previously existing domains. The elementary events that create new domain architectures may be categorized into three classes, namely domain(s) insertion or deletion (indel), exchange and repetition. Using ‘DomainTeam’, a tool dedicated to the search for microsyntenies of domains, we quantified the relative contribution of these events. This tool allowed us to collect homologous bacterial genes encoding proteins that have obviously evolved by modular assembly of domains. We show that indels are the most frequent elementary events and that they occur in most cases at either the N- or C-terminus of the proteins. As revealed by the genomic neighbourhood/context of the corresponding genes, we show that a substantial number of these terminal indels are the consequence of gene fusions/fissions. We provide evidence showing that the contribution of gene fusion/fission to the evolution of multi-domain bacterial proteins is lower-bounded by 27% and upper-bounded by 64%. We conclude that gene fusion/fission is a major contributor to the evolution of multi-domain bacterial proteins.

Contact:  pasek@genopole.cnrs.fr

Supplementary information: Supplementary data are available at
Non-omnivorous generality promotes population stability
Authors: Romanuk Tamara N , Beisner Beatrix E , Martinez Neo D , Kolasa Jurek
Published: April 2006

Using a combination of stable isotope analysis of δ
13
C and δ
15
N and long-term census data on population abundances for meiofauna in tropical aquatic rock pools, we provide evidence that species which exhibit greater variation in δ
13
C, an indication of a greater range of distinct carbon sources in their diet, have more stable populations than species with lower variation in δ
13
C. This link between increased isotope variability and reduced population variability, however, did not hold for δ
15
N. This suggests that increases in population stability were due to non-omnivorous feeding on multiple carbon sources within a trophic level rather than omnivorous feeding on multiple carbon sources across trophic levels. Our findings corroborate MacArthur's original hypothesis that populations that can access a greater range of resources are more stable than those which consume a more restricted range of resources.
Discrete vector on-site vortices
Authors: Kevrekidis P.G , Pelinovsky D.E
Published: April 2006

We study discrete vortices in coupled discrete nonlinear Schrödinger equations. We focus on the vortex cross configuration that has been experimentally observed in photorefractive crystals. Stability of the single-component vortex cross in the anti-continuum limit of small coupling between lattice nodes is proved. In the vector case, we consider two coupled configurations of vortex crosses, namely the charge-one vortex in one component coupled in the other component to either the charge-one vortex (forming a double-charge vortex) or the charge-negative-one vortex (forming a, so-called, hidden-charge vortex). We show that both vortex configurations are stable in the anti-continuum limit, if the parameter for the inter-component coupling is small and both of them are unstable when the coupling parameter is large. In the marginal case of the discrete two-dimensional Manakov system, the double-charge vortex is stable while the hidden-charge vortex is linearly unstable. Analytical predictions are corroborated with numerical observations that show good agreement near the anti-continuum limit, but gradually deviate for larger couplings between the lattice nodes.
Dynamic non-null magnetic reconnection in three dimensions. I. Particular solutions
Authors: Wilmot-Smith Antonia , Hornig Gunnar , Priest Eric
Published: April 2006

A stationary model of three-dimensional magnetic reconnection in the absence of a null point is presented, with a non-ideal region that is localized in space. Analytical solutions to the resistive magnetohydrodynamic equations are obtained, with the momentum equation included so that the model is fully dynamic, and thus extends the previous kinematic solutions. A splitting of variables allows solutions to be written in terms of a particular non-ideal solution, on which ideal solutions may be superposed. For the non-ideal solution alone, it is shown that only the field lines linking the diffusion region are affected by the reconnection process, and counter-rotating flows above and below the diffusion region are present. It is only the dimensions of the diffusion region along the reconnection line that are important for the reconnection rate. Many features of the previous stationary kinematic model are also observed here.
The evolution of hexapod engrailed-family genes: evidence for conservation and concerted evolution
Authors: Peel Andrew D , Telford Maximilian J , Akam Michael
Published: April 2006

Phylogenetic analyses imply that multiple engrailed-family gene duplications occurred during hexapod evolution, a view supported by previous reports of only a single engrailed-family gene in members of the grasshopper genusSchistocercaand in the beetleTribolium castaneum. Here, we report the cloning of a second engrailed-family gene fromSchistocerca gregariaand present evidence for two engrailed-family genes from four additional hexapod species. We also report the existence of a second engrailed-family gene in theTriboliumgenome. We suggest that theengrailedandinvectedgenes ofDrosophila melanogasterhave existed as a conserved gene cassette throughout holometabolous insect evolution. In total 11 phylogenetically diverse hexapod orders are now known to contain species that possess two engrailed-family paralogues, with in each case only one paralogue encoding the RS-motif, a characteristic feature of holometabolous insect invected proteins. We propose that the homeoboxes of hexapod engrailed-family paralogues are evolving in a concerted fashion, resulting in gene trees that overestimate the frequency of gene duplication. We present new phylogenetic analyses using non-homeodomain amino acid sequence that support this view. TheS. gregariaengrailed-family paralogues provide strong evidence that concerted evolution might in part be explained by recurrent gene conversion. Finally, we hypothesize that the RS-motif is part of a serine-rich domain targeted for phosphorylation.
Sex-specific development of cell-mediated immunity under experimentally altered rearing conditions in blue tit nestlings
Authors: Dubiec Anna , Cichoń Mariusz , Deptuch Kinga
Published: April 2006

In birds, poor rearing conditions usually have negative effects on T-cell-mediated immune response. However, earlier studies demonstrate that fitness-related traits such as body mass may show sex-specific patterns when subject to alteration of rearing conditions. Therefore, to investigate whether deterioration of rearing conditions influences the development of immune function differently in male and female nestlings, we performed brood size manipulation experiments on blue tit (
Parus caeruleus
) nestlings. To alter rearing conditions, some broods were increased by three nestlings soon after hatching, while other broods were left non-manipulated. Immune response was assessed as a hypersensitivity reaction to phytohaemagglutinin in 11-day-old nestlings. Additionally, we studied the consequences of brood size manipulation for fledgling body mass and tarsus length. The enlargement of brood size had different effects on the cellular immune responses of male and female nestlings, with males being more negatively affected than their female nest-mates. Sex-specific effects of poor rearing conditions were also recorded for tarsus length, such that tarsus growth was more retarded in female than in male nestlings. We discuss the effects of deterioration of rearing conditions on sex-specific development of cell-mediated immunity with respect to sexual dimorphism of size and developmental strategies in male and female nestlings.
Role of avidity and breadth of the CD4 T cell response in progression to AIDS
Authors: Korthals Altes Hester , de Boer Rob , Boerlijst Maarten
Published: April 2006

The great variability in the time between infection with HIV and the onset of AIDS has been the object of intense study. In the current work, we examine a mathematical model that focuses on the role of immune response variability between patients. We study the effect of variation in both the avidity and the breadth of the immune response on within-patient disease dynamics, viral setpoint and time to AIDS.

We conclude that immune response variability can explain the observed variability in disease progression to a large extent. It turns out that the avidity, more than the breadth of the immune response, determines disease progression, and that the average avidity of the five best clones is a much better correlate for disease progression than the total number of clones responding. For the design of vaccines, this would suggest that, if given the choice between stimulating a broader, but average avidity response or a narrower high-avidity response, the latter option would yield better control of virus load and consequently slow down disease progression.
Relationship between retroviral vector membrane and vector stability
Authors: Carmo M. , Faria T. Q. , Falk H. , Coroadinha A. S. , Teixeira M. , Merten O.-W. , Gény-Fiamma C. , Alves P. M. , Danos O. , Panet A. , Carrondo M. J. T. , Cruz P. E.
Published: April 2006

The present work studies the physico-chemical properties of retroviral vector membrane, in order to provide some explanation for the inactivation kinetics of these vectors and to devise new ways of improving transduction efficiency. For this purpose, vectors with an amphotropic envelope produced by TE Fly A7 cells at two culture temperatures (37 and 32 °C) were characterized by different techniques. Electron paramagnetic resonance (EPR) results showed that vectors produced at 32 °C are more rigid than those produced at 37 °C. Further characterization of vector membrane composition allowed us to conclude that the vector inactivation rate increases with elevated cholesterol to phospholipid ratio. Differential scanning calorimetry (DSC) showed that production temperature also affects the conformation of the membrane proteins. Transduction studies using HCT116 cells and tri-dimensional organ cultures of mouse skin showed that vectors produced at 37 °C have higher stability and thus higher transduction efficiency in gene therapy relevant cells as compared with vectors produced at 32 °C. Overall, vectors produced at 37 °C show an increased stability at temperatures below 4 °C. Since vector membrane physico-chemical properties are affected in response to changes in culture temperature, such changes, along with alterations in medium composition, can be used prospectively to improve the stability and the transduction efficiency of retroviral vectors for therapeutic purposes.
Ebola virus glycoprotein GP is not cytotoxic when expressed constitutively at a moderate level
Authors: Alazard-Dany Nathalie , Volchkova Valentina , Reynard Olivier , Carbonnelle Caroline , Dolnik Olga , Ottmann Michèle , Khromykh Alexander , Volchkov Viktor E.
Published: April 2006

Transient expression of Ebola virus (EBOV) glycoprotein GP causes downregulation of surface proteins, cell rounding and detachment, a phenomenon believed to play a central role in the pathogenicity of the virus. In this study, evidence that moderate expression of GP does not result in such morphological changes was provided. It was shown that GP continuously produced in 293T cells from the Kunjin virus replicon was correctly processed and transported to the plasma membrane without affecting the surface expression of β1 and α5 integrins and major histocompatibility complex I molecules. The level of GP expression in Kunjin replicon GP-expressing cells was similar to that observed in cells infected with EBOV early in infection and lower than that produced in cells transfected with plasmid DNA, phCMV-GP, expressing GP from a strong promoter. Importantly, transient transfection of Kunjin replicon GP-expressing cells with GP-coding plasmid DNA resulted in overexpression of GP, which lead to the downregulation of surface molecules and massive rounding and detachment of transfected cells. Here, it was also demonstrated that cell rounding and downregulation of the surface markers are the late events in EBOV infection, whereas synthesis and massive release of virus particles occur at early steps and do not cause significant cytotoxic effects. These findings indicate that the synthesis of EBOV GP in virus-infected cells is controlled well by several mechanisms that do not allow GP overexpression and hence the early appearance of its cytotoxic properties.
Acid inactivation of prions: efficient at elevated temperature or high acid concentration
Authors: Appel Thomas R. , Lucassen Ralf , Groschup Martin H. , Joncic Marion , Beekes Michael , Riesner Detlev
Published: April 2006

Scrapie prion rods isolated from hamster and non-infectious aggregates of the corresponding recombinant protein rPrP(90–231) were incubated with hydrochloric acid. The amount of PrP and of infectivity that survived incubation in HCl at varying times, acid concentrations and temperatures was quantified by Western blot densitometry and bioassays, respectively. Prion rods and rPrP aggregates showed similar HCl hydrolysis kinetics of PrP, indicating structural homology. For 1 M HCl and 25 °C, the rate of PrP hydrolysis follows first-order kinetics at 0·014 h−1; the rate of infectivity inactivation is 0·54 h−1. Hydrolysis for 1 h at 25 °C was only slightly proportional to HCl concentration up to 5 M, but complete loss of infectivity and PrP reduction to <2 % was observed at 8 M HCl. The temperature dependence of unhydrolysed PrP, as well as infectivity at 1 M HCl for 1 h, showed a slight decrease up to 45 °C, but a sigmoidal decrease by several orders of magnitude at higher temperatures. The slow hydrolysis of PrP and inactivation of infectivity by acid treatment at room temperature are attributed to solvent inaccessibility of prion rods and rPrP aggregates, respectively. The more effective hydrolysis and inactivation at temperatures above 45 °C are interpreted as thermally induced disaggregation with an activation energy of 50–60 kJ mol−1. Most importantly, infectivity was always inactivated faster or to a higher extent than PrP was hydrolysed at several incubation times, HCl concentrations and temperatures.
Identification of an allelic variant of the goat PrP gene associated with resistance to scrapie
Authors: Vaccari Gabriele , Bari Michele A. Di , Morelli Luisella , Nonno Romolo , Chiappini Barbara , Antonucci Giovanni , Marcon Stefano , Esposito Elena , Fazzi Paola , Palazzini Nadia , Troiano Pasquale , Petrella Antonio , Guardo Giovanni Di , Agrimi Umberto
Published: April 2006

The association between PrP gene variations and scrapie susceptibility was studied in a single herd of Ionica breed goats. The entire herd comprised 100 animals, 11 of which were clinically affected and showed pathological prion protein (PrPSc) deposition in both their central nervous system (CNS) and lymphoreticular system (LRS). Among asymptomatic goats, nine harboured PrPSc in both CNS and LRS, 19 showed PrPSc only at the LRS level and 61 animals had no PrPSc deposition. Genetic analysis of the PrP gene coding sequence revealed the presence of several polymorphisms, namely G37V, T110P, H143R, R154H, Q222K and P240S. Silent polymorphisms were also found at codons 42, 138, 219 and 232. The effect of PrP polymorphism on scrapie susceptibility was assessed by comparing the genotype distribution at each locus among animals with different pathogenetic and clinical disease stages. Significant differences in the distribution of genotypes were observed for codons 154 and 222, with polymorphism at codon 154 modulating susceptibility to scrapie and lysine at codon 222 being associated with scrapie resistance. The allelic variant encoding lysine at position 222 could be a valuable candidate to select in the framework of appropriate breeding programmes for scrapie resistance in goats.
Mixed infection with multiple strains of murine cytomegalovirus occurs following simultaneous or sequential infection of immunocompetent mice
Authors: Gorman Shelley , Harvey Nicole L. , Moro Dorian , Lloyd Megan L. , Voigt Valentina , Smith Lee M. , Lawson Malcolm A. , Shellam Geoffrey R.
Published: April 2006

As with human cytomegalovirus (HCMV) infection of humans, murine CMV (MCMV) infection is widespread in its natural host, the house mouse Mus domesticus, and may consist of mixed infection with different CMV isolates. The incidence and mechanisms by which mixed infection occurs in free-living mice are unknown. This study used two approaches to determine whether mixed infection with MCMV could be established in laboratory mice. The first utilized two naturally occurring MCMV strains, N1 and G4, into which the lacZ gene was inserted by homologous recombination. The lacZ gene was used to track recombinant and parental viruses in simultaneously coinfected mice. In the second approach, a real-time quantitative PCR (qPCR) assay was used to detect viral immediate-early 1 (ie1) gene sequences in mice successively coinfected with G4 and then with the K181 MCMV strain. In both systems, mixed infection was detected in the salivary glands and lungs of experimentally infected mice. MCMV-specific antibody in sera and G4 IE1-specific cytotoxic lymphocyte responses in the spleens of twice-infected mice did not prevent reinfection. Finally, the prevalence of mixed infection in free-living mice trapped in four Australian locations was investigated using real-time qPCR to detect ie1 DNA sequences of N1, G4 and K181. Mixed infection with MCMVs containing the G4 and K181 ie1 sequences was detected in the salivary glands of 34·2 % of trapped mice. The observations that mixed infections are common in free-living M. domesticus and are acquired by immunocompetent mice through simultaneous or successive infections are important for vaccine development.
Phylogenetic analysis of the precore/core gene of hepatitis B virus genotypes E and A in West Africa: new subtypes, mixed infections and recombinations
Authors: Olinger Christophe M. , Venard Véronique , Njayou Mounjohou , Oyefolu Akeeb O. Bola , Maïga Ibrahim , Kemp Alain J. , Omilabu Sunday A. , le Faou Alain , Muller Claude P.
Published: April 2006

One hundred and twenty-two new hepatitis B virus (HBV) preC/C sequences and three complete genomes from three major countries in West Africa were analysed. The majority of sequences were of genotype E and the only other genotype found was genotype A. Although for genotype E sequences, the genetic diversity of the preC/C gene was about two to three times higher than that of the preS/S gene, it was still considerably lower than that for genotype A sequences. The HBV/E preC/C gene was related most closely to subgenotype D1 and D2 sequences. Evidence of recombination was found in two strains that were of genotype A in the preS/S gene and of genotype E in the preC/C gene. The genotype A strains from Cameroon, Mali and Nigeria could be divided phylogenetically into three subtypes, A3 and two new subtypes, tentatively designated A4 and A5. Each subtype presented a genetic diversity of 2·19–3·85 % and intersubtype distances of 4·47–5·97 %. Interestingly, one sample from Nigeria showed evidence of a triple recombination of genotypes E/D and A, separated by a genotype G-specific insert of 36 bp. Of 110 patients, 19 (17·3 %) showed a coinfection of genotypes A and E, mostly in human immunodeficiency virus-positive children from Cameroon. Thus, in Cameroon, where both genotypes coexist, 37 % of all individuals tested had mixed infections. The low genetic variability in the preC/C gene of genotype E supports our previous speculation about a relatively short evolutionary history of this genotype, in contrast to the subtype-rich African genotype A strains.
Raf/MEK/ERK signalling triggers reactivation of Kaposi's sarcoma-associated herpesvirus latency
Authors: Ford Patrick W. , Bryan Benjaman A. , Dyson Ossie F. , Weidner Douglas A. , Chintalgattu Vishnu , Akula Shaw M.
Published: April 2006

Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma, primary effusion lymphoma and multicentric Castleman's disease. KSHV infection of cells produces both latent and lytic cycles of infection. In vivo, the virus is found predominantly in the latent state. In vitro, a lytic infection can be induced in KSHV-infected cells by treating with phorbol ester (TPA). However, the exact signalling events that lead to the reactivation of KSHV lytic infection are still elusive. Here, a role is demonstrated for B-Raf/MEK/ERK signalling in TPA-induced reactivation of KSHV latent infection. Inhibiting MEK/ERK signalling by using MEK-specific inhibitors decreased expression of the TPA-induced KSHV lytic-cycle gene ORF8. Transfection of BCBL-1 cells with B-Raf small interfering RNA inhibited TPA-induced KSHV lytic infection significantly. Additionally, overexpression of MEK1 induced a lytic cycle of KSHV infection in BCBL-1 cells. The significance of these findings in understanding the biology of KSHV-associated pathogenesis is discussed.
Tracing the origin and co-phylogeny of the caliciviruses
Authors: Etherington Graham J. , Ring Susan M. , Charleston Michael A. , Dicks Jo , Rayward-Smith Vic J. , Roberts Ian N.
Published: April 2006

Caliciviruses infect a wide range of mammalian hosts and include the genusNorovirus, the major cause of food-borne viral gastroenteritis in humans. Using publicly available sequence data and phylogenetic analysis tools, the origins and virus–host co-phylogeny of these viruses were investigated. Here, evidence is presented in support of host switching by caliciviruses, but showing that zoonotic transfer does not appear to have occurred in the history of these viruses. The age or demography of the caliciviruses cannot yet be estimated with any firm degree of support, but further studies of this family, as new dated sequences become available, could provide key information of importance to human health and in understanding the emergence of food-borne disease.
In primary human monocyte-derived macrophages exposed to Human immunodeficiency virus type 1, does the increased intracellular growth of Leishmania infantum rely on its enhanced uptake?
Authors: Zhao Chenqi , Thibault Sandra , Messier Nadine , Ouellette Marc , Papadopoulou Barbara , Tremblay Michel J.
Published: April 2006

Concurrent uncontrolled development of human immunodeficiency virus type 1 (HIV-1) andLeishmaniaspp. is regarded as an emerging pathogenic combination in countries where human beings are exposed to these two micro-organisms. The present study was aimed at exploring whether HIV-1 development within a culture of human monocyte-derived macrophages (MDMs) affected the further development of luciferase-encodingLeishmania infantumusing the luciferase activity as a readout assay. It was demonstrated that, in cultures of HIV-1-loaded MDMs exposed to axenic amastigotes, the luciferase activity was higher than in HIV-1-free MDMs. As a preliminary approach to deciphering the possible mechanism through which HIV-1 can affectLeishmania infantum, attention was focused on the very early processes that could underlie this increased luciferase activity. Using GFP-labelled parasites, it was possible to establish that, in HIV-1-infected MDMs, the percentage of GFP-expressing MDMs was higher (10–20 %) than in cell cultures not exposed to HIV-1 (5 %). Two-colour immunofluorescence staining suggested that HIV-1 indirectly affects the uptake of parasites inside MDMs. Thus, the observed phenomenon seems to be linked with a higher uptake of parasites within MDMs. Taken together, the data reported here may contribute to our understanding of disseminatedLeishmaniainfection in HIV-1-infected individuals.
Emergence of a resistance-breaking isolate of Rice yellow mottle virus during serial inoculations is due to a single substitution in the genome-linked viral protein VPg
Authors: Hébrard Eugénie , Pinel-Galzi Agnès , Bersoult Anne , Siré Christelle , Fargette Denis
Published: April 2006

The recessive gene rymv-1, responsible for the high resistance of Oryza sativa ‘Gigante’ to Rice yellow mottle virus (genus Sobemovirus), was overcome by the variant CI4*, which emerged after serial inoculations of the non-resistance-breaking (nRB) isolate CI4. By comparison of the full-length sequences of CI4 and CI4*, a non-synonymous mutation was identified at position 1729, localized in the putative VPg domain, and an assay was developed based on this single-nucleotide polymorphism. The mutation G1729T was detected as early as the first passage in resistant plants and was found in all subsequent passages. Neither reversion nor any additional mutation was observed. The substitution G1729T, introduced by mutagenesis into the VPg of an nRB infectious clone, was sufficient to induce symptoms in uninoculated leaves of O. sativa ‘Gigante’. This is the first evidence that VPg is a virulence factor in plants with recessive resistance against viruses outside the family Potyviridae.
Arenavirus Z protein as an antiviral target: virus inactivation and protein oligomerization by zinc finger-reactive compounds
Authors: García Cybele C. , Djavani Mahmoud , Topisirovic Ivan , Borden Katherine L. B. , Salvato María S. , Damonte Elsa B.
Published: April 2006

Several disulfide-based and azoic compounds have shown antiviral and virucidal properties against arenaviruses in virus yield-inhibition and inactivation assays, respectively. The most effective virucidal agent, the aromatic disulfide NSC20625, was able to inactivate two strains of the prototype arenavirus species Lymphocytic choriomeningitis virus (LCMV). Inactivated viral particles retained the biological functions of the virion envelope glycoproteins in virus binding and uptake, but were unable to perform viral RNA replication. Furthermore, in inactivated virions, the electrophoretic profile of the Z protein was altered when analysed under non-reducing conditions, whereas the patterns of the proteins NP and GP1 remained unaffected. Treatment of a recombinant LCMV Z protein with the virucidal agents induced unfolding and oligomerization of Z to high-molecular-mass aggregates, probably due to metal-ion ejection and the formation of intermolecular disulfide bonds through the cysteine residues of the Z RING finger. NSC20625 also exhibited antiviral properties in LCMV-infected cells without affecting other cellular RING-motif proteins, such as the promyelocytic leukaemia protein PML. Altogether, the investigations described here illustrate the potential of the Z protein as a promising target for therapy and the prospects of the Z-reactive compounds to prevent arenavirus dissemination.