bluuebunny/crossref_metadata_2025 huggingface dataset:
Dense flows of bidisperse assemblies of disks down an inclined plane
Authors: Rognon Pierre G. , Roux Jean-Noël , Naaïm Mohamed , Chevoir François
Published: May 2007

Using discrete numerical simulations, we have studied the flow down a rough inclined plane of a bidisperse assembly of frictional cohesionless disks. Our study focuses on steady uniform flows, once a stable segregation has developed inside the flowing layer. The material is segregated in three layers: a basal layer (small grains), a superficial layer (large grains), and a mixed layer in the center, so that the average diameter of the grains increases from the bottom to the top. From the measurement of the profiles of velocity, solid fraction, and stress components, we show that the rheological law of such a polydisperse material may be described by a local friction law, which extends the result obtained for quasimonodisperse granular flows. This law states that the effective friction coefficient depends approximately linearly on a generalized inertial number, taking into account the average diameter of the grains.
Heterogeneous multicomponent nucleation theorems for the analysis of nanoclusters
Authors: Vehkamäki Hanna , Määttänen Anni , Lauri Antti , Kulmala Markku , Winkler Paul , Vrtala Aron , Wagner Paul E.
Published: May 2007

In this paper we present a new form of the nucleation theorems applicable to heterogeneous nucleation. These heterogeneous nucleation theorems allow, for the first time, direct determination of properties of nanoclusters formed on pre-existing particles from measured heterogeneous nucleation probabilities. The theorems can be used to analyze the size (first theorem) and the energetics (second theorem) of heterogeneous clusters independent of any specific nucleation model. We apply the first theorem to the study of small water and n-propanol clusters formed at the surface of 8 nm silver particles. According to the experiments the size of the two-component critical clusters is found to be below 90 molecules, and only less than 20 molecules for pure water, less than 300 molecules for pure n-propanol. These values are drastically smaller than the ones predicted by the classical nucleation theory, which clearly indicates that the nucleating clusters are too small to be quantitatively described using a macroscopic theory.
A new breakup regime of liquid drops identified in a continuous and uniform air jet flow
Authors: Cao Xian-Kui , Sun Zhi-Gang , Li Wei-Feng , Liu Hai-Feng , Yu Zun-Hong
Published: May 2007

A new breakup regime of liquid drops, named the dual-bag breakup regime, in a continuous and uniform air jet flow is identified at We ranging from 28 to 41 at the present investigation. The dual-bag breakup regime is characterized by two successive bag breakup processes; the first one is suffered by the initial main drop, and the second one is suffered by the core drop produced in the first bag breakup process. Shadowgraph and high-speed cameras were used to record the temporal properties of liquid drops in the dual-bag breakup regime. Parameters including breakup time, drop deformation rate, and volume fraction of core drop, are measured and given as a function of Weber numbers in the dual-bag breakup regime.
Vascularization with trees that alternate with upside-down trees
Authors: Zhang Houlei , Lorente Sylvie , Bejan Adrian
Published: May 2007

This article describes the generation of dendritic flow architectures that provide maximum side-to-side flow access, across a vascularized body. The flow architecture consists of trees that alternate with upside-down trees (a,b,a,b,…). If in tree “a” the flow is from root to canopy, in tree “b” the flow is from canopy to root. This means that the flow proceeds in the same direction through all the trees, i.e., the flow is oriented side-to-side, or line-to-line. The channel cross sections are rectangular, and they all have the same depth. The article shows under what conditions the tree vascularization offers greater flow access than parallel single-scale channels oriented perpendicularly to the two parallel lines. The analytical part of the work is based on the assumption of fully developed laminar flow in every channel. The numerical part consists of simulations of three-dimensional laminar flow through the entire tree architecture and its many bifurcations. It is shown that tree vascularization is more attractive than parallel channels when the number of bifurcation levels increases, the global porosity of the vascularized body decreases, and the global svelteness (Sv) of the flow architecture increases. The nonuniformity (maldistribution) of flow rates through ramifications of the same rank becomes nonnegligible when the pressure drop number (Be) exceeds 109. The optimal step in the sizes of cross-sectional areas from one channel to the channel of the next rank is closely approximated by 22∕3 even when the cross section is not square or round. The agreement between analysis and numerical simulation and optimization is good.
Anomalous reduction in thrust/reaction of water jets issuing from microapertures
Authors: Hasegawa Tomiichi , Watanabe Hiroshi , Sato Takashi , Watanabe Tohru , Takahashi Masanao , Narumi Takatsune , Tiu Carlos
Published: May 2007

Thrusts and reactions of water jets issuing through small orifices and thin slots were measured and compared with the predictions from numerical solutions of the Navier-Stokes equations. Reasonable agreements were obtained between the experimental and numerical results for orifices and slots with openings of the order of 1mm size, but not with those of 10μm or less. The experimental results were found to be well below the predictions for apertures of the order of 10μm. The difference between the numerically calculated and the measured thrusts/reactions for the small apertures was found to be proportional to the square of the mean velocity. Several possible causes for the observed reduction in jet thrust/reaction in small apertures were examined, but none of them could adequately explain the flow anomaly.
Co-doped anatase TiO2 nanofibers fabricated by electrospinning
Authors: Jia C. W. , Xie E. Q. , Zhao J. G. , Duan H. G.
Published: May 2007

Co-doped TiO2 nanofibers with an average diameter of ∼70nm were fabricated with electrospinning method. X-ray diffraction measurements show that the nanofibers possess pure anatase structure. The obtained nanofibers exhibit evident room temperature ferromagnetism through magnetic measurement. The photoluminescence of the Co-doped TiO2 nanofibers is composed of two emission bands attributed to self-trapped excitons and oxygen vacancies, different from that of pure TiO2 nanofibers which only includes emission due to self-trapped excitons. Photoluminescence intensity due to oxygen vacancies vary with annealing atmosphere and Co concentration, and the ferromagnetic moment increases with the increment of oxygen vacancies.
Inert gas condensation of evaporated Ni and laser ablated CoO
Authors: Ceylan Abdullah , Rumaiz Abdul K. , Ismat Shah S.
Published: May 2007

Magnetic core/shell nanoparticles have been prepared using a method that is modified version of inert gas condensation (IGC) technique. Using resistive evaporation and laser ablation techniques combined in an IGC system, we have shown that it is possible to synthesize core/shell nanostructures made of different materials. Resistively evaporated Ni and laser ablated CoO have formed the core/shell particles. It has been found that these particles have improved magnetic properties due to their layered structures that form as a result of oxidation of Ni core before it gets coated by CoO. Investigation of magnetic properties of the particles has revealed that the particles are single domain and have superparamagnetic behavior at room temperature as a result of their small sizes. However, low temperature measurements showed that due to the exchange interactions of the different magnetically ordered layers, there is a shift of hysteresis loops for field cooled magnetization measurements. The exchange bias at 5K obtained by 2T field cooling of the sample was 778Oe.
Growth dynamics and characterization of SiC quantum dots synthesized by low-frequency inductively coupled plasma assisted rf magnetron sputtering
Authors: Cheng Q. J. , Long J. D. , Xu S.
Published: May 2007

Self-assembled SiC quantum dots (QDs) are grown on Si substrates at a low substrate temperature of 400°C by means of low-frequency, inductively coupled plasma assisted rf magnetron sputtering from a sintered SiC target in a reactive Ar+H2 gas mixture. Effects of SiC target power and working gas pressure on the surface morphology and structural properties of SiC QDs are investigated. The growth dynamics of the QDs obeys cubic root-law behavior. With the increase of SiC target power, the growth rate increases greatly, resulting in nonuniform surface morphology and higher intensity of Si–C transmittance band. Scanning electron microscopy shows that (i) at pressure below 1Pa, SiC quantum dots are highly uniform and the average size of quantum dots increases with the increase of pressure; (ii) at pressure above 1Pa, SiC quantum dots are nonuniform, and the size of quantum dots decreases with the increase of pressure. These behaviors are explained by the scattering effects and the surface mobility of the sputtered atoms. X-ray photoelectron and Fourier transform infrared spectroscopic results show that the predominant bonds are Si–C and the elemental composition of Si and C atoms is near stoichiometric.
A constant magnetocaloric response in FeMoCuB amorphous alloys with different Fe∕B ratios
Authors: Franco V. , Conde C. F. , Blázquez J. S. , Conde A. , Švec P. , Janičkovič D. , Kiss L. F.
Published: May 2007

The magnetocaloric effect of Fe91−xMo8Cu1Bx (x=15,17,20) amorphous alloys has been studied. The temperature of the peak of magnetic entropy change can be tuned by altering the Fe∕B ratio in the alloy, without changing its magnitude, ∣ΔSMpk∣. The average contribution of the Fe atoms to ∣ΔSMpk∣ increases with increasing B content. This is correlated with the increase in the low temperature mean magnetic moment of Fe. A recently proposed master curve behavior for the magnetic entropy change is also followed by these alloys and is common for all of them.
Collisional diffusion in toroidal plasmas with elongation and triangularity
Authors: Martín P. , Castro E. , Haines M. G.
Published: May 2007

Collisional diffusion is analyzed for plasma tokamaks with different ellipticities and triangularities. Improved nonlinear equations for the families of magnetic surfaces are used here. Dimensionless average velocities are calculated as a function of the inductive electric field, elongation, triangularity, and Shafranov shift. Confinement has been found to depend significantly on triangularity.
Kinetic properties of magnetic merging in the coalescence process
Authors: Pritchett P. L.
Published: May 2007

The magnetic merging process associated with pairwise magnetic island coalescence is investigated using two-dimensional particle-in-cell simulations for the case where the initial island separation ζ is in the range of 3–12c∕ωpi, where c∕ωpi is the ion inertia length. In this regime the coalescence process is driven by the electrons, the electron and ion bulk flows decouple on the global island scale (the electron flows are much larger than those for the ions), there is no magnetic flux pileup near the merging line, and the X-O line separation drops smoothly to zero on a time scale of the order of twice the linear e-folding time for the coalescence instability. For fixed island aspect ratio, the scaling of the merging electric field Ey as a function of ζ is rather weak; i.e., ∼ζ−0.5. The magnitude of Ey, however, is strongly dependent on the magnitude of the current concentration at the initial O lines, suggesting that driven merging does not exhibit a universal rate. These kinetic results support the existence of a regime with merging rates faster than the linear Alfvén scaling with island size, but we were not able to observe the transition between these two regimes.
Eigenfunctions and eigenvalues of the Dougherty collision operator
Authors: Anderson M. W. , O’Neil T. M.
Published: May 2007

The Dougherty collision operator is a simplified Fokker-Planck collision operator that conserves particle number, momentum, and energy. In this paper, a complete set of orthogonal eigenfunctions of the linearized Dougherty operator is obtained. Five of the eigenfunctions have zero eigenvalue and correspond to the five conserved quantities (particle number, three components of momentum, and energy). The connection between the eigenfunctions and fluid modes in the limit of strong collisionality is demonstrated; in particular, the sound speed, thermal conductivity, and viscosity predicted by the Dougherty operator are identified.
Diameter control of gallium nitride nanowires
Authors: Simpkins B. S. , Pehrsson P. E. , Taheri M. L. , Stroud R. M.
Published: May 2007

Gallium nitride (GaN) nanowires are grown with controlled diameter and position by combining electron-beam lithography and naturally occurring surface tension forces. Lithographically defined particle diameters were held constant while only the film thickness was varied. Annealing drives as-deposited metal disks toward hemispheres according to conservation of volume constraints, resulting in well-controlled catalyst particles with radii smaller than those of the as-deposited particles. Transmission electron microscopy and electron diffraction confirm that the nanowires are highly crystalline wurtzite GaN. The ability to structurally control the GaN nanowire size yields effective modulation of NW-FET conductivity.
Direct writing of molecularly imprinted microstructures using a nanofountain pen
Authors: Belmont Anne-Sophie , Sokuler Mordechai , Haupt Karsten , Gheber Levi A.
Published: May 2007

Molecularly imprinted polymers (MIPs) constitute a very appealing avenue to parallel sensors of a multitude of small target molecules due to their stability, relative ease of preparation, and their ability to recognize targets for which natural capture molecules do not exist. The authors present here a way of arraying MIP structures with micrometer dimensions, using nanofountain pen, and demonstrate their functionality using a fluorescent template molecule.
Isotopic study of the nitrogen-related modes in N+-implanted ZnO
Authors: Artús L. , Cuscó R. , Alarcón-Lladó E. , González-Díaz G. , Mártil I. , Jiménez J. , Wang B. , Callahan M.
Published: May 2007

Micro-Raman measurements were performed to study the nitrogen-related modes in ZnO samples implanted with N+. The two stable N isotopes, N14 and N15, were implanted. Distinct peaks at 277 and 512cm−1 are observed irrespective of the implanted isotope, both before and after rapid thermal annealing. The insensitivity of the mode frequencies to the implanted isotope rules out the explanation of these modes as local vibrational modes involving N motion. These modes were not detected in ZnO samples implanted with Zn+, O+, or P+, which suggests that they may be associated with distortions∕defects favored by the presence of N.
Dimensional transition of CdxZn1−xTe nanostructures grown on ZnTe layers
Authors: Lee H. S. , Park H. L. , Kim T. W.
Published: May 2007

The atomic force microscopy images showed that the dimensional structural transformation from CdxZn1−xTe quantum dots (QDs) with Cd mole fractions of 0.5 and 0.6 to CdxZn1−xTe quantum wires occurred at a Cd mole fraction of 0.8. Photoluminescence spectra showed that the excitonic peak corresponding to the transition from the ground electronic subband to the ground heavy-hole band in CdxZn1−xTe∕ZnTe nanostructures shifted to a lower energy with increasing Cd mole fraction. The activation energy of the electrons confined in the CdxZn1−xTe∕ZnTe QDs with a Cd mole fraction of 0.6 was higher than those of electrons in CdxZn1−xTe∕ZnTe nanostructures.
Surface plasmon enhanced silicon solar cells
Authors: Pillai S. , Catchpole K. R. , Trupke T. , Green M. A.
Published: May 2007

Thin-film solar cells have the potential to significantly decrease the cost of photovoltaics. Light trapping is particularly critical in such thin-film crystalline silicon solar cells in order to increase light absorption and hence cell efficiency. In this article we investigate the suitability of localized surface plasmons on silver nanoparticles for enhancing the absorbance of silicon solar cells. We find that surface plasmons can increase the spectral response of thin-film cells over almost the entire solar spectrum. At wavelengths close to the band gap of Si we observe a significant enhancement of the absorption for both thin-film and wafer-based structures. We report a sevenfold enhancement for wafer-based cells at λ=1200 nm and up to 16-fold enhancement at λ=1050 nm for 1.25 μm thin silicon-on-insulator (SOI) cells, and compare the results with a theoretical dipole-waveguide model. We also report a close to 12-fold enhancement in the electroluminescence from ultrathin SOI light-emitting diodes and investigate the effect of varying the particle size on that enhancement.
Energy dissipation of materials at high pressure and high temperature
Authors: Li Li , Weidner Donald J.
Published: May 2007

We report an experimental method to study the anelastic properties of materials at high pressure and high temperature. The multianvil high pressure deformation device, used to apply a cyclic loading force onto the sample, can reach 15GPa and 2000K. A synchrotron x-ray radiation source provides time resolved images of the sample and reference material. The images yield stress and strain as a function of time; stresses are derived from the reference material, and strains from the sample. This method has been tested by applying a sinusoidal stress at megahertz to hertz frequency on a San Carlos olivine specimen at 5GPa and up to 2000K. Strain as small as 10−5 can be resolved. We have obtained experimental results which exhibit resolvable attenuation factor (Q−1) and shear modulus (M) at deep Earth conditions. These results are in quantitative agreement with previously reported lower pressure data and suggest that temperature and grain size have dominating effect on these properties.
Stable electro-optic striation grating produced by programed periodic modulation of the growth temperature
Authors: Agranat Aharon J. , Kaner Roy , Perpelitsa Galina , Garcia Yehudit
Published: May 2007

Electrically controlled Bragg gratings implemented by periodic striations that were produced during the crystal growth are demonstrated in potassium lithium tantalate niobate crystals. The striations were generated by blowing air with periodic flow at the flux surface. The gratings were investigated by measurements of the diffraction efficiency versus the applied electric field. It was found that the composition grating induced correlated gratings of the refractive index and the low frequency dielectric constant. The latter, under the application of a uniform electric field, produced an electrically controlled birefringence grating through the quadratic electro-optic effect.
Stability and tunability of the gyrotron backward-wave oscillator
Authors: Chang T. H. , Fan C. T. , Pao K. F. , Chu K. R. , Chen S. H.
Published: May 2007

To fulfill the broadband tunability of the gyrotron backward-wave oscillator (gyro-BWO), stability issues are studied and displayed in the form of stability maps. These maps serve as a guide for the identification and optimization of stable windows for broadband tuning. A Ka-band gyro-BWO experiment was conducted accordingly. In the case of a short interaction length, stable and smooth tunability of 1.3GHz was demonstrated with a peak interaction efficiency of 29.8%. In the longer length case, piecewise-stable tuning curves were obtained, as predicted in theory.
Midinfrared doping-tunable extraordinary transmission from sub-wavelength Gratings
Authors: Wasserman D. , Shaner E. A. , Cederberg J. G.
Published: May 2007

The authors demonstrate doping-tunable extraordinary transmission from subwavelength apertures in a periodic two-dimensional metallic grating deposited upon n-doped GaAs. By varying the doping of the underlying GaAs epilayer, they demonstrate wavelength tunability of ∼23cm−1 or approximately 0.15μm. The authors have achieved transmission peaks as narrow as 18cm−1 with such gratings, which suggests that devices based on midinfrared extraordinary transmission gratings could be used in external cavity structures for quantum cascade lasers, or as tunable filters or modulators for midinfrared applications.
Single glass substrate liquid crystal device using electric field-enforced phase separation and photoinduced polymerization
Authors: Ren Hongwen , Wu Shin-Tson , Lin Yi-Hsin
Published: May 2007

An in-plane switching liquid crystal (LC) cell using a glass substrate and a photoinduced polymer layer is demonstrated. The fabrication process is based on the electrodynamics of dielectric fluids. When the fringing field is present, the LC molecules tend to aggregate in the strong electric field regions while the monomers diffuse to the weak field regions. After photopolymerization, the LC molecules are confined by a thin polymer layer and polymer walls which define the cell gap. This approach enables single-substrate large panel display devices to be fabricated.
Efficient coupling of photonic crystal microcavity modes to a ridge waveguide
Authors: Banaee M. G. , Pattantyus-Abraham A. G. , McCutcheon M. W. , Rieger G. W. , Young Jeff F.
Published: May 2007

The unidirectional coupling of a microcavity mode to a ridge waveguide in a slab photonic crystal structure was investigated for the first time. Experimental observation of the coupling efficiency for the signal coupled out of the structure is in good agreement with the result of three-dimensional finite-difference time-domain simulations. The coupling efficiency of the cavity mode to the output channel is ∼60%.
Mechanical strengths of silicon nitrides studied byab initiocalculations
Authors: Zhang R. F. , Sheng S. H. , Veprek S.
Published: May 2007

The stress-strain relationships under tensile and shear loads are calculated for hcp(β)-Si3N4 and fcc(NaCl)-SiN by means of ab initio density functional theory. The ideal shear strengths for fcc-SiN are much lower than those for hcp-Si3N4. This is in agreement with experiments which show that the interfacial fcc-SiN can strengthen the TiN∕SiN heterostructures only when its thickness is about 1–2 ML. Based on the calculated electronic density of states, the physical origin of the mechanical strengths is addressed.
Metamaterials with dendriticlike structure at infrared frequencies
Authors: Liu Hui , Zhao Xiaopeng
Published: May 2007

The authors present a planar medium composed of the copper dendriticlike structure and silver film at infrared frequencies. The dendriticlike copper, which has quasiperiodic hexagonal cells, and silver film were prepared using the electrochemical deposition method. It is shown that the transmission spectra of the copper dendriticlike structure and the planar medium appear to have a stop band and a passband in the range of 1.28–2.5μm. A clear image is also observed at the wavelength near 1.92μm, as expected, with our lens composed of copper dendritic cells and silver film.
Midinfrared, optically pumped, unstable resonator lasers
Authors: Ongstad A. P. , Kaspi R. , Dente G. C. , Tilton M. L. , Chavez J.
Published: May 2007

The authors describe high-brightness, broad area midinfrared semiconductor lasers. These devices were fabricated in the authors’ laboratory using a commercial solid-source molecular beam epitaxial system. The laser structures incorporated 14 type-II quantum wells embedded in thick waveguide/absorber regions composed of In0.2Ga0.8As0.18Sb0.82. The optically pumped devices achieved higher brightness operation as unstable resonators. Each unstable resonator was realized by polishing a diverging cylindrical mirror at one of the facets. For an unstable resonator semiconductor laser operating at ∼4.6μm, near 84K, and at a peak power of 6.7W, the device was observed to be nearly diffraction limited at 25 times threshold. In comparison, a standard Fabry-Pérot laser was observed to be many times diffraction limited when operated under similar conditions.
Continuous control of liquid crystal pretilt angle from homeotropic to planar
Authors: Vaughn Karen E. , Sousa Matthew , Kang Daeseung , Rosenblatt Charles
Published: May 2007

A mixture of two polyamic acids, one having an alkyl side chain and ordinarily used for vertical liquid crystal alignment and the other without a side chain and ordinarily used for planar alignment, is deposited on two substrates and baked at high temperatures. When the resulting cell is filled with the liquid crystal pentyl cyanobiphenyl, it is found that the pretilt angle θ0 is a function of the baking temperature, and can be controlled continuously over the range of 0°⩽θ0≲90°.
Control of core-shell structure and elemental composition of binary quantum dots
Authors: Levchenko I. , Rider A. E. , Ostrikov K.
Published: May 2007

The possibility of initial stage control of the elemental composition and core/shell structure of binary SiC quantum dots by optimizing temporal variation of Si and C incoming fluxes and surface temperatures is shown via hybrid numerical simulations. Higher temperatures and influxes encourage the formation of a stoichiometric outer shell over a small carbon-enriched core, whereas lower temperatures result in a larger carbon-enriched core, Si-enriched undershell, and then a stoichiometric SiC outer shell. This approach is generic and is applicable to a broad range of semiconductor materials and nanofabrication techniques.
A substrate-independent, 14:3:3 protein-mediated plastid import pathway of NADPH:protochlorophyllide oxidoreductase A
Authors: Schemenewitz Andreas , Pollmann Stephan , Reinbothe Christiane , Reinbothe Steffen
Published: May 2007

Plastids are semiautonomous organelles that contain only limited coding information in their own DNA. Because most of their genome was transferred to the nucleus after their endosymbiotic origin, plastids must import the major part of their protein constituents from the cytosol. The exact role of cytosolic targeting factors in the regulation of plastid protein import has not been determined. Here, we report that the nucleus-encoded NADPH:protochlorophyllide (Pchlide) oxidoreductase A plastid precursor (pPORA) can use two different plastid import pathways that differ by the requirements for cytosolic 14:3:3 proteins and Hsp70. pPORA synthesized in a wheat germ lysate segregated into different precursor fractions. While import of free pPORA and only Hsp70-complexed pPORA was Pchlide-dependent and involved the previously identified Pchlide-dependent translocon, 14:3:3 protein- and Hsp70-complexed pPORA was transported into Pchlide-free chloroplasts through the Toc75-containing standard translocon at the outer chloroplast membrane/translocon at the inner chloroplast membrane machinery. A 14:3:3 protein binding site was identified in the mature region of the
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S-pPORA, which governed 14:3:3 protein- and Hsp70-mediated, Pchlide-independent plastid import. Collectively, our results reveal that the import of pPORA into the plastids is tightly regulated and involves different cytosolic targeting factors and plastid envelope translocon complexes.
Endosomal recycling controls plasma membrane area during mitosis
Authors: Boucrot Emmanuel , Kirchhausen Tomas
Published: May 2007

The shape and total surface of a cell and its daughters change during mitosis. Many cells round up during prophase and metaphase and reacquire their extended and flattened shape during cytokinesis. How does the total area of plasma membrane change to accommodate these morphological changes and by what mechanism is control of total membrane area achieved? Using single-cell imaging methods, we have found that the amount of plasma membrane in attached cells in culture decreases at the beginning of mitosis and recovers rapidly by the end. Clathrin-based endocytosis is normal throughout all phases of cell division, whereas recycling of internalized membranes back to the cell surface slows considerably during the rounding up period and resumes at the time at which recovery of cell membrane begins. Interference with either one of these processes by genetic or chemical means impairs cell division. The total cell-membrane area recovers even in the absence of a functional Golgi apparatus, which would be needed for export of newly synthesized membrane lipids and proteins. We propose a mechanism by which modulation of endosomal recycling controls cell area and surface expression of membrane-bound proteins during cell division.
DNA methylation affects nuclear organization, histone modifications, and linker histone binding but not chromatin compaction
Authors: Gilbert Nick , Thomson Inga , Boyle Shelagh , Allan James , Ramsahoye Bernard , Bickmore Wendy A.
Published: May 2007

DNA methylation has been implicated in chromatin condensation and nuclear organization, especially at sites of constitutive heterochromatin. How this is mediated has not been clear. In this study, using mutant mouse embryonic stem cells completely lacking in DNA methylation, we show that DNA methylation affects nuclear organization and nucleosome structure but not chromatin compaction. In the absence of DNA methylation, there is increased nuclear clustering of pericentric heterochromatin and extensive changes in primary chromatin structure. Global levels of histone H3 methylation and acetylation are altered, and there is a decrease in the mobility of linker histones. However, the compaction of both bulk chromatin and heterochromatin, as assayed by nuclease digestion and sucrose gradient sedimentation, is unaltered by the loss of DNA methylation. This study shows how the complete loss of a major epigenetic mark can have an impact on unexpected levels of chromatin structure and nuclear organization and provides evidence for a novel link between DNA methylation and linker histones in the regulation of chromatin structure.
Integrin-linked kinase is required for epidermal and hair follicle morphogenesis
Authors: Lorenz Katrin , Grashoff Carsten , Torka Robert , Sakai Takao , Langbein Lutz , Bloch Wilhelm , Aumailley Monique , Fässler Reinhard
Published: May 2007

Integrin-linked kinase (ILK) links integrins to the actin cytoskeleton and is believed to phosphorylate several target proteins. We report that a keratinocyte-restricted deletion of the ILK gene leads to epidermal defects and hair loss. ILK-deficient epidermal keratinocytes exhibited a pronounced integrin-mediated adhesion defect leading to epidermal detachment and blister formation, disruption of the epidermal–dermal basement membrane, and the translocation of proliferating, integrin-expressing keratinocytes to suprabasal epidermal cell layers.

The mutant hair follicles were capable of producing hair shaft and inner root sheath cells and contained stem cells and generated proliferating progenitor cells, which were impaired in their downward migration and hence accumulated in the outer root sheath and failed to replenish the hair matrix. In vitro studies with primary ILK-deficient keratinocytes attributed the migration defect to a reduced migration velocity and an impaired stabilization of the leading-edge lamellipodia, which compromised directional and persistent migration. We conclude that ILK plays important roles for epidermis and hair follicle morphogenesis by modulating integrin-mediated adhesion, actin reorganization, and plasma membrane dynamics in keratinocytes.
v-SNARE cellubrevin is required for basolateral sorting of AP-1B–dependent cargo in polarized epithelial cells
Authors: Fields Ian C. , Shteyn Elina , Pypaert Marc , Proux-Gillardeaux Véronique , Kang Richard S. , Galli Thierry , Fölsch Heike
Published: May 2007

The epithelial cell–specific adaptor complex AP-1B is crucial for correct delivery of many transmembrane proteins from recycling endosomes to the basolateral plasma membrane. Subsequently, membrane fusion is dependent on the formation of complexes between SNARE proteins located at the target membrane and on transport vesicles. Although the t-SNARE syntaxin 4 has been localized to the basolateral membrane, the v-SNARE operative in the AP-1B pathway remained unknown. We show that the ubiquitously expressed v-SNARE cellubrevin localizes to the basolateral membrane and to recycling endosomes, where it colocalizes with AP-1B. Furthermore, we demonstrate that cellubrevin coimmunoprecipitates preferentially with syntaxin 4, implicating this v-SNARE in basolateral fusion events. Cleavage of cellubrevin with tetanus neurotoxin (TeNT) results in scattering of AP-1B localization and missorting of AP-1B–dependent cargos, such as transferrin receptor and a truncated low-density lipoprotein receptor, LDLR-CT27. These data suggest that cellubrevin and AP-1B cooperate in basolateral membrane trafficking.
Syndecan-4–dependent Rac1 regulation determines directional migration in response to the extracellular matrix
Authors: Bass Mark D. , Roach Kirsty A. , Morgan Mark R. , Mostafavi-Pour Zohreh , Schoen Tobias , Muramatsu Takashi , Mayer Ulrike , Ballestrem Christoph , Spatz Joachim P. , Humphries Martin J.
Published: May 2007

Cell migration in wound healing and disease is critically dependent on integration with the extracellular matrix, but the receptors that couple matrix topography to migratory behavior remain obscure. Using nano-engineered fibronectin surfaces and cell-derived matrices, we identify syndecan-4 as a key signaling receptor determining directional migration. In wild-type fibroblasts, syndecan-4 mediates the matrix-induced protein kinase Cα (PKCα)–dependent activation of Rac1 and localizes Rac1 activity and membrane protrusion to the leading edge of the cell, resulting in persistent migration. In contrast, syndecan-4–null fibroblasts migrate randomly as a result of high delocalized Rac1 activity, whereas cells expressing a syndecan-4 cytodomain mutant deficient in PKCα regulation fail to localize active Rac1 to points of matrix engagement and consequently fail to recognize and respond to topographical changes in the matrix.
Emi1 is needed to couple DNA replication with mitosis but does not regulate activation of the mitotic APC/C
Authors: Di Fiore Barbara , Pines Jonathon
Published: May 2007

Ubiquitin-mediated proteolysis is critical for the alternation between DNA replication and mitosis and for the key regulatory events in mitosis. The anaphase-promoting complex/cyclosome (APC/C) is a conserved ubiquitin ligase that has a fundamental role in regulating mitosis and the cell cycle in all eukaryotes. In vertebrate cells, early mitotic inhibitor 1 (Emi1) has been proposed as an important APC/C inhibitor whose destruction may trigger activation of the APC/C at mitosis. However, in this study, we show that the degradation of Emi1 is not required to activate the APC/C in mitosis. Instead, we uncover a key role for Emi1 in inhibiting the APC/C in interphase to stabilize the mitotic cyclins and geminin to promote mitosis and prevent rereplication. Thus, Emi1 plays a crucial role in the cell cycle to couple DNA replication with mitosis, and our results also question the current view that the APC/C has to be inactivated to allow DNA replication.
Tripin/hSgo2 recruits MCAK to the inner centromere to correct defective kinetochore attachments
Authors: Huang Haomin , Feng Jie , Famulski Jakub , Rattner Jerome B. , Liu Song Tao , Kao Gary D. , Muschel Ruth , Chan Gordon K.T. , Yen Tim J.
Published: May 2007

hSgo2 (previously annotated as Tripin) was recently reported to be a new inner centromere protein that is essential for centromere cohesion (Kitajima et al., 2006). In this study, we show that hSgo2 exhibits a dynamic distribution pattern, and that its localization depends on the BUB1 and Aurora B kinases. hSgo2 is concentrated at the inner centromere of unattached kinetochores, but extends toward the kinetochores that are under tension. This localization pattern is reminiscent of MCAK, which is a microtubule depolymerase that is believed to be a key component of the error correction mechanism at kinetochores. Indeed, we found that hSgo2 is essential for MCAK to localize to the centromere. Delocalization of MCAK accounts for why cells depleted of hSgo2 exhibit kinetochore attachment defects that go uncorrected, despite a transient delay in the onset of anaphase. Consequently, these cells exhibit a high frequency of lagging chromosomes when they enter anaphase. We confirmed that hSgo2 is associated with PP2A, and we propose that it contributes to the spatial regulation of MCAK activity within inner centromere and kinetochore.
Glycoprotein I of herpes simplex virus type 1 contains a unique polymorphic tandem-repeated mucin region
Authors: Norberg Peter , Olofsson Sigvard , Tarp Mads Agervig , Clausen Henrik , Bergström Tomas , Liljeqvist Jan Åke
Published: May 2007

Glycoprotein I (gI) of herpes simplex virus type 1 (HSV-1) contains a tandem repeat (TR) region including the amino acids serine and threonine, residues that can be utilized forO-glycosylation. The length of this TR region was determined for 82 clinical HSV-1 isolates and the results revealed a polymorphic distribution of two to six or eight repeated blocks with a majority harbouring between two and four repeats. Assessment of theO-glycosylation capacity of an acceptor peptide (STPSTTTSTPSTTT), representing two of the gI blocks, showed that the peptide was a universal substrate forO-glycosylation not only for the two most commonly expressedN-acetyl-d-galactosamine (GalNAc)-T1 and -T2 transferases, but also for the GalNAc-T3, -T4 and -T11 transferases. Immunoblotting of virus-infected cells showed that gI was exclusivelyO-glycosylated with GalNAc monosaccharides (Tn antigen). A polymorphic mucin region has not been described previously for HSV-1 and is a unique finding, as repeated blocks within gI homologues are lacking in other alphaherpesviruses.
Control of Rta expression critically determines transcription of viral and cellular genes following gammaherpesvirus infection
Authors: Hair James R. , Lyons Paul A. , Smith Kenneth G. C. , Efstathiou Stacey
Published: May 2007

The replication and transcriptional activator (Rta), encoded by ORF50 of gammaherpesviruses, initiates the lytic cycle of gene expression; therefore understanding the impact of Rta on viral and cellular gene expression is key to elucidating the transcriptional events governing productive infection and reactivation from latency. To this end, the impact of altering Rta transcription on viral and cellular gene expression was studied in the context of a whole virus infection. Recombinant murine gammaherpesvirus (MHV)-68 engineered to overexpress Rta greatly accelerated expression of specific lytic cycle ORFs, but repressed transcription of the major latency gene, ORF73. Increased expression of Rta accelerated the dysregulation in transcription of specific cellular genes when compared with cells infected with wild-type and revertant viruses. A subset of cellular genes was dysregulated only in cells infected with Rta-overexpressing virus, and never in those infected with non-overexpressing viruses. These data highlight the critical role of Rta abundance in governing viral and cellular gene transcription, and demonstrate the importance of understanding how the relative expression of ORF50 during the virus life cycle impacts on these processes.
Reduced susceptibility to bovine spongiform encephalopathy prions in transgenic mice expressing a bovine PrP with five octapeptide repeats
Authors: Brun Alejandro , Gutiérrez-Adán Alfonso , Castilla Joaquín , Pintado Belén , Díaz-San Segundo Fayna , Cano María J. , Alamillo Elia , Espinosa Juan C. , Torres Juan M.
Published: May 2007

In this work, transgenic (Tg) mice were generated expressing a bovine prion protein containing five octarepeats (BoPrP5OR-Tg). After intracerebral inoculation of bovine spongiform encephalopathy (BSE) inoculum, these mice suffered a BSE-like neuropathology but survived longer compared with homologous Tg mice expressing similar levels of a six octarepeat BoPrP protein (BoPrP6OR-Tg). De novo-generated five octarepeat (5OR) PrPSc showed no biochemical differences from 6OR-PrPSc, and the proteinase K-resistant core (PrPres) was biochemically indistinguishable from the 6OR counterpart. Lower susceptibility to BSE is suggested for BoPrP5OR-Tg mice, as they were not as efficient at replicating BSE prions from the same natural source inoculum as BoPrP6OR-Tg mice expressing similar PrPC levels. These results raise the possibility of selecting cattle breeds bearing the 5OR Prnp allele that are less susceptible to prion infection.
Type I feline coronavirus spike glycoprotein fails to recognize aminopeptidase N as a functional receptor on feline cell lines
Authors: Dye Charlotte , Temperton Nigel , Siddell Stuart G.
Published: May 2007

There are two types of feline coronaviruses that can be distinguished by serology and sequence analysis. Type I viruses, which are prevalent in the field but are difficult to isolate and propagate in cell culture, and type II viruses, which are less prevalent but replicate well in cell culture. An important determinant of coronavirus infection, in vivo and in cell culture, is the interaction of the virus surface glycoprotein with a cellular receptor. It is generally accepted that feline aminopeptidase N can act as a receptor for the attachment and entry of type II strains, and it has been proposed that the same molecule acts as a receptor for type I viruses. However, the experimental data are inconclusive. The aim of the studies reported here was to provide evidence for or against the involvement of feline aminopeptidase N as a receptor for type I feline coronaviruses. Our approach was to produce retroviral pseudotypes that bear the type I or type II feline coronavirus surface glycoprotein and to screen a range of feline cell lines for the expression of a functional receptor for attachment and entry. Our results show that type I feline coronavirus surface glycoprotein fails to recognize feline aminopeptidase N as a functional receptor on three continuous feline cell lines. This suggests that feline aminopeptidase N is not a receptor for type I feline coronaviruses. Our results also indicate that it should be possible to use retroviral pseudotypes to identify and characterize the cellular receptor for type I feline coronaviruses.
Search for DNA of exogenous mouse mammary tumor virus-related virus in human breast cancer samples
Authors: Bindra A. , Muradrasoli S. , Kisekka R. , Nordgren H. , Wärnberg F. , Blomberg J.
Published: May 2007

Earlier reports of a human exogenous retrovirus (HMTV) related closely to mouse mammary tumor virus (MMTV) led us to search for these viral sequences in breast cancer tissues and normal tissues. A real-time PCR was developed based on MMTV and published HMTV envelope sequences. The real-time PCR method can detect one to ten copies of MMTV target DNA. Tissue samples were collected prospectively from 18 breast cancer patients and 11 non-malignant control cases, as well as peripheral blood leukocytes from the same women. Despite the high sensitivity of the real-time PCR method used, none of the samples were positive for HMTV DNA or RNA. The absence of HMTV DNA in both breast cancer samples and controls indicates either that the concentration of putative HMTV DNA in the breast cancers was too low for detection or that it did not exist there.
Functional and structural studies of the vaccinia virus virulence factor N1 reveal a Bcl-2-like anti-apoptotic protein
Authors: Cooray Samantha , Bahar Mohammad W. , Abrescia Nicola G. A. , McVey Colin E. , Bartlett Nathan W. , Chen Ron A.-J. , Stuart David I. , Grimes Jonathan M. , Smith Geoffrey L.
Published: May 2007

Vaccinia virus (VACV) encodes many immunomodulatory proteins, including inhibitors of apoptosis and modulators of innate immune signalling. VACV protein N1 is an intracellular homodimer that contributes to virus virulence and was reported to inhibit nuclear factor (NF)-κB signalling. However, analysis of NF-κB signalling in cells infected with recombinant viruses with or without the N1L gene showed no difference in NF-κB-dependent gene expression. Given that N1 promotes virus virulence, other possible functions of N1 were investigated and this revealed that N1 is an inhibitor of apoptosis in cells transfected with the N1L gene and in the context of VACV infection. In support of this finding virally expressed N1 co-precipitated with endogenous pro-apoptotic Bcl-2 proteins Bid, Bad and Bax as well as with Bad and Bax expressed by transfection. In addition, the crystal structure of N1 was solved to 2.9 Å resolution (0.29 nm). Remarkably, although N1 shows no sequence similarity to cellular proteins, its three-dimensional structure closely resembles Bcl-xL and other members of the Bcl-2 protein family. The structure also reveals that N1 has a constitutively open surface groove similar to the grooves of other anti-apoptotic Bcl-2 proteins, which bind the BH3 motifs of pro-apoptotic Bcl-2 family members. Molecular modelling of BH3 peptides into the N1 surface groove, together with analysis of their physico-chemical properties, suggests a mechanism for the specificity of peptide recognition. This study illustrates the importance of the evolutionary conservation of structure, rather than sequence, in protein function and reveals a novel anti-apoptotic protein from orthopoxviruses.
Functional characterization of the M-type K15-encoded membrane protein of Kaposi's sarcoma-associated herpesvirus
Authors: Wang Linding , Brinkmann Melanie M. , Pietrek Marcel , Ottinger Matthias , Dittrich-Breiholz Oliver , Kracht Michael , Schulz Thomas F.
Published: May 2007

Kaposi's sarcoma-associated herpesvirus (KSHV) or human herpesvirus 8 is the causative agent of Kaposi's sarcoma, primary effusion lymphoma and the plasma-cell variant of multicentric Castleman's disease. Its alternatively spliced K15 gene encodes several membrane proteins with varying numbers of transmembrane domains. Two highly diverged alleles of the K15 gene, termed predominant (P) and minor (M), exist and share only 33 % amino acid identity with one another, but retain conserved putative src homology (SH) 2- and SH3-binding motifs. K15-M is thought to have entered the KSHV genome as the result of recombination with a related γ
2-herpesvirus. The more common K15-P allele has been shown to activate the mitogen-activated protein kinases Erk2 and JNK1 and the nuclear factor κB (NF-κB) pathway. To explore possible functional differences between K15-P and K15-M that might have influenced their spread in the KSHV population, here, the ability of the M form of K15 to activate these pathways was investigated. Similarly to K15-P, K15-M induces the activation of the Erk2 and JNK1 kinases, the NF-κB transcription factor and the expression of a similar range of cellular inflammatory genes, as assessed by gene-expression microarray studies and reporter assays. In epithelial cells, the activation of most K15-M target genes is impaired by mutagenesis of Y490 in its SH2-binding motif Y490EEV, although this motif appears less important in endothelial cells. Therefore, K15-M and K15-P can trigger similar intracellular signalling pathways, despite their extensive sequence divergence.