bluuebunny/crossref_metadata_2025 huggingface dataset:
Wave coupling in sheet- and multiple-beam traveling-wave tubes
Authors: Nusinovich Gregory S. , Cooke Simon J. , Botton Moti , Levush Baruch
Published: June 2009

To increase the power level of the sources of coherent electromagnetic radiation at frequencies from 100 GHz up to the terahertz range it makes sense to develop devices with a spatially extended interaction space. Sheet-beam and multiple-beam devices belong to the category. In the present paper the small-signal theory of traveling-wave tubes with sheet-beam and multiple sheet-beam configurations is developed. It is shown that in such tubes the wave coupling on electron beams may occur even in small-signal regimes. The wave coupling and its role for amplification of forward and excitation of backward waves in such amplifiers is studied. Also the effect of transverse nonuniformity of the electromagnetic field on the device operation is analyzed and illustrated by several examples.
A spin-wave frequency doubler by domain wall oscillation
Authors: Hermsdoerfer Sebastian J. , Schultheiss Helmut , Rausch Christopher , Schäfer Sebastian , Leven Britta , Kim Sang-Koog , Hillebrands Burkard
Published: June 2009

We present a mechanism for spin-wave excitation using a pinned domain wall, which is forced to oscillate at its eigenfrequency and radiates spin waves. The domain wall acts as a frequency doubler as the excited spin waves have twice the frequency of the domain wall oscillation. The investigations have been carried out using micromagnetic simulations and enable the determination of the main characteristics of the excited spin waves such as frequency, wavelength, and velocity. This behavior is understood by the oscillation in the perpendicular magnetization, which shows two antinodes oscillating out of phase with respect to each other.
Stability of supercooled binary liquid mixtures
Authors: Toxvaerd Søren , Pedersen Ulf R. , Schrøder Thomas B. , Dyre Jeppe C.
Published: June 2009

Recently, the supercooled Wahnström binary Lennard-Jones mixture was partially crystallized into MgZn2 phase crystals in lengthy molecular dynamics simulations. We present molecular dynamics simulations of a modified Kob–Andersen binary Lennard-Jones mixture that also crystallizes in lengthy simulations here, however, by forming pure fcc crystals of the majority component. The two findings motivate this paper that gives a general thermodynamic and kinetic treatment of the stability of supercooled binary mixtures, emphasizing the importance of negative mixing enthalpy whenever present. The theory is used to estimate the crystallization time in a Kob–Andersen mixture from the crystallization time in a series of related systems. At T=0.40 we estimate this time to be 5×107 time units (≈0.1 ms). A new binary Lennard-Jones mixture is proposed that is not prone to crystallization and faster to simulate than the two standard binary Lennard-Jones mixtures. This is obtained by removing the like-particle attractions by switching to Weeks–Chandler–Andersen type potentials, while maintaining the unlike-particle attraction.
In-plane electric field induced by polarization and lateral photovoltaic effect in a-plane GaN
Authors: Hu Weiguo , Ma Bei , Li Dabing , Miyake Hideto , Hiramatsu Kazumasa
Published: June 2009

A lateral photovoltaic effect was observed in a-plane GaN films grown on r-plane sapphire at room temperature. Under various light sources illuminations, contacts along the c-axis exhibited about ten times the photovoltage than those along the m-axis, which kept linear relationship with the illumination intensity. It was attributed to anisotropic in-plane electrical field induced by the intrinsic spontaneous/piezoelectric polarization, which spatially separated photogenerated carriers to produce the photovoltage.
Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol
Authors: Velez-Vega Camilo , Borrero Ernesto E. , Escobedo Fernando A.
Published: June 2009

Forward flux sampling (FFS) simulations were used to study the kinetics of alanine dipeptide both in vacuum and in explicit solvent. The recently proposed FFS least-squares estimation approach and an algorithm that optimizes the position of the interfaces were implemented to determine a reaction coordinate that adequately describes the transition dynamics. A new method is also introduced to try to ensure that the ensemble of “starting points” (for the trial trajectories) is properly sampled. The rate constant estimates for the C7eq⇒C5 transition of alanine dipeptide in vacuum were used to demonstrate the consistency between Monte Carlo and molecular dynamics (MD) simulations. FFS-MD simulations were then performed for the study of the β2/αR⇒C5/C7eq transition in explicit solvent. The kinetic results for both systems in vacuum and explicit solvent are in general agreement with previous experimental and computational studies for this peptide. In vacuum, an additional dihedral angle besides the one typically used as order parameter is identified as a significant variable in the reaction coordinate model. In solution, several dihedral angles and variables that describe the solvent action on the molecule’s dynamics are found to play a significant role in the description of the system’s dynamics.
Structural growth behavior and polarizability of CdnTen (n=1–14) clusters
Authors: Wang Jianguang , Ma Li , Zhao Jijun , Jackson Koblar Alan
Published: June 2009

The lowest-energy structures of CdnTen (n=1–14) clusters have been studied by an unbiased simulated annealing search using first-principles molecular dynamics along with local optimization of “handmade” structures using density functional theory. After n≥6, three-dimensional cage geometries are the lowest-energy configurations. Two families of low-lying structures, hollow cages, and endohedral or core-shell cages are found. The endohedral cages begin to appear from n=10, and they become more energetically preferred than the hollow cages for n≥12. Cd13Te13 with the core-shell cage structure is particularly stable. At the same size, the hollow cages possess smaller dipole moments and larger polarizabilities than the endohedral ones. The polarizabilities for the three-dimensional cage structures are insensitive to cluster size. The anisotropies in the polarizabilities mirror the anisotropies in cluster shapes.
A Mach number study of the Richtmyer–Meshkov instability in a varicose, heavy-gas curtain
Authors: Orlicz G. C. , Balakumar B. J. , Tomkins C. D. , Prestridge K. P.
Published: June 2009

A varicose-perturbed, thin, heavy-gas curtain is impulsively accelerated by a planar shock wave of varying strength and investigated experimentally using concentration field visualization. Experiments were performed with Mach 1.2 and 1.5 incident shock waves, acquiring images of the initial conditions, and 18 different times after shock interaction in each case. Repeatability of the initial conditions allows for visualization of flow feature development over time for both Mach numbers despite capturing only one dynamic, postshock image per run of the experiment. Good agreement between integral width experimental data and a mixing width model is demonstrated for early to intermediate times in the flow. Integral width growth rates for Mach 1.2 and 1.5 are shown to collapse using a scaling based upon the convection velocity of the curtain. The diffusion driven instantaneous mixing rate, χ, is also estimated and compared between experiments. Results from this gradient based metric show differences in mixing trends between Mach numbers that do not scale in the same way as integral width, suggesting that integral width alone is insufficient for completely describing the flow. An experiment with a Mach 2.0 incident shock was carried out for the first time in the experimental facility. The resulting image provides further evidence for the mixing trends observed in this paper as Mach number is increased.
Large-scale lognormal fluctuations in turbulence velocity fields
Authors: Mouri Hideaki , Hori Akihiro , Takaoka Masanori
Published: June 2009

For several flows of laboratory turbulence, we obtain long records of velocity data. These records are divided into numerous segments. In each segment, we calculate the mean rate of energy dissipation, the mean energy at each scale, and the mean total energy. Their values fluctuate significantly among the segments. The fluctuations are lognormal, if the segment length lies within the range of large scales where the velocity correlations are weak but not yet absent. Since the lognormality is observed regardless of the Reynolds number and the configuration for turbulence production, it is expected to be universal. The likely origin is some multiplicative stochastic process related to interactions among scales through the energy transfer.
Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation
Authors: Niklasson Anders M. N. , Steneteg Peter , Odell Anders , Bock Nicolas , Challacombe Matt , Tymczak C. J. , Holmström Erik , Zheng Guishan , Weber Valery
Published: June 2009

Stability and dissipation in the propagation of the electronic degrees of freedom in time-reversible extended Lagrangian Born–Oppenheimer molecular dynamics [Niklasson et al., Phys. Rev. Lett. 97, 123001 (2006); Phys. Rev. Lett. 100, 123004 (2008)] are analyzed. Because of the time-reversible propagation the dynamics of the extended electronic degrees of freedom is lossless with no dissipation of numerical errors. For long simulation times under “noisy” conditions, numerical errors may therefore accumulate to large fluctuations. We solve this problem by including a dissipative external electronic force that removes noise while keeping the energy stable. The approach corresponds to a Langevin-like dynamics for the electronic degrees of freedom with internal numerical error fluctuations and external, approximately energy conserving, dissipative forces. By tuning the dissipation to balance the numerical fluctuations the external perturbation can be kept to a minimum.
Phase and strain distributions associated with reactive contaminants inside of a solid oxide fuel cell
Authors: Liu Di-Jia , Almer Jonathan
Published: June 2009

A microfocused synchrotron x-ray diffraction method was used to reveal the quantitative distributions of phase fractions, internal strains, and their interdependences at different layer depths inside of a planar solid oxide fuel cell, which was deactivated by chromium contamination through direct contact with the metallic interconnect under typical operating conditions. These observations provide insight into the mechanism of Cr poisoning. The method can serve as a versatile tool for studying the electrochemical devices with thin-layered construction such as batteries and fuel cells under static or in situ conditions.
Modulation doping in ZnO nanorods for electrical nanodevice applications
Authors: Yoo Jinkyoung , Lee Chul-Ho , Doh Yong-Joo , Jung Hye Seong , Yi Gyu-Chul
Published: June 2009

We introduce a modulation-doping method to control electrical characteristics of ZnO nanorods. Compared with a conventional homogeneous doping method, the modulation-doping method generates localized doping layers along the circumference in ZnO nanorods, useful for many device applications. Here, we investigated electrical, structural, and optical characteristics of Ga-doped ZnO nanorods with the dopant modulation layers. Electrical conductivity of ZnO nanorods was controlled by changing either dopant mole fraction or the number of modulation-doped layers. Furthermore, the modulation-doped nanorod field effect transistors exhibited precisely controlled conductance in the order of magnitude without degradation of electron mobility. The effects of the doping on structural and optical characteristics of the nanorods are also discussed.
Vapor-liquid critical and interfacial properties of square-well fluids in slit pores
Authors: Jana Subimal , Singh Jayant K. , Kwak Sang Kyu
Published: June 2009

Vapor-liquid phase equilibria of square-well (SW) fluids of variable interaction range: λσ=1.25, 1.75, 2.0, and 3.0 in hard slit pores are studied by means of grand-canonical transition-matrix Monte Carlo (GC-TMMC) simulation. Critical density under confinement shows an oscillatory behavior as slit width, H, reduced from 12σ to 1σ. Two linear regimes are found for the shift in the critical temperature with the inverse in the slit width. The first regime is seen for H>2.0σ with linear increase in the slope of shift in the critical temperature against inverse slit width with increasing interaction range. Subsequent decrease in H has little consequence on the critical temperature and it remains almost constant. Vapor-liquid surface tensions of SW fluids of variable well extent in a planar slit pore of variable slit width are also reported. GC-TMMC results are compared with that from slab based canonical Monte Carlo and molecular dynamics techniques and found to be in good agreement. Although, vapor-liquid surface tension under confinement is found to be lower than the bulk surface tension, the behavior of surface tension as a function of temperature is invariant with the variable pore size. Interfacial width, ξ, calculated using a hyperbolic function increases with decreasing slit width at a given temperature, which is contrary to what is being observed recently for cylindrical pores. Inverse scaled interfacial width (ξ/H), however, linearly increases with increase in the scaled temperature (Tc,bulk−T)/Tc,bulk.
Solvent-mediated interactions between nanoparticles at fluid interfaces
Authors: Bresme Fernando , Lehle Hartwig , Oettel Martin
Published: June 2009

We investigate the solvent-mediated interactions between nanoparticles adsorbed at a liquid-vapor interface in comparison to the solvent-mediated interactions in the bulk liquid and vapor phases of a Lennard–Jones solvent. Molecular dynamics simulation data for the latter are in good agreement with results from integral equations in the reference functional approximation and a simple geometric approximation. Simulation results for the solvent-mediated interactions at the interface differ markedly from the interactions of the particles in the corresponding bulk phases. We find that at short interparticle distances, the interactions are considerably more repulsive than those in either bulk phase. At long interparticle distances we find evidence for a long-ranged attraction. We discuss these observations in terms of interfacial interactions, namely, the three-phase line tension that would operate at short distances and capillary wave interactions for longer interparticle distances.
Planar superconductor/ferromagnet hybrids: Anisotropy of resistivity induced by magnetic templates
Authors: Aladyshkin A. Yu. , Fritzsche J. , Moshchalkov V. V.
Published: June 2009

We investigated experimentally the transport properties of a superconducting cross-shaped aluminum microbridge fabricated on top of a ferromagnetic BaFe12O19 single crystal. It was demonstrated that a one-dimensional domain structure in the ferromagnetic substrate can induce the formation of superconducting channels above magnetic domains. This leads to a giant anisotropy of resistivity of the superconducting bridge, caused by the appearance of continuous paths of supercurrents flowing along domain walls.
Effect of 16-mercaptohexadecanoic acid modification on liquid transport in a nanoporous carbon
Authors: Lu Weiyi , Han Aijie , Kim Taewan , Qiao Yu
Published: June 2009

The inner surfaces of a nanoporous carbon are modified by 16-mercaptohexadecanioic acid. The degree of wettability is electrically controllable: by applying a negative potential difference across the solid-liquid interface, the ion transport pressure in the nanopores can be considerably lowered; while the effect of applying a positive potential difference is negligible. These phenomena can be attributed to the unique surface chain configuration in the confining nanoenvironment.
High-resolution surface plasmon coupled resonant filter for monitoring of fluorescence emission from molecular multiplexes
Authors: R Sai Sathish , Kostov Yordan , Rao Govind
Published: June 2009

Nanoscale photonic devices made of plasmonic structures can control the reflection, transmission, and polarization properties of the electromagnetic field to achieve high-spectral-resolution of light. Here we experimentally demonstrate the use of a real time plasmonic optical filter for photon sorting of fluorescence emission from nanoenvironments in a multispecies system. This was achieved by utilizing surface plasmon-coupled emission associated with nanometer thick metal films for the fluorescence spectral resolution of monomer, dimer, and higher order aggregates of Rhodamine-6G. We highlight the ability to resolve individual emissions from nanostructures in a complex system in its native state without requiring specialized cryogenic and/or high pressure platforms.
Large-scale molecular dynamics simulations of normal shock waves in dilute argon
Authors: Valentini Paolo , Schwartzentruber Thomas E.
Published: June 2009

Large-scale molecular dynamics (MD) simulations using the Lennard-Jones potential are performed to study the structure of normal shock waves in dilute argon. Nonperiodic boundary conditions in the flow direction are applied by coupling the MD domain with a two-dimensional finite-volume computational fluid dynamics (CFD) solver to correctly generate the inflow and outflow particle reservoirs. Detailed comparisons are made with direct simulation Monte Carlo (DSMC) solutions using the variable-hard-sphere (VHS) collision model. By performing realistic MD simulations of full shock waves, this article presents a more sensitive evaluation of the VHS model parameters (via temperature and velocity distribution functions) than is possible using available experimental density measurements. In the high temperature range (300–8000 K), where the Chapman–Enskog theory supports the VHS model assumptions, near-perfect agreement between MD and DSMC solutions is demonstrated and inverse shock thickness predictions reproduce experimental measurements. In the low temperature range (16–300 K), theory predicts and MD simulation confirms that the VHS collision model becomes less valid.
Epilayer control of photodeposited materials during UV photocatalysis
Authors: Takahashi R. , Katayama M. , Dahl Ø. , Grepstad J. K. , Matsumoto Y. , Tybell T.
Published: June 2009

Epilayer control of photoassisted oxidation and reduction on the ferroelectric PbTiO3 polar surface was investigated. Photo-oxidation of a AgNO3 electrolyte resulting in formation of Ag7NO11 particles was observed on the PbTiO3/Nb:SrTiO3 film surface; whereas PbTiO3/SrRuO3/SrTiO3 leads to AgNO3 reduction under UV illumination. The oxidation reaction resulting in the formation of Ag7NO11 is explained in terms of a rectifying interface between PbTiO3 and Nb:SrTiO3, controlling the charge transport during UV photocatalysis.
Electrical control of the exciton spin in nitride semiconductor quantum dots
Authors: Sénès Mathieu , Lagarde Delphine , Smith Katherine L. , Balocchi Andrea , Hooper Stewart E. , Amand Thierry , Heffernan Jonathan , Marie Xavier
Published: June 2009

We report on the experimental evidence of the manipulation of the exciton spin in InGaN quantum dots through the application of an external electric field up to room temperature. Furthermore, we have found the exciton spin relaxation to be independent of temperature. These findings are highly promising for the potential future use of nitride semiconductor quantum dots in practical spintronic devices.
Resonant transmission of light through surface plasmon structures
Authors: Gurel Kemal , Kaplan Burkan , Guner Hasan , Bayindir Mehmet , Dana Aykutlu
Published: June 2009

Plasmonics enables the realization of new optical components. Here, we report yet another plasmonic component based on a pair of surfaces displaying grating coupled plasmon enhanced transmission. We observe high quality factor transmission peaks as high as 100 through our plasmonic filter based on gratings obtained directly from optical storage disks. Wavelength and polarization dependent transmission is also demonstrated in the visible and infrared portions of the spectrum. The resonance wavelength of this filter can be tuned by simply changing the angle of incidence. Numerical calculations agree well with measurements. Our work can open up directions toward disposable optical components such as filters and polarizers.
Charge transport mechanism in amorphous alumina
Authors: Novikov Yu. N. , Gritsenko V. A. , Nasyrov K. A.
Published: June 2009

The charge transport mechanism in amorphous Al2O3 was examined both experimentally and theoretically. We have found that electrons are dominant charge carriers in Al2O3. A satisfactory agreement between the experimental and calculated data was obtained assuming the multiphonon ionization mechanism for deep traps in Al2O3. For the thermal and optical trap ionization energies in Al2O3, the values WT=1.5 eV and Wopt=3.0 eV were obtained.
Mapping cavity modes of ZnO nanobelts
Authors: Xu Xiulai , Brossard Frederic S. F. , Williams David A. , Collins Daniel P. , Holmes Mark J. , Taylor Robert A. , Zhang Xitian
Published: June 2009

ZnO nanostructures attract current interest because they have the potential to implement cavity quantum electrodynamics at room temperature. We report a photoluminescence mapping of ZnO nanobelts both at room temperature and 4.2 K. The multicavity modes were observed all over the belt surface, which were induced by Fabry–Pérot interference. The emission from the belt surface is enhanced at both the ends and the sides of the belt, and is highly linearly polarized in the direction perpendicular to the long axis of the belt. The results are explained using finite-difference time-domain simulations.
Atomic-scale structural evolution in amorphous Nd9Fe85B6 subjected to severe plastic deformation at room temperature
Authors: Li Wei , Li Xiaohong , Guo Defeng , Sato Kiminori , Gunderov Dmitry V. , Stolyarov Vladimir V. , Zhang Xiangyi
Published: June 2009

Understanding the deformation-induced nanocrystallization in amorphous alloys at room temperature is proved to be a great challenge. In the present study, the formation of vacancy-type defects richly surrounded with Fe atoms in amorphous Nd9Fe85B6 subjected to room-temperature high-pressure torsion deformation is directly evidenced by positron lifetime measurements combined with a coincident Doppler broadening measurement of the positron-electron annihilation photons. This demonstrates a direct experimental evidence for shear inducing the enrichment of Fe atoms in the deformed amorphous alloy. These results presented here are of importance for understanding the deformation-induced nanocrystallization and for the technique development of nanocrystalline materials.
Hydrogen diffusion in bulk and nanoclusters of MgH2 and the role of catalysts on the basis of ab initio molecular dynamics
Authors: Ramzan M. , Hussain T. , Ahuja R.
Published: June 2009

We present ab initio molecular dynamics calculations based on density functional theory to study the hydrogen-deuterium exchange in bulk and nanoclusters of MgH2. Our calculations reveal the important role of catalysts to diffuse the hydrogen at low temperatures and increase the diffusion rate. We determine the diffusion constants, ⟨D⟩ of deuterium, and show the single hydrogen-deuterium exchange in bulk and nanocluster of MgH2. Our calculated value of diffusion constant of deuterium in bulk MgH2 is in excellent agreement with the experimental value. Furthermore, we show the edge site importance of catalysts in the fast diffusion of hydrogen.
Coherent beam combination of two-dimensional high power fiber amplifier array using stochastic parallel gradient descent algorithm
Authors: Zhou Pu , Liu Zejin , Wang Xiaolin , Ma Yanxing , Ma Haotong , Xu Xiaojun
Published: June 2009

We demonstrate coherent beam combination of two-dimensional high power fiber amplifier array using stochastic parallel gradient descent (SPGD) algorithm. Four polarization-maintained fiber amplifiers are tiled side by side into a 2×2 laser array with a fill factor of 54% in the near-field. Phase control on the fiber amplifiers are performed by running SPGD algorithm on a digital dignal processor with updating rate of 50 000 Hz/channel. Coherent beam combination of the four fiber amplifiers with a total output power of 60.1 W using SPGD algorithm is demonstrated. Beam quality of the combined beam is computed to be BQ<1.4.
Low-threshold ablation of dielectrics irradiated by picosecond soft x-ray laser pulses
Authors: Faenov A. Ya. , Inogamov N. A. , Zhakhovskii V. V. , Khokhlov V. A. , Nishihara K. , Kato Y. , Tanaka M. , Pikuz T. A. , Kishimoto M. , Ishino M. , Nishikino M. , Nakamura T. , Fukuda Y. , Bulanov S. V. , Kawachi T.
Published: June 2009

Ablation of LiF crystal by soft x-ray laser (XRL) pulses with wavelength λ=13.9 nm and duration TL=7 ps is studied experimentally and theoretically. It is found that a crater appears on a surface of LiF for XRL fluence, exceeding the ablation threshold Fa∼10.2 mJ/cm2 in one shot, or 5 mJ/cm2 in each of the three XRL shots. This is substantially below the ablation thresholds obtained with other lasers having longer pulse duration and/or longer wavelength. A mechanism of thermomechanical ablation in large bandgap dielectrics is proposed. The theory explains the low Fa via small attenuation depth, absence of light reflection, and electron heat conductivity.
Doping selective lateral electrochemical etching of GaN for chemical lift-off
Authors: Park Joonmo , Song Kwang Min , Jeon Seong-Ran , Baek Jong Hyeob , Ryu Sang-Wan
Published: June 2009

An electrochemical etching based on oxalic acid was developed for use in the chemical lift-off of GaN epitaxial structures. It was shown that only the Si-doped n-GaN layer was etched away, while the p-type and undoped GaN layers were not etched at all. The etch rate and the remaining structure were analyzed for various doping concentrations and etching voltages. A lateral etch rate of 12 μm/min was achieved under 60 V for n-type doping concentration of 8×1018 cm−3. This doping selective etching was used to lift-off a GaN epitaxial layer patterned into 300×300 μm2 squares.
Recent Developments in Glycoside Synthesis with Glycosynthases and Thioglycoligases
Authors: Rakić Bojana , Withers Stephen G.
Published: June 2009

Glycosynthases are hydrolytically incompetent engineered glycosidases that catalyze the high-yielding synthesis of glycoconjugates from glycosyl fluoride donor substrates and appropriate acceptors. Glycosynthases from more than 10 glycoside hydrolase families have now been generated, allowing the synthesis of a wide range of oligosaccharides. Recent examples include glycosynthase-mediated syntheses of xylo-oligosaccharides, xyloglucans, glycolipids, and aryl glycosides. Glycosynthases have also now been generated from inverting glycosidases, increasing the range of enzyme scaffolds. Improvement of glycosynthase activity and broadening of specificity has been achieved through directed evolution approaches, and several novel high-throughput screens have been developed to allow this. Finally, metabolically stable glycoside analogues have been generated using another class of mutant glycosidases: thioglycoligases. Recent developments in all these aspects are discussed.
Early Eocene Ripogonum (Liliales: Ripogonaceae) leaf macrofossils from southern Australia
Authors: Conran John G. , Carpenter Raymond J. , Jordan Gregory J.
Published: June 2009

We present evidence that fossil leaves from an early Eocene estuarine mudstone deposit at Lowana Road in western Tasmania include the oldest records of the extant monocot genus, Ripogonum (Ripogonaceae). These fossils are similar to the extant eastern Australian and Papua New Guinean R. album R.Br. and New Zealand R. scandens J.R. et G.Forst., and are described as a new species, R. tasmanicum Conran, R.J.Carp. & G.J.Jord. The venation, cuticular and other leaf features of this fossil are included in a morphology-based phylogenetic analysis for the genus, and character evolution is discussed in relation to the ecology of the extant species and the palaeoenvironments of known Ripogonaceae fossil sites. The fossil (albeit on leaf characters) was placed close to the base of a black-fruited, Australian endemic Ripogonum clade. This suggests that the family have a long and conservative evolutionary history in association with moist forests, with the fossil locality showing palaeoclimate similar to the environments that most Ripogonum species still occupy today.
Tie2cre
-induced inactivation of the miRNA-processing enzyme Dicer disrupts invariant NKT cell development
Authors: Zhou Li , Seo Kook-Heon , He Hong-Zhi , Pacholczyk Rafal , Meng Dong-Mei , Li Chang-Gui , Xu Jianrui , She Jin-Xiong , Dong Zheng , Mi Qing-Sheng
Published: June 2009

MicroRNAs (miRNAs) are a class of evolutionarily conserved small noncoding RNAs that are increasingly being recognized as important regulators of gene expression. The ribonuclease III enzyme Dicer is essential for the processing of miRNAs. CD1d-restricted invariant natural killer T (
i
NKT) cells are potent regulators of diverse immune responses. The role of Dicer-generated miRNAs in the development and function of immune regulatory
i
NKT cells is unknown. Here, we generated a mouse strain with a tissue-specific disruption of Dicer, and showed that lack of miRNAs after the deletion of Dicer by Tie2-Cre (expressed in hematopoietic cells and endothelial cells) interrupted the development and maturation of
i
NKT cells in the thymus and significantly decreased the number of
i
NKT cells in different immune organs. Thymic and peripheral
i
NKT cell compartments were changed in miRNA-deficient mice, with a significantly increased frequency of CD4
+
CD8
+
i
NKT cells in the thymus and a significantly decreased frequency of CD4
+
i
NKT cells in the spleen. MiRNA-deficient
i
NKT cells display profound defects in α-GalCer-induced activation and cytokine production. Bone marrow (BM) from miRNA-deficient mice poorly reconstituted
i
NKT cells compared to BM from WT mice. Also, using a thymic iNKT cell transfer model, we found that
i
NKT cell homeostasis was impaired in miRNA-deficient recipient mice. Our data indicate that miRNAs expressed in hematopoietic cells and endothelial cells are potent regulators of
i
NKT cell development, function, and homeostasis.
JFK, a Kelch domain-containing F-box protein, links the SCF complex to p53 regulation
Authors: Sun Luyang , Shi Lei , Li Wenqian , Yu Wenhua , Liang Jing , Zhang Hua , Yang Xiaohan , Wang Yan , Li Ruifang , Yao Xingrong , Yi Xia , Shang Yongfeng
Published: June 2009

The p53 tumor suppressor plays a central role in integrating cellular responses to various stresses. Tight regulation of p53 is thus essential for the maintenance of genome integrity and normal cell proliferation. Currently, several ubiquitin ligases, including the single-subunit RING-finger types—MDM2, Pirh2, and COP1—and the HECT-domain type—ARF-BP1—have been reported to target p53 for degradation. Here, we report the identification of a human Kelch domain-containing F-box protein, JFK. We showed that JFK promotes ubiquitination and degradation of p53. But unlike MDM2, Pirh2, COP1, and ARF-BP1, all of which possess an intrinsic ubiquitin ligase activity, JFK destabilizes p53 through the assembly of a Skp1-Cul1-F-box complex. Significantly, JFK inhibits p53-dependent transcription, and depletion of JFK stabilizes p53, promotes cell apoptosis, arrests cells in the G
1
phase, and sensitizes cells to ionizing radiation-induced cell death. These data indicate that JFK is a critical negative regulator of p53 and represents a pathway for the maintenance of p53 levels in unstressed cells. Our experiments link the Skp1-Cul1-F-box system to p53 regulation.
Matthew Krummel: Visions enumerated
Authors: Maxmen Amy
Published: June 2009

By snapping shots in real time, Matthew “Max” Krummel catches inflammation in the act.
The Sequence Alignment/Map format and SAMtools
Authors: Li Heng , Handsaker Bob , Wysoker Alec , Fennell Tim , Ruan Jue , Homer Nils , Marth Gabor , Abecasis Goncalo , Durbin Richard ,   1000 Genome Project Data Processing Subgroup
Published: June 2009

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.

Availability:  http://samtools.sourceforge.net

Contact:  rd@sanger.ac.uk
Synthesis of Cellulase by Mucor pusillus and Mucor miehei
Authors: Somkuti G. A.
Published: June 2009

Strains of Mucor pusillus and M. miehei were found to synthesize β-1,4-glucan glucanohydrolase (cellulase) in a complex medium. The inducible enzyme complex hydrolysed carboxymethylcellulose, acid-swollen cellulose and unmodified cellulose.
Effect of Lactose on Soluble-glucan Production and on the Ultrastructure of Sclerotium rolfsii Sacc. Grown in Submerged Culture
Authors: Okon Y. , Chet I. , Kislev Naomi , Henis Y.
Published: June 2009

SUMMARY A significant increase in mycelial dry weight and a decrease in production of extracellular glucan were observed when lactose was added to a submerged culture of Sclerotium rolfsii grown in a liquid glucose-synthetic medium. When added as a sole carbon source, lactose at 2·5% (w/v) induced the formation of dark, spherical, compact bodies. The ultrastructure of these bodies is compared with that of sclerotia formed on solid media.
Populations of Spore-forming Bacteria in an Acid Forest Soil, with Special Reference to Bacillus subtilis
Authors: Siala A. , Hill I. R. , Gray T. R. G.
Published: June 2009

The distribution of Bacillus subtilis in a pine-forest soil has been investigated by using the fluorescent-antibody technique and dilution plating. In the acid, mineral horizon of the soil, the organism occurred mainly in the vegetative condition, while in the alkaline, mineral horizon it was mostly present as spores. Within these soil horizons, the bulk of the vegetative bacteria was found on organic matter particles, but of those found on mineral particle surfaces, almost all were on cryptocrystalline quartz particles with iron oxide inclusions.
The Effect on Virulence of Converting the O Antigen of Salmonella cholerae-suis from 627 to 617 by Phage
Authors: Smith H. Williams , Parsell Zoe
Published: June 2009

Of 86 strains of Salmonella cholerae-suis isolated in the U.K., 83 possessed the O antigen 617 and three the O antigen 627. All the O 617 strains were latently infected with the same phage which was active on the O 627 strains; during lyso-genization this phage converted O 627 strains to O 617. None of 900 strains of Escherichia coli was latently infected with this phage; nor were they susceptible to it.

Two O 627 strains converted to O 617 by lysogenization were significantly more virulent for chicks than were their O 627 parent strains; lysogenization of one of these O 627 strains by two different non-converting phages was not accompanied by an increase in virulence. One of the converted strains tested in mice was more virulent for these animals than was the O 627 strain from which it was derived.

The O 617 organisms were found at higher concentrations in the blood and liver of chickens into which they had been injected intravenously than were organisms of the O 627 strain from which they were derived. No difference was detected between the survival rates of the two kinds of organisms in normal chicken serum.
Studies on Membranes Isolated from Extracts of Fusarium culmorum
Authors: Nombela C. , Uruburu F. , Villanueva J. R.
Published: June 2009

A method was developed for the fractionation of Fusarium culmorum homogenates in order to obtain purified cytoplasmic membranes. The fractions obtained were characterized by studying their ultrastructure and enzymic properties. Since ATPase is an enzyme present in the cytoplasmic membrane, we studied the levels of this activity in our fractions as an indication of the presence of cytoplasmic membrane fragments. Since this activity is also present in mitochondria, we determined the levels of fumarase, a mitochondrial enzyme, and took the ratio of the two activities as an index of the purity of the membrane preparations.

The sediment obtained by centrifuging the cell-free extract at 40000 g was fractionated in a discontinuous sucrose gradient. This led to three types of fractions. The most dense had a high ATPase/fumarase ratio and its ultrastructure showed that it contained membrane fragments having a triple-layered structure. We concluded that this fraction was rich in cytoplasmic membrane fragments; it was clearly distinguishable from the intermediate and less dense fractions. These latter fractions had a much lower ATPase/fumarase ratio and, judging by their ultrastructure, they were respectively a mitochondrial fraction and a fraction consisting of vesicles probably related to the endoplasmic reticulum. Analysis of the cytoplasmic membrane-rich fraction showed that it consisted of protein, lipid and 30 % carbohydrate
The Pathway of Glucose Catabolism in Sporocytophaga myxococcoides
Authors: Hanstveit A. O. , Goksøyr J.
Published: June 2009

The pathway of glucose metabolism in Sporocytophaga myxococcoides was studied by a radiorespirometric technique and assays of enzyme activity in cell-free extracts. The primary catabolic pathways in the organism were examined by measurement of relative rates of 14CO2-production from different carbon atoms of labelled glucose, pyruvic acid and acetic acid. These substrates appeared to be degraded solely by enzymes of the Embden-Meyerhof-Parnas pathway in conjunction with the tricarboxylic acid cycle. The results were confirmed by studies of enzyme activity, which showed a lack of two enzymes, glucose-6-phosphate dehydrogenase (D-glucose-6-phosphate dehydrogenase, EC. 1.1.1.49) and 6-phospho-gluconate dehydrogenase [6-phospho-D-gluconate: NADP oxidoreductase (decarboxylating), EC. 1.1.1.44], in the pentose pathway, which indicated a biosynthetic function of the non-oxidative part of this pathway.
In vitro Protein Synthesis and Measurement of the Stability of Messenger RNA in the Blue-green Alga, Anabaena variabilis
Authors: Leach C. K. , Carr N. G.
Published: June 2009

A cell-free preparation of the blue-green alga, Anabaena variabilis, that incorporates 14C-labelled amino acids into protein has been prepared and characterized. The activation of amino acids to amino acid transfer RNAs was characterized, and assembly of these into peptides has been described with respect to cofactor requirements and antibiotic sensitivity. The properties of these systems and the effect of antibiotics on them are similar to those of bacteria. Both natural and synthetic messenger RNA were effective in peptide formation. The kinetics of incorporation of [14C]uracil into RNA has been examined and the stability of labelled RNA from A. variabilis measured by radioactivity loss and by its role in directing peptide synthesis. The half-life of messenger RNA from this organism is approximately 12 min, and as such is comparable to that of bacteria when based upon the mean generation time of the respective organisms.
The Presence and Function of Cytochromes in Selenomonas ruminantium, Anaerovibrio lipolytica and Veillonella alcalescens
Authors: de Vries Wytske , van Wijck-Kapteyn Willemina M. C. , Oosterhuis S. K. H.
Published: June 2009

Strains of Selenomonas ruminantium, Anaerovibrio lipolytica and Veillonella alcalescens contained cytochrome b. Peaks corresponding to cytochromes a and a carbon monoxide-binding pigment were also observed. By means of dual-wavelength experiments with crude membrane fractions it was established that cytochrome b functioned in anaerobic electron transport to fumarate. In V. alcalescens and one strain of S. ruminantium which reduced nitrate, anaerobic electron transport to nitrate was found. Glycerol 1-phosphate and NADH were active as hydrogen donors for cytochrome b reduction in glycerol-grown A. lipolytica, lactate and pyruvate were active in lactate-grown V. alcalescens, and NADH was active in lactose-grown S. ruminantium. Oxidative phosphorylation associated with these electron transfer systems might explain the high molar growth yields previously found for these micro-organisms. Fermentation products were measured in supernatant fluids of cultures grown in the presence and absence of nitrate. Nitrate did not influence the fermentation of lactose to lactate by S. ruminantium, and inhibited propionate formation by V. alcalescens.
The Occurrence of Mycorrhizas in Halophytes, Hydrophytes and Xerophytes, and of Endogone Spores in Adjacent Soils
Authors: Khan A. G.
Published: June 2009

The incidence of mycorrhizas in the roots and Endogone spores in rhizosphere soil of 52 xerophytes, 21 halophytes and 16 hydrophytes from Pakistan was investigated. Vesicular-arbuscular mycorrhizas were of general occurrence in all plants examined except hydrophytes and members of the families Urticaceae, Casuarinaceae, Nyctaginaceae, Portulaceae, Caryophyllaceae, Amaranthaceae, Chenopodiaceae, Capparaceae, Oleaceae, Elaeagnaceae, Zygophyllaceae, Tamaricaceae, Euphorbiaceae and Palmae. Mycorrhizas were found mainly in the surface and subsurface horizons of the soil, and they were much less abundant in the deeper layers, although the abundance of Endogone spores did not decrease with depth. Endogone spores were rare in permanently waterlogged soils, which suggested that soil moisture affected spore number. Most other soil samples contained Endogone spores, including some from rhizospheres of non-mycorrhizal plants. In some soils an increase in spore numbers was recorded in the autumn and winter and a decrease in the spring and summer.
A New Killer Factor Produced by a Killer/Sensitive Yeast Strain
Authors: WOODS D. R. , ROSS I. W. , HENDRY D. A.
Published: June 2009

Summary: The isolation of a new killer/sensitive phenotype of the yeast, Saccharomyces cerevisiae, is described. Killer/sensitive yeast cells are killed by the killer factor (KF1) secreted by killer yeast cells. The killer/sensitive cells also secrete a new killer factor (KF2) which kills sensitive cells. The production of KF2 by killer/sensitive cells renders them less sensitive to KF1, than sensitive cells. Sensitive cells are most susceptible to the action of KF2 in log phase. KF2 is a thermostable protein-containing killer factor.
Nuclear Behaviour and Spindle-pole Bodies During Ascosporogenesis in Peziza quelepidotia
Authors: O'DONNELL K. L. , TAI W. , BENEKE E. S.
Published: June 2009

Summary: The behaviour of nuclei and spindle-pole bodies in Peziza quelepidotia Korf & O'Donnell, a homothallic Discomycete, was investigated by light microscopy from ontogeny of the crozier up to ascosporogenesis. All nuclear divisions appeared to be intranuclear. Plaque-shaped spindle-pole bodies were discernible during the synchronous mitotic division in the crozier, the reductional division in the ascus and the mitotic division preceding sporogenesis. The intranuclear reductional division was of the Neurospora type with no time interval between karyogamy and the onset of meiosis. This type of meiosis is further characterized by the presence of highly contracted homologues at synapsis and the absence of leptotene. A comparison of the behaviour of spindle-pole bodies in this species with other members of the Euascomycetidae is presented.
The Mode of Action of Polyene Antibiotics; Induced Entry of Hydrogen Ions as a Consequence of Polyene Action on the Cell Membrane of Candida albicans
Authors: HAMMOND S. M. , LAMBERT P. A. , KLIGER B. N.
Published: June 2009

Summary: The polyene antibiotic candicidin is a potent antifungal agent acting upon the cell membrane of Candida albicans. Destruction of selective permeability by polyenes allows cations to leak into the environment and permits the entry of protons to neutralize the charge so created, causing internal acidification. Quantitive studies on proton entry reveal that K+ leakage alone is not sufficient to account for the degree of acidification recorded. Extracts of untreated C. albicans, when acidified to the same extent, precipitated. Electron micrographs of candicidin treated C. albicans cells confirm this precipitation.
The Inducible Quinate-Shikimate Catabolic Pathway in Neurospora crassa: Induction and Regulation of Enzyme Synthesis
Authors: CHALEFF R. S.
Published: June 2009

Summary: The regulation of the synthesis of the first three enzymes of the quinate-shikimate catabolic pathway in Neurospora crassa has been studied. Induction of these enzymes is promoted efficiently by quinate and less so by 5-dehydroquinate and/or 5-dehydroshikimate. Shikimate has little or no inducing ability. The kinetics and steady-state rates of synthesis of the three catabolic enzymes have been examined. It is suggested that quinate-shikimate dehydrogenase, catabolic dehydro-quinase, and 5-dehydroshikimate dehydrase are regulated coordinately.
Infiuence of Dilution Rate on Enzyme Synthesis in Aspergillus niger in Continuous Culture
Authors: NG A. M. L. , SMITH J. E. , McINTOSH A. F.
Published: June 2009

Summary: Aspergillus niger was grown in continuous culture under steady-state conditions in citrate-limiting or glucose-limiting medium. The specific activities of hexokinase, phosphofructokinase, pyruvate kinase, fructose diphosphatase, 6-phosphogluconate dehydrogenase and, to a limited extent, citrate synthase under citrate limitation remained at a relatively constant steady-state level irrespective of the dilution rate (0.01 to 0.5 h-1). Increase in dilution rate led to an increase in the specific activities of aconitase, NAD(P) isocitrate dehydrogenase, malate dehydrogenase, and glucose-6-phosphate dehydrogenase in both citrate and glucose limiting culture, and to an increase in citrate synthase, hexokinase, phosphofructokinase, pyruvate kinase, and 6-phosphogluconate dehydrogenase only in glucose limitation. A decrease in specific activity with increasing dilution rate occurred with isocitrate lyase in both citrate and glucose limitation and for fructose diphosphatase only in glucose limitation. The specific activity of malate synthetase showed a peak activity in the middle range of dilution rates.
α-1,3 Glucan Synthesis Correlated with α-1,3 Glucanase Synthesis, Conidiation and Fructification in Morphogenetic Mutants of Aspergillus nidulans
Authors: ZONNEVELD B. J. M.
Published: June 2009

Summary: Nine mutants of Aspergillus nidulans differing in cleistothecia and/or conidia production were investigated. The strains were grown on four media with different levels of glucose (0.8, 3, and 4%) and nitrate (0.6 and 0.15%). The mycelia were analysed on the basis of the dry weight of the total mycelium and the alkali-soluble fraction (containing the α-1,3 glucan) as well as enzyme activities lytic to α-1,3 glucan, laminarin, and starch. Low quantities of α-1,3 glucan present on the third day are correlated with low α-1,3 glucanase activity and absence of cleistothecia formation on the sixth day. α-1,3 Glucan and cleistothecium formation seemed to be inversely related to conidiation.