bluuebunny/crossref_metadata_2025 huggingface dataset:
Relaxor behavior and dielectric relaxation in Pb(Ba1/3Nb2/3)O3: A phase pure new relaxor material
Authors: Bajpai P. K. , Pastor Mukul , Singh K. N.
Published: January 2011

Pb ( Ba 1 / 3 Nb 2 / 3 ) O 3 was prepared by two steps solid state reaction route. Material stabilized in orthorhombic perovskite phase with lattice constants a=4.0849(3) Å, b=11.8469(4) Å, and c=10.6818(9) Å. The scanning electron micrograph exhibits heterogeneous grain distribution with average grain size of 1–3 μm. Temperature dependent dielectric constant exhibits a broad peak at 316 K (εm=2250) that shows frequency dependent shifts toward higher temperature—typical relaxor behavior. Modified Curie–Weiss law is used to fit the dielectric data that exhibits almost complete diffuse phase transition characteristics. The dielectric relaxation obeys the Vogel–Fulcher relationship with the freezing temperature 286 K. In addition to relaxation observed due to transformation of the material into ergodic relaxor phase below Burn temperature, significant dielectric dispersion is observed in low frequency regime in both components of dielectric response and a small dielectric relaxation peak is observed in the temperature range (423–598 K) that is associated with defect related hopping process. Cole–Cole plots indicate polydispersive nature of this dielectric relaxation; the relaxation distribution increasing with temperature.
Atmospheric pressure cold plasma as an antifungal therapy
Authors: Sun Peng , Sun Yi , Wu Haiyan , Zhu Weidong , Lopez Jose L. , Liu Wei , Zhang Jue , Li Ruoyu , Fang Jing
Published: January 2011

A microhollow cathode based, direct-current, atmospheric pressure, He/O2 (2%) cold plasma microjet was used to inactive antifungal resistants Candida albicans, Candida krusei, and Candida glabrata in air and in water. Effective inactivation (>90%) was achieved in 10 min in air and 1 min in water. Antifungal susceptibility tests showed drastic reduction of the minimum inhibitory concentration after plasma treatment. The inactivation was attributed to the reactive oxygen species generated in plasma or in water. Hydroxyl and singlet molecular oxygen radicals were detected in plasma-water system by electron spin resonance spectroscopy. This approach proposed a promising clinical dermatology therapy.
Numerical simulations of electrical asymmetry effect on electronegative plasmas in capacitively coupled rf discharge
Authors: Zhang Quan-Zhi , Jiang Wei , Hou Lu-Jing , Wang You-Nian
Published: January 2011

Recently a so-called electrical asymmetry effect (EAE), which could achieve high-degree separate control of ion flux and energy in dual-frequency capacitively coupled radio-frequency (CCRF) discharges, was discovered theoretically by Heil et al. [J. Phys. D: Appl. Phys. 41, 165202 (2008)] and was confirmed by experiments and theory/numerical simulations later on for electropositive argon discharges. In this work simulations based on particle-in-cell/Monte Carlo collision are performed to study the EAE on electronegative oxygen plasmas in geometrically symmetric CCRF discharges. Dual frequency discharges operating at 13.56 and 27.12 MHz are simulated for different pressures and the results are compared with those of electropositive argon discharges at the same conditions. It is found that in general the EAE on oxygen discharges has similar behavior as on argon discharge: The self-bias voltage η increases monotonically and almost linearly with the increase in the phase angle θ between the two driving voltages in the range 0<θ<90°, and the maximum ion energy varies by a factor of 3 by adjusting θ. However, the ion flux varies with θ by ±12% for low pressure and by ±15% for higher pressure, due primarily to an enhanced plasma series resonance, which then leads to dramatic changes in plasma density, power absorption and consequently the electronegativity. This may place a limitation for achieving separate control of ion energy and flux for electronegative plasma via the EAE.
Rheology of oscillating suspensions of noncolloidal spheres at small and large accumulated strains
Authors: Park Hyun-Ok , Bricker Jonathan M. , Roy Michael J. , Butler Jason E.
Published: January 2011

The oscillatory rheology of a noncolloidal suspension of spheres is studied for volume fractions up to 0.50 and strain amplitudes of oscillation between 0.05 and 5.0. The stress responses to the imposed oscillatory strain can deviate from a linear response, even at the smallest strain amplitude, as quantified by both a Fourier decomposition and a least-squares analysis. The stress component that is in phase with the strain can decay by an order of magnitude over the first 15–20 oscillations, depending upon the concentration and strain amplitude. Over the same number of oscillations, the stress component in phase with the rate of strain remains nearly constant, but does change significantly over a large number of oscillations. Furthermore, the apparent values of the complex viscosity of the suspensions at steady state demonstrate a nonmonotonic dependence on strain amplitude for volume fractions larger than 0.2, confirming previously published data limited to the volume fraction of 0.4.
Surface flows of inelastic spheres
Authors: Berzi Diego , Jenkins James T.
Published: January 2011

We study flows of inelastic spheres on the surface of an erodible bed between frictional sidewalls and distinguish two regions in such flows: a dilute, diffuse region, neighboring the free surface, for which we solve a boundary-value problem based on the kinetic theory, and a dense algebraic layer, in which there is an approximate algebraic balance between production and dissipation of fluctuation energy. We take into account correlated motions between the particles at high volume fractions and employ the trapezoidal rule to solve, in an approximate way, for the flow quantities in the diffuse layer. Using boundary conditions of no-slip and yield at the bed and vanishing of the stresses and the energy flux at the free surface, we obtain analytical predictions of flow depth and mass flow rate that compare favorably with the results of experiments performed on glass spheres flowing on the surface of a heap and in half-filled rotating drums.
Viscoelastic drop falling through a viscous medium
Authors: Mukherjee Swarnajay , Sarkar Kausik
Published: January 2011

Deformation and sedimentation velocities of a viscoelastic drop falling through a Newtonian medium are numerically investigated using a front-tracking finite difference method. In contrast to a viscous drop, viscoelasticity deforms an initially spherical drop into an oblate shape and decreases its sedimentation velocity. Further increase of elasticity results in a dimple at the rear end, as the viscoelastic stress at the trailing end of the drop pulls the drop interface inward. The dimple becomes more prominent with increasing Deborah number, amount of polymeric viscosity, and capillary number. An approximate analysis is performed to model the stress development along the axis of symmetry, specifically its increase at the rear end that governs the dimple formation. For even higher values of Deborah number, the interfacial tension cannot balance the viscoelastic stresses leading to an unstable situation toward a toroidal shape. We numerically find the critical Deborah number for the transition. It shows an approximate inverse scaling with capillary number. For unstable cases, downward progressing dimple develops a globular end. Development of the globular end results in a sudden increase in the cross-sectional area of the drop and a sharp decrease of the settling velocity.
High-capacity hydrogen storage medium: Ti doped fullerene
Authors: Guo Jun , Liu Zhiguo , Liu Suqin , Zhao Xuehui , Huang Kelong
Published: January 2011

Using density functional theory, it is shown that titanium doped heterofullerene has superior property of hydrogen storage. The single titanium atom lies at a double bond position of C60 and bonds to four carbons by Dewar interaction. Each titanium atom binds up to six hydrogen molecules. The first and second hydrogen molecules are dissociated to form carbon hydrides with binding energy of −0.43 eV/H. The other four adsorptions are molecular with binding energy of −0.14 eV/H2. For substitutionally dope C60 with six titanium atoms, the gravimetric density of hydrogen reaches the 7.7 wt % limit necessary for applications in the mobile industry.
Plus–minus construction leads to perfect invisibility
Authors: Nacher J. C. , Ochiai T.
Published: January 2011

Recent theoretical advances applied to metamaterials have opened new avenues to design a coating that hides objects from electromagnetic radiation and even the sight. Here, we propose a new design of cloaking devices that creates perfect invisibility in isotropic media. A combination of positive and negative refractive indices, called plus–minus construction, is essential to achieve perfect invisibility (i.e., no time delay and total absence of reflection). Contrary to the common understanding that between two isotropic materials having different refractive indices the electromagnetic reflection is unavoidable, our method shows that surprisingly the reflection phenomena can be completely eliminated. The invented method, different from the classical impedance matching, may also find electromagnetic applications outside of cloaking devices, wherever distortions are present arising from reflections.
Numerical simulation of a liquid bridge in a coaxial gas flow
Authors: Herrada Miguel A. , López-Herrera José M. , Vega Emilio J. , Montanero José M.
Published: January 2011

The dynamical response of an isothermal liquid bridge to a coaxial gas stream is examined from axisymmetric numerical simulations of the Navier–Stokes equations. The simulation method is previously validated by calculating the temporal evolution of the first oscillation mode in both cylindrical and axisymmetric liquid bridges. The comparison with other theoretical approaches and experiments shows good agreement in most cases, although significant discrepancies are found between the simulation and the experimental values of the damping rate for hexadecane. The simulation of a liquid bridge in a coaxial gas stream shows that a recirculation cell always appears in the liquid driven by the gas viscous stress on the free surface. The recirculation cell speed depends quasilinearly on the gas velocity for the range of gas flow rates considered. If the gas stream and gravity have the same direction, then the speed of the recirculation cell increases considerably due to the free surface deformation of the liquid bridge at equilibrium. This effect does not occur when gravity has the opposite direction because viscous dissipation in the liquid increases in this case. If the gas stream and gravity point downward, the liquid bridge shrinks at the upper part and bulges at the lower owing to the accumulation of momentum there. The same occurs for zero gravity, but noncylindrical liquid bridges deform more than cylindrical shapes with the same slenderness. If one inverts the direction of the gravity force, the interface deformation caused by the gas stream is the opposite, and its magnitude is smaller. The magnitude of the free surface deformation depends almost linearly on the gas stream velocity for both zero and normal gravity conditions.
The effect of intensity of excitation on CdSe/ZnS quantum dots: Opportunities in luminescence sensing
Authors: Sutter Jens U. , Birch David J. S. , Rolinski Olaf J.
Published: January 2011

We report changes in the photophysical properties of core-shell type CdSe/ZnS quantum dots (QDs) under optical irradiation. QDs either in aqueous solution or immobilized in a silica sol gel matrix have been excited at different wavelengths and fluxes. Illumination of the sample with 140 fs 700 nm Ti:sapphire laser pulses of the peak power of the order of 4 GW/cm2 caused gradual increase in the luminescence lifetime from an initial value of 3.5 increasing to 4.5 ns and an increase in luminescence intensity by ∼8%. Using about 16 GW/cm2 peak power resulted in a shortening of the luminescence lifetime to 3 ns and a decrease in intensity by ∼75%. Both photobrightening and photodarkening were fully reversible. We discuss the kinetics of photobrightening and photodarkening and investigate the suitability of QDs as luminescence lifetime sensors with tunable parameters.
Correlating structure, strain, and morphology of self-assembled InAs quantum dots on GaAs
Authors: Kumah D. P. , Wu J. H. , Husseini N. S. , Dasika V. D. , Goldman R. S. , Yacoby Y. , Clarke R.
Published: January 2011

We report on the use of a direct x-ray phase retrieval method, coherent Bragg rod analysis, to characterize self-assembled InAs quantum dots (QDs) grown epitaxially on GaAs substrates. Electron density maps obtained close to the x-ray absorption edges of the constituent elements are compared to deconvolute composition and atomic spacing information. Our measurements show no evidence of a wetting layer and reveal bowing of the atomic layers throughout the QD, extending from the QD-substrate interface. This leads to a half-layer stacking shift which may act to partially decouple the QDs electronically from the substrate.
Coupling of a surface plasmon with localized subwavelength microcavity modes
Authors: Jouy P. , Todorov Y. , Vasanelli A. , Colombelli R. , Sagnes I. , Sirtori C.
Published: January 2011

Midinfrared photonic modes of a periodically patterned metal-dielectric-metal structure have been investigated theoretically and experimentally. We have observed an anticrossing behavior between cavity modes localized in the double-metal regions and the surface plasmon polariton, signature of a hybridization between the two modes.
Band gap engineering in graphene and hexagonal BN antidot lattices: A first principles study
Authors: Zhang Aihua , Teoh Hao Fatt , Dai Zhenxiang , Feng Yuan Ping , Zhang Chun
Published: January 2011

The effects of antidot lattices on electronic structures of graphene and hexagonal BN (h-BN) are investigated using the first principles method based on density functional theory. For graphene, we find that when the antidot lattice is along the zigzag direction, the band gap opening can be related to the intervalley scattering and does not follow the simple scaling rule previously proposed in the literature for the antidot lattice along the armchair direction. For h-BN, our calculations show that the antidot lattice results in reducing of band gaps. Coupled with doping of carbon atoms, the band gap of a h-BN antidot lattice can be reduced to below 2 eV, which might have implications in light-emitting devices or photoelectrochemistry.
Influence of annular magnet on discharge characteristics in enhanced glow discharge plasma immersion ion implantation
Authors: Li Liu He , Wang Zhuo , Lu Qiu Yuan , Pang En Jing , Dun Dan Dan , He Fu Shun , Li Fen , Fu Ricky K. Y. , Chu Paul K.
Published: January 2011

A permanent annular magnet positioned at the grounded anode alters the discharge characteristics in enhanced glow discharge plasma immersion ion implantation (EGD-PIII). The nonuniform magnetic field increases the electron path length and confines electron motion due to the magnetic mirror effect and electron-neutral collisions thus occur more frequently. The plasma potential and ion density measured by a Langmuir probe corroborate that ionization is improved near the grounded anode. This hybrid magnetic field EGD-PIII method is suitable for implantation of gases with low ionization rates.
Implications of elastic constants, fragility, and bonding on permanent deformation in metallic glass
Authors: Plummer J. D. , Todd I.
Published: January 2011

Ratios of elastic constants C12/C11 and C44/C11 are compared for a representative group of bulk metallic glasses (BMGs) via a Blackman diagram [M. Blackman, Proc. R. Soc. London, Ser. A 164, 62 (1938)]. By the application of bounding limits to the elastic data, with respect to the Born mechanical-instability criterion and the extent of deviation from zero Cauchy pressure, a physical picture emerges of the required structural nature of a BMG if plasticity is to be prevalent, suggesting the need for a large kinetic glass fragility index m as well as nondirectional interatomic bonds.
Polarization-independent filters for luminescent solar concentrators
Authors: de Boer Dick K. G. , Lin Chi-Wen , Giesbers Merijn P. , Cornelissen Hugo J. , Debije Michael G. , Verbunt Paul P. C. , Broer Dirk J.
Published: January 2011

The efficiency of luminescent solar concentrators could be enhanced by use of wavelength-selective filters, reducing the amount of luminescent light lost. To accomplish this, polarization-independent filters with reflectivity >97% were made by combining layers of cholesteric liquid crystals, either a right- with a left-handed layer, or two right-handed layers with a half-lambda waveplate. Normal cholesteric filters have a reflection bandwidth which is narrower than the spectral and angular range of the luminescent emission. The reflection band is broadened from 80 to 200 nm by employing a pitch gradient in the cholesteric layer. The measured transmission bands compare well with calculations.
Epitaxial VO2/Cr2O3/sapphire heterostructure for multifunctional applications
Authors: Yang Tsung-Han , Mal S. , Jin C. , Narayan R. J. , Narayan J.
Published: January 2011

In this letter, we report integration of magnetic and ultrafast-transition properties of VO2 films with antiferromagnetic (AFM) Cr2O3 template layer in the epitaxial VO2/Cr2O3/Al2O3 heterostructure The Cr2O3 is an AFM material, which can pin the spin momentum of ferromagnetic VO2, in addition to providing epitaxial template. Thus, the magnetic properties of VO2 films grown with Cr2O3 buffer layer can be improved for multifunctional magnetic tunnel junctions and sensor applications. Electrical resistivity measurements as a function of temperature showed a sharp transition width (1.94 °C), with a small hysteresis width (5.7 °C), and large resistance change (∼3.8×104) across the semiconductor to metal transition (SMT). We discuss the correlations of the magnetic properties and SMT characteristics with epitaxial growth and formation of twins.
Inheritance of resistance to root-lesion nematode (Pratylenchus thornei) in wheat landraces and cultivars from the West Asia and North Africa (WANA) region
Authors: Thompson J. P. , Seymour N. P.
Published: January 2011

The root-lesion nematode Pratylenchus thornei causes substantial loss to bread wheat production in the northern grain region of Australia and other parts of the world. West Asia and North Africa (WANA) wheat accessions with partial resistance to P. thornei were analysed for mode of inheritance in a half-diallel crossing design of F1 hybrids (10 parents) and F2 populations (7 parents). General combining ability was more important than specific combining ability as indicated by components of variance ratios of 0.93 and 0.95 in diallel ANOVA of the F1 and F2 generations, respectively. General combining ability values of the ‘resistant’ parents were predictive of the mean nematode numbers of their progeny in crosses with the susceptible Australian cv. Janz at the F1 (R2 = 0.86, P < 0.001, 8 crosses), F2 (R2 = 0.83, P < 0.001, 9 populations) and F∞ (R2 = 0.71, P < 0.05, 5 doubled-haploid populations). The F2 and F∞ populations showed relatively continuous distributions. Heritability was 0.68 for F2 populations in the half-diallel of resistant parents and 0.82–0.92 for 5 ‘resistant’ parent/Janz doubled-haploid populations (narrow-sense heritability on a line mean basis). The results indicate polygenic inheritance of P. thornei resistance with a minimum of from 2 to 6 genes involved in individual F∞ populations of 5 resistant parents crossed with Janz. Morocco 426 and Iraq 43 appear to be the best of the parents tested for breeding for resistance to P. thornei. None of the P. thornei-resistant WANA accessions was resistant to Pratylenchus neglectus.
Violation of the Leggett–Garg inequality with weak measurements of photons
Authors: Goggin M. E. , Almeida M. P. , Barbieri M. , Lanyon B. P. , O’Brien J. L. , White A. G. , Pryde G. J.
Published: January 2011

By weakly measuring the polarization of a photon between two strong polarization measurements, we experimentally investigate the correlation between the appearance of anomalous values in quantum weak measurements and the violation of realism and nonintrusiveness of measurements. A quantitative formulation of the latter concept is expressed in terms of a Leggett–Garg inequality for the outcomes of subsequent measurements of an individual quantum system. We experimentally violate the Leggett–Garg inequality for several measurement strengths. Furthermore, we experimentally demonstrate that there is a one-to-one correlation between achieving strange weak values and violating the Leggett–Garg inequality.
Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution
Authors: Fujii Sota , Bond Charles S. , Small Ian D.
Published: January 2011

Eukaryotic cells have harbored mitochondria for at least 1.5 billion years in an apparently mutually beneficial symbiosis. Studies on the agronomically important crop trait cytoplasmic male sterility (CMS) have suggested the semblance of a host–parasite relationship between the nuclear and mitochondrial genomes, but molecular evidence for this is lacking. Key players in CMS systems are the fertility restorer (
Rf
) genes required for the development of a functional male gametophyte in plants carrying a mitochondrial CMS gene. In the majority of cases,
Rf
genes encode pentatricopeptide repeat (PPR) proteins. We show that most angiosperms for which extensive genomic sequence data exist contain multiple PPR genes related to
Rf
genes. These
Rf
-like genes show a number of characteristic features compared with other PPR genes, including chromosomal clustering and unique patterns of evolution, notably high rates of nonsynonymous to synonymous substitutions, suggesting diversifying selection. The highest probabilities of diversifying selection were seen for amino acid residues 1, 3, and 6 within the PPR motif. PPR proteins are involved in RNA processing, and mapping the selection data to a predicted consensus structure of an array of PPR motifs suggests that these residues are likely to form base-specific contacts to the RNA ligand. We suggest that the selection patterns on
Rf
-like genes reveal a molecular “arms-race” between the nuclear and mitochondrial genomes that has persisted throughout most of the evolutionary history of angiosperms.
Spontaneous voice–face identity matching by rhesus monkeys for familiar conspecifics and humans
Authors: Sliwa Julia , Duhamel Jean-René , Pascalis Olivier , Wirth Sylvia
Published: January 2011

Recognition of a particular individual occurs when we reactivate links between current perceptual inputs and the previously formed representation of that person. This recognition can be achieved by identifying, separately or simultaneously, distinct elements such as the face, silhouette, or voice as belonging to one individual. In humans, those different cues are linked into one complex conceptual representation of individual identity. Here we tested whether rhesus macaques (Macaca mulatta) also have a cognitive representation of identity by evaluating whether they exhibit cross-modal individual recognition. Further, we assessed individual recognition of familiar conspecifics and familiar humans. In a free preferential looking time paradigm, we found that, for both species, monkeys spontaneously matched the faces of known individuals to their voices. This finding demonstrates that rhesus macaques possess a cross-modal cognitive representation of individuals that extends from conspecifics to humans, revealing the adaptive potential of identity recognition for individuals of socioecological relevance.
Nonheme oxo-iron(IV) intermediates form an oxyl radical upon approaching the C–H bond activation transition state
Authors: Ye Shengfa , Neese Frank
Published: January 2011

Oxo-iron(IV) species are implicated as key intermediates in the catalytic cycles of heme and nonheme oxygen activating iron enzymes that selectively functionalize aliphatic C–H bonds. Ferryl complexes can exist in either quintet or triplet ground states. Density functional theory calculations predict that the quintet oxo-iron(IV) species is more reactive toward C–H bond activation than its corresponding triplet partner, however; the available experimental data on model complexes suggests that both spin multiplicities display comparable reactivities. To clarify this ambiguity, a detailed electronic structure analysis of alkane hydroxylation by an oxo-iron(IV) species on different spin-state potential energy surfaces is performed. According to our results, the lengthening of the Fe–oxo bond in ferryl reactants, which is the part of the reaction coordinate for H-atom abstraction, leads to the formation of oxyl-iron(III) species that then perform actual C–H bond activation. The differential reactivity stems from the fact that the two spin states have different requirements for the optimal angle at which the substrate should approach the (FeO)
2+
core because distinct electron acceptor orbitals are employed on the two surfaces. The H-atom abstraction on the quintet surface favors the “σ-pathway” that requires an essentially linear attack; by contrast a “π-channel” is operative on the triplet surface that leads to an ideal attack angle near 90°. However, the latter is not possible due to steric crowding; thus, the attenuated orbital interaction and the unavoidably increased Pauli repulsion result in the lower reactivity of the triplet oxo-iron(IV) complexes.
Widespread crown condition decline, food web disruption, and amplified tree mortality with increased climate change-type drought
Authors: Carnicer Jofre , Coll Marta , Ninyerola Miquel , Pons Xavier , Sánchez Gerardo , Peñuelas Josep
Published: January 2011

Climate change is progressively increasing severe drought events in the Northern Hemisphere, causing regional tree die-off events and contributing to the global reduction of the carbon sink efficiency of forests. There is a critical lack of integrated community-wide assessments of drought-induced responses in forests at the macroecological scale, including defoliation, mortality, and food web responses. Here we report a generalized increase in crown defoliation in southern European forests occurring during 1987–2007. Forest tree species have consistently and significantly altered their crown leaf structures, with increased percentages of defoliation in the drier parts of their distributions in response to increased water deficit. We assessed the demographic responses of trees associated with increased defoliation in southern European forests, specifically in the Iberian Peninsula region. We found that defoliation trends are paralleled by significant increases in tree mortality rates in drier areas that are related to tree density and temperature effects. Furthermore, we show that severe drought impacts are associated with sudden changes in insect and fungal defoliation dynamics, creating long-term disruptive effects of drought on food webs. Our results reveal a complex geographical mosaic of species-specific responses to climate change–driven drought pressures on the Iberian Peninsula, with an overwhelmingly predominant trend toward increased drought damage.
Pack-
Mutator
–like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition
Authors: Jiang Ning , Ferguson Ann A. , Slotkin R. Keith , Lisch Damon
Published: January 2011

In monocots, many genes demonstrate a significant negative GC gradient, meaning that the GC content declines along the orientation of transcription. Such a gradient is not observed in the genes of the dicot plant
Arabidopsis
. In addition, a lack of homology is often observed when comparing the 5′ end of the coding region of orthologous genes in rice and
Arabidopsis
. The reasons for these differences have been enigmatic. The presence of GC-rich sequences at the 5′ end of genes may influence the conformation of chromatin, the expression level of genes, as well as the recombination rate. Here we show that Pack-
Mutator
–like transposable elements (Pack-MULEs) that carry gene fragments specifically acquire GC-rich fragments and preferentially insert into the 5′ end of genes. The resulting Pack-MULEs form independent, GC-rich transcripts with a negative GC gradient. Alternatively, the Pack-MULEs evolve into additional exons at the 5′ end of existing genes, thus altering the GC content in those regions. We demonstrate that Pack-MULEs modify the 5′ end of genes and are at least partially responsible for the negative GC gradient of genes in grasses. Such a unique and global impact on gene composition and gene structure has not been observed for any other transposable elements.
Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors
Authors: Kim Keunhwa , Shin Jieun , Lee Sang-Hee , Kweon Hee-Seok , Maloof Julin N. , Choi Giltsu
Published: January 2011

Phytochromes are red and far-red light photoreceptors that regulate various aspects of plant development. One of the less-understood roles of phytochromes is the inhibition of hypocotyl negative gravitropism, which refers to the loss of hypocotyl gravitropism and resulting random growth direction in red or far-red light. This light response allows seedlings to curve toward blue light after emergence from the soil and enhances seedling establishment in the presence of mulch. Phytochromes inhibit hypocotyl negative gravitropism by inhibiting four phytochrome-interacting factors (PIF1, PIF3, PIF4, PIF5), as shown by hypocotyl agravitropism of dark-grown
pif1 pif3 pif4 pif5
quadruple mutants. We show that phytochromes inhibit negative gravitropism by converting starch-filled gravity-sensing endodermal amyloplasts to other plastids with chloroplastic or etioplastic features in red or far-red light, whereas PIFs promote negative gravitropism by inhibiting the conversion of endodermal amyloplasts to etioplasts in the dark. By analyzing transgenic plants expressing
PIF1
with an endodermis-specific
SCARECROW
promoter, we further show that endodermal
PIF1
is sufficient to inhibit the conversion of endodermal amyloplasts to etioplasts and hypocotyl negative gravitropism of the
pif
quadruple mutant in the dark. Although the functions of phytochromes in gravitropism and chloroplast development are normally considered distinct, our results indicate that these two functions are closely related.
Chromosomal amplification of leucine-rich repeat kinase-2 (LRRK2) is required for oncogenic MET signaling in papillary renal and thyroid carcinomas
Authors: Looyenga Brendan D. , Furge Kyle A. , Dykema Karl J. , Koeman Julie , Swiatek Pamela J. , Giordano Thomas J. , West Andrew B. , Resau James H. , Teh Bin T. , MacKeigan Jeffrey P.
Published: January 2011

The receptor tyrosine kinase MET is frequently amplified in human tumors, resulting in high cell surface densities and constitutive activation even in the absence of growth factor stimulation by its endogenous ligand, hepatocyte growth factor (HGF). We sought to identify mechanisms of signaling crosstalk that promote MET activation by searching for kinases that are coordinately dysregulated with wild-type MET in human tumors. Our bioinformatic analysis identified leucine-rich repeat kinase-2 (
LRRK2
), which is amplified and overexpressed in papillary renal and thyroid carcinomas. Down-regulation of LRRK2 in cultured tumor cells compromises MET activation and selectively reduces downstream MET signaling to mTOR and STAT3. Loss of these critical mitogenic pathways induces cell cycle arrest and cell death due to loss of ATP production, indicating that MET and LRRK2 cooperate to promote efficient tumor cell growth and survival in these cancers.
Structural basis for the nucleotide-dependent dimerization of the large G protein atlastin-1/SPG3A
Authors: Byrnes Laura J. , Sondermann Holger
Published: January 2011

The large GTPase atlastin belongs to the dynamin superfamily that has been widely implicated in facilitating membrane tubulation, fission, and in select cases, fusion. Mutations spread across atlastin isoform 1 (atlastin-1) have been identified in patients suffering from hereditary spastic paraplegia (HSP), a neurodegenerative disorder affecting motor neuron function in the lower extremities. On a molecular level, atlastin-1 associates with high membrane curvature and fusion events at the endoplasmic reticulum and
cis
-Golgi. Here we report crystal structures of atlastin-1 comprising the G and middle domains in two different conformations. Although the orientation of the middle domain relative to the G domain is different in the two structures, both reveal dimeric assemblies with a common, GDP-bound G domain dimer. In contrast, dimer formation in solution is observed only in the presence of GTP and transition state analogs, similar to other G proteins that are activated by nucleotide-dependent dimerization. Analyses of solution scattering data suggest that upon nucleotide binding, the protein adopts a somewhat extended, dimeric conformation that is reminiscent of one of the two crystal structures. These structural studies suggest a model for nucleotide-dependent regulation of atlastin with implications for membrane fusion. This mechanism is affected in several mutants associated with HSP, providing insights into disease pathogenesis.
Mating behavior and the evolution of sperm design
Authors: Schärer Lukas , Littlewood D. Timothy J. , Waeschenbach Andrea , Yoshida Wataru , Vizoso Dita B.
Published: January 2011

Sperm are the most diverse of all animal cell types, and much of the diversity in sperm design is thought to reflect adaptations to the highly variable conditions under which sperm function and compete to achieve fertilization. Recent work has shown that these conditions often evolve rapidly as a consequence of multiple mating, suggesting a role for sexual selection and sexual conflict in the evolution of sperm design. However, very little of the striking diversity in sperm design is understood functionally, particularly in internally fertilizing organisms. We use phylogenetic comparative analyses covering 16 species of the hermaphroditic flatworm genus
Macrostomum
to show that a complex sperm design is associated with reciprocal mating and that this complexity is lost secondarily when hypodermic insemination—sperm injection through the epidermis—evolves. Specifically, the complex sperm design, which includes stiff lateral bristles, is likely a male persistence trait associated with sexual conflicts over the fate of received ejaculates and linked to female resistance traits, namely an intriguing postcopulatory sucking behavior and a thickened epithelium of the sperm-receiving organ. Our results suggest that the interactions between sperm donor, sperm, and sperm recipient can change drastically when hypodermic insemination evolves, involving convergent evolution of a needle-like copulatory organ, a simpler sperm design, and a simpler female genital morphology. Our study documents that a shift in the mating behavior may alter fundamentally the conditions under which sperm compete and thereby lead to a drastic change in sperm design.
Detection of a ternary complex of NF-κB and IκBα with DNA provides insights into how IκBα removes NF-κB from transcription sites
Authors: Sue Shih-Che , Alverdi Vera , Komives Elizabeth A. , Dyson H. Jane
Published: January 2011

It has been axiomatic in the field of NF-κB signaling that the formation of a stable complex between NF-κB and the ankyrin repeat protein IκBα precludes the interaction of NF-κB with DNA. Contradicting this assumption, we present stopped-flow fluorescence and NMR experiments that give unequivocal evidence for the presence of a ternary DNA–NF-κB–IκBα complex in solution. Stepwise addition of a DNA fragment containing the κB binding sequence to the IκBα–NF-κB complex results in changes in the IκBα NMR spectrum that are consistent with dissociation of the region rich in proline, glutamate, serine, and threonine (PEST) and C-terminal ankyrin repeat sequences of IκBα from the complex. However, even at high concentrations of DNA, IκBα remains associated with NF-κB, indicated by the absence of resonances of the free N-terminal ankyrin repeats of IκBα. The IκBα-mediated release of NF-κB from its DNA-bound state may be envisioned as the reverse of this process. The initial step would consist of the coupled folding and binding of the intrinsically disordered nuclear localization sequence of the p65 subunit of NF-κB to the well-structured N-terminal ankyrin repeats of IκBα. Subsequently the poorly folded C-terminal ankyrin repeats of IκBα would fold upon binding to the p50 and p65 dimerization domains of NF-κB, permitting the negatively charged C-terminal PEST sequence of IκBα to displace the bound DNA through a process of local mass action.
Vibrio vulnificus rtxA1
gene recombination generates toxin variants with altered potency during intestinal infection
Authors: Kwak Jayme S. , Jeong Hee-Gon , Satchell Karla J. F.
Published: January 2011

Vibrio vulnificus
is a food-borne bacterial pathogen associated with 1% of all food-related deaths, predominantly because of consumption of contaminated seafood. The ability of
V. vulnificus
to cause disease is linked to the production of a large cytotoxin called the “multifunctional-autoprocessing RTX” (MARTX
Vv
) toxin, a factor shown here to be an important virulence factor by the intragastric route of infection in mice. In this study, we examined genetic variation of the
rtxA1
gene that encodes MARTX
Vv
in 40
V. vulnificus
Biotype 1 strains and found four distinct variants of
rtxA1
that encode toxins with different arrangements of effector domains. We provide evidence that these variants arose by recombination either with
rtxA
genes carried on plasmids or with the
rtxA
gene of
Vibrio anguillarum
. Contrary to expected results, the most common
rtxA1
gene variant in clinical-type
V. vulnificus
encodes a toxin with reduced potency and is distinct from the toxin produced by strains isolated from market oysters. These results indicate that an important virulence factor of
V. vulnificus
is undergoing significant genetic rearrangement and may be subject to selection for reduced virulence in the environment. This finding would imply further that in the future on-going genetic variation of the MARTX
Vv
toxins could result in the emergence of novel strains with altered virulence in humans.
Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping
Authors: Cheng Lingpeng , Sun Jingchen , Zhang Kai , Mou Zongjun , Huang Xiaoxing , Ji Gang , Sun Fei , Zhang Jingqiang , Zhu Ping
Published: January 2011

The cytoplasmic polyhedrosis virus (CPV) from the family
Reoviridae
belongs to a subgroup of “turreted” reoviruses, in which the mRNA capping activity occurs in a pentameric turret. We report a full atomic model of CPV built from a 3D density map obtained using cryoelectron microscopy. The image data for the 3D reconstruction were acquired exclusively from a CCD camera. Our structure shows that the enzymatic domains of the pentameric turret of CPV are topologically conserved and that there are five unique channels connecting the guanylyltransferase and methyltransferase regions. This structural organization reveals how the channels guide nascent mRNA sequentially to guanylyltransferase, 7-N-methyltransferase, and 2′-O-methyltransferase in the turret, undergoing the highly coordinated mRNA capping activity. Furthermore, by fitting the deduced amino acid sequence of the protein VP5 to 120 large protrusion proteins on the CPV capsid shell, we confirmed that this protrusion protein is encoded by CPV RNA segment 7.
Inositol polyphosphate multikinase is a physiologic PI3-kinase that activates Akt/PKB
Authors: Maag David , Maxwell Micah J. , Hardesty Douglas A. , Boucher Katie L. , Choudhari Namrata , Hanno Adam G. , Ma Jenny F. , Snowman Adele S. , Pietropaoli Joseph W. , Xu Risheng , Storm Phillip B. , Saiardi Adolfo , Snyder Solomon H. , Resnick Adam C.
Published: January 2011

The second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP
3
), formed by the p110 family of PI3-kinases, promotes cellular growth, proliferation, and survival, in large part by activating the protein kinase Akt/PKB. We show that inositol polyphosphate multikinase (IPMK) physiologically generates PIP
3
as well as water soluble inositol phosphates. IPMK deletion reduces growth factor-elicited Akt signaling and cell proliferation caused uniquely by loss of its PI3-kinase activity. Inhibition of p110 PI3-kinases by wortmannin prevents IPMK phosphorylation and activation. Thus, growth factor stimulation of Akt signaling involves PIP
3
generation through the sequential activations of the p110 PI3-kinases and IPMK. As inositol phosphates inhibit Akt signaling, IPMK appears to act as a molecular switch, inhibiting or stimulating Akt via its inositol phosphate kinase or PI3-kinase activities, respectively. Drugs regulating IPMK may have therapeutic relevance in influencing cell proliferation.
WNK1 is required for mitosis and abscission
Authors: Tu Szu-wei , Bugde Abhijit , Luby-Phelps Katherine , Cobb Melanie H.
Published: January 2011

WNK [with no lysine (K)] protein kinases are found in all sequenced multicellular and many unicellular organisms. WNKs influence ion balance. Two WNK family members are associated with a single gene form of hypertension. RNA interference screens have implicated WNKs in survival and growth, and WNK1 is essential for viability of mice. We found that the majority of WNK1 is localized on cytoplasmic puncta in resting cells. During cell division, WNK1 localizes to mitotic spindles. Therefore, we analyzed mitotic phenotypes in WNK1 knockdown cells. A large percentage of WNK1 knockdown cells fail to complete cell division, displaying defects in mitotic spindles and also in abscission and cell survival. One of the best-characterized WNK1 targets is the protein kinase OSR1 (oxidative stress responsive 1). OSR1 regulates ion cotransporters, is activated in response to osmotic stress by WNK family members, and is largely associated with WNK1. In resting cells, the majority of OSR1, like WNK1, is on cytoplasmic puncta. OSR1 is also in nuclei. In contrast to WNK1, however, OSR1 does not concentrate around spindles during mitosis and does not show a WNK1-like localization pattern in mitotic cells. Knockdown of OSR1 has only a modest effect on cell survival and does not lead to spindle defects. We conclude that decreased cell survival associated with loss of WNK1 is attributable to defects in chromosome segregation and abscission and is independent of the effector kinase OSR1.
Late Pleistocene adult mortality patterns and modern human establishment
Authors: Trinkaus Erik
Published: January 2011

The establishment of modern humans in the Late Pleistocene, subsequent to their emergence in eastern Africa, is likely to have involved substantial population increases, during their initial dispersal across southern Asia and their subsequent expansions throughout Africa and into more northern Eurasia. An assessment of younger (20–40 y) versus older (>40 y) adult mortality distributions for late archaic humans (principally Neandertals) and two samples of early modern humans (Middle Paleolithic and earlier Upper Paleolithic) provides little difference across the samples. All three Late Pleistocene samples have a dearth of older individuals compared with Holocene ethnographic/historical samples. They also lack older adults compared with Holocene paleodemographic profiles that have been critiqued for having too few older individuals for subsistence, social, and demographic viability. Although biased, probably through a combination of preservation, age assessment, and especially Pleistocene mobility requirements, these adult mortality distributions suggest low life expectancy and demographic instability across these Late Pleistocene human groups. They indicate only subtle and paleontologically invisible changes in human paleodemographics with the establishment of modern humans; they provide no support for a life history advantage among early modern humans.
Local microbleeding facilitates IL-6– and IL-17–dependent arthritis in the absence of tissue antigen recognition by activated T cells
Authors: Murakami Masaaki , Okuyama Yuko , Ogura Hideki , Asano Shogo , Arima Yasunobu , Tsuruoka Mineko , Harada Masaya , Kanamoto Minoru , Sawa Yukihisa , Iwakura Yoichiro , Takatsu Kiyoshi , Kamimura Daisuke , Hirano Toshio
Published: January 2011

Cognate antigen recognition by CD4+ T cells is thought to contribute to the tissue specificity of various autoimmune diseases, particularly those associated with class II MHC alleles. However, we show that localized class II MHC–dependent arthritis in F759 mice depends on local events that result in the accumulation of activated CD4+ T cells in the absence of cognate antigen recognition. In this model, transfer of in vitro polarized Th17 cells combined with the induction of experimental microbleeding resulted in CCL20 production, the accumulation of T cells in the joints, and local production of IL-6. Disease induction required IL-17A production by transferred T cells, IL-6 and CCL20 expression, and STAT3 signaling in type I collagen–expressing cells. Our data suggest a model in which the development of autoimmune disease in F759 mice depends on four events: CD4+ T cell activation regardless of antigen specificity, local events that induce T cell accumulation, enhanced sensitivity to T cell–derived cytokines in the tissue, and activation of IL-6 signaling in the tissue. This model provides a possible explanation for why tissue-specific antigens recognized by activated CD4+ T cells have not been identified in many autoimmune diseases, especially those associated with class II MHC molecules.
Human B1 cells in umbilical cord and adult peripheral blood express the novel phenotype CD20+CD27+CD43+CD70−
Authors: Griffin Daniel O. , Holodick Nichol E. , Rothstein Thomas L.
Published: January 2011

B1 cells differ in many ways from conventional B cells, most prominently in the production of natural immunoglobulin, which is vitally important for protection against pathogens. B1 cells have also been implicated in the pathogenesis of autoimmune dyscrasias and malignant diseases. It has been impossible to accurately study B1 cells during health and illness because the nature of human B1 cells has not been successfully defined. This has produced controversy regarding the existence of human B1 cells. Here, we determined the phenotype of human B1 cells by testing sort-purified B cell fractions for three fundamental B1 cell functions based on mouse studies: spontaneous IgM secretion, efficient T cell stimulation, and tonic intracellular signaling. We found that a small population of CD20+CD27+CD43+ cells present in both umbilical cord and adult peripheral blood fulfilled these criteria and expressed a skewed B cell receptor repertoire. These B cells express little or no surface CD69 and CD70, both of which are markedly up-regulated after activation of CD20+CD27−CD43− (naive) and CD20+CD27+CD43− (memory) B cells. This work identifies human B1 cells as CD20+CD27+CD43+CD70−. We determined that the proportion of B1 cells declines with age, which may contribute to disease susceptibility. Identification of human B1 cells provides a foundation for future studies on the nature and role of these cells in human disease.