bluuebunny/crossref_metadata_2025 huggingface dataset:
Phototunable reflection notches of cholesteric liquid crystals
Authors: Hrozhyk Uladzimir A. , Serak Svetlana V. , Tabiryan Nelson V. , Bunning Timothy J.
Published: September 2008

The reflection notch of cholesteric liquid crystals (CLCs) formed from highly photosenstive azobenzene nematic liquid crystals doped with light-insensitive, large helical twisting power chiral dopants is shown to be widely phototunable by green laser beams. The nonlinear transmission properties of these materials were studied. We have shown that the relative shift in Bragg wavelength is independent of the chiral dopant concentration and develop a predictive theory of such behavior. The theory describes the dynamics of phototuning as well. Reflection shifts greater than 150 nm were driven with low power, cw of 532 nm in these photosensitive CLCs, previously attainable only through UV pre-exposure. A nonlinear feedback mechanism was demonstrated for CLCs of left, right, and both handedness upon laser-induced blueshifting of the reflection notch from a red wavelength using a green cw laser.
Do non-centro-symmetric linear X-Y-X molecules exist? The case for the (I)Π2u state of CuCl2
Authors: Zou Wenli , Bersuker Isaac B. , Boggs James E.
Published: September 2008

The potential energy surface of the low-lying excited state (I)Π2u of CuCl2 is constructed by using the ionization potential equation-of-motion coupled-cluster method and also the RASPT2 method with a large active space of 21 electrons in 17 orbitals to improve the results. It is found by the multiconfiguration calculation that this state has a barrier of 53 cm−1 between two equivalent minima in which the linear molecule has a dipole moment. In our computations artifactual symmetry breaking is carefully avoided. Further refinement, including consideration of interaction between the two excited Π2 states, yields a somewhat higher barrier between 100 and 500 cm−1. The mechanism of formation of the double-minimum potential is explained by the pseudo–Jahn–Teller effect theory. Computed spectroscopic constants are in good agreement with experimental ones.
Developing the random phase approximation into a practical post-Kohn–Sham correlation model
Authors: Furche Filipp
Published: September 2008

The random phase approximation (RPA) to the density functional correlation energy systematically improves upon many limitations of present semilocal functionals, but was considered too computationally expensive for widespread use in the past. Here a physically appealing reformulation of the RPA correlation model is developed that substantially reduces its computational complexity. The density functional RPA correlation energy is shown to equal one-half times the difference of all RPA electronic excitation energies computed at full and first order coupling. Thus, the RPA correlation energy may be considered as a difference of electronic zero point vibrational energies, where each eigenmode corresponds to an electronic excitation. This surprisingly simple result is intimately related to plasma theories of electron correlation. Differences to electron pair correlation models underlying popular correlated wave function methods are discussed. The RPA correlation energy is further transformed into an explicit functional of the Kohn–Sham orbitals. The only nontrivial ingredient to this functional is the sign function of the response operator. A stable iterative algorithm to evaluate this sign function based on the Newton–Schulz iteration is presented. Integral direct implementations scale as the fifth power of the system size, similar to second order Møller–Plesset calculations. With these improvements, RPA may become the long-sought robust and efficient zero order post-Kohn–Sham correlation model.
Nanoscale uniform self-assembled monolayers of fluorescent zinc(II) complexes on the Si(100) surface
Authors: Di Bella Santo , Consiglio Giuseppe , La Spina Giuseppe , Oliva Cecilia , Cricenti Antonio
Published: September 2008

The synthesis of self-assembled monolayers on Si(100) substrates of a new fluorescent ZnII Schiff-base complex is reported. Chemisorbed species are characterized by the combination of fluorescence scanning near-field optical/atomic force microscopy (SNOM/AFM), and by fluorescence spectroscopy. Both SNOM/AFM results indicate the existence of a monolayer on the surface, while optical SNOM images highlight the contribution of the monolayer to the local fluorescence. While chemisorbed molecular monolayers exhibit a distinct fluorescence, analogous to that observed in solution, cast thin films do not show any emission. Photoluminescent properties of the monolayer can be related to its nanoscale uniform, ordered structure.
Effect of substrate geometry on liquid-crystal-mediated nanocylinder-substrate interactions
Authors: Cheung David L. , Allen Michael P.
Published: September 2008

Using classical density functional theory, the liquid crystal (LC)-mediated interaction between a cylindrical nanoparticle and a structured substrate is studied. The surface is structured by cutting a rectangular groove into the surface. In the absence of the nanoparticle, a range of defect structures is formed in the vicinity of the groove. By varying the groove width and depth, the LC-mediated interaction changes from repulsive to attractive. This interaction is strongest when the groove is of comparable size to the nanoparticle. For narrow grooves the nanoparticle is attracted to the center of the groove, while for wider grooves there is a free energy minimum near the sidewalls.
Accurate determination of crystal structures based on averaged local bond order parameters
Authors: Lechner Wolfgang , Dellago Christoph
Published: September 2008

Local bond order parameters based on spherical harmonics, also known as Steinhardt order parameters, are often used to determine crystal structures in molecular simulations. Here we propose a modification of this method in which the complex bond order vectors are averaged over the first neighbor shell of a given particle and the particle itself. As demonstrated using soft particle systems, this averaging procedure considerably improves the accuracy with which different crystal structures can be distinguished.
Crystal-like low frequency phonons in the low-density amorphous and high-density amorphous ices
Authors: Belosludov R. V. , Subbotin O. S. , Mizuseki H. , Rodger P. M. , Kawazoe Y. , Belosludov V. R.
Published: September 2008

The structure and vibrational properties of high- and low-density amorphous (HDA and LDA, respectively) ices have been determined using reverse Monte Carlo, molecular dynamics, and lattice dynamics simulations. This combined approach leads to a more accurate and detailed structural description of HDA and LDA ices when compared to experiment than was previously possible. The water molecules in these ices form well connected hydrogen-bond networks that exhibit modes of vibration that extend throughout the solid and can involve up to 70% of all molecules. However, the networks display significant differences in their dynamical behavior. In HDA, the extended low-frequency vibrational modes occur in dense parallel two dimensional layers of water that are approximately 10 nm thick. In contrast, the extended modes in LDA resemble a holey structure that encapsulates many small pockets of nonparticipating water molecules.
Statistics of beam-driven waves in plasmas with ambient fluctuations: Reduced-parameter approach
Authors: Tyshetskiy Yu. , Cairns I. H. , Robinson P. A.
Published: September 2008

A reduced-parameter (RP) model of quasilinear wave-plasma interactions is used to analyze statistical properties of beam-driven waves in plasmas with ambient density fluctuations. The probability distribution of wave energies in such a system is shown to have a relatively narrow peak just above the thermal wave level, and a power-law tail at high energies, the latter becoming progressively more evident for increasing characteristic amplitude of the ambient fluctuations. To better understand the physics behind these statistical features of the waves, a simplified model of stochastically driven thermal waves is developed on the basis of the RP model. An approximate analytic solution for stationary statistical distribution of wave energies W is constructed, showing a good agreement with that of the original RP model. The “peak” and “tail” features of the wave energy distribution are shown to be a result of contributions of two groups of wave clumps: those subject to either very slow or very fast random variations of total wave growth rate (due to fluctuations of ambient plasma density), respectively. In the case of significant ambient plasma fluctuations, the overall wave energy distribution is shown to have a clear power-law tail at high energies, P(W)∝W−α, with nontrivial exponent 1<α<2, while for weak fluctuations it is close to the lognormal distribution predicted by pure stochastic growth theory. The model’s wave statistics resemble the statistics of plasma waves observed by the Ulysses spacecraft in some interplanetary type III burst sources. This resemblance is discussed qualitatively, and it is suggested that the stochastically driven thermal waves might be a candidate for explaining the power-law tails in the observed wave statistics without invoking mechanisms such as self-organized criticality or nonlinear wave collapse.
A novel feature of intramolecular vibrational redistribution in propargyl alcohol and propargyl amine
Authors: Makarov A. A. , Malinovsky A. L. , Ryabov E. A.
Published: September 2008

Intramolecular vibrational redistribution (IVR) from the terminal acetylene mode νHC has been studied for four molecules: H–CC–CH3 (propyne), H–CC–CH2Cl (propargyl chloride), H–CC–CH2OH (propargyl alcohol), and H–CC–CH2NH2 (propargyl amine). The experiments were performed with the room-temperature gases. The transition ∣0⟩→∣1⟩ in the mode νHC was pumped by a short laser pulse. Anti-Stokes spontaneous Raman scattering was used as a probe. The measured parameters were the de-excitation rate W and the dilution factor σ defined as the relative level of the residual energy in the νHC mode at long pump-probe delay times. The pair of these values {W,σ} allowed us to determine the density ρeff of those vibrational-rotational states, which are involved in IVR from state ∣1⟩. For two molecules, HCCCH3 and HCCCH2Cl, the experimental results were consistent with the suggestion that all close vibrational-rotational states with the same total angular momentum J and symmetry participate in the IVR regardless of the other rotator quantum number K (in the case of HCCCH3) or Ka (in the case of HCCCH2Cl) and the vibrational quantum numbers as well. For the other two molecules, HCCCH2OH and HCCCH2NH2, this effect was also present, yet the experimental results revealed certain restrictions. We have obtained a satisfactory theoretical fit with the assumption that the low-frequency torsion vibration of the hydrogen atom in the hydroxyl group (in the case of HCCCH2OH) or hydrogen atoms in the amine group (in the case of HCCCH2NH2) does not participate in the IVR. This assumption can be treated as a challenge to future studies of these molecules by high-resolution spectroscopy and various double-resonance and pump-probe techniques.
The influence of desorption gas to high power microwave window multipactor
Authors: Chang Chao , Liu Guozhi , Tang Chuanxiang , Chen Changhua , Qiu Shi , Fang Jinyong , Hou Qin
Published: September 2008

Gas desorbed by electrons plays a key role in multipactor saturation and final plasma breakdown at the vacuum side of the window in high power microwave systems. A multipactor model involving electron-neutral collision and ionization is established. When desorption gas pressure reaches 1Torr, the electron impact energy apparently decreases, multipactor saturates at a lower surface charging field, and multipactor saturation meets easier, compared to vacuum. Experiments for different material windows of high power microwave, with the power of 1GW, frequency of 9.4GHz, and 20ns single and multiple pulses was conducted. It was discovered that gas pressure rose prominently in the horn, when breakdown occurred. The increase in local gas pressure during the 20ns pulse is estimated from the experiment to reach several Torr, a pressure that is consistent with the presented dynamic model.
Fully nonadiabatic properties of all H2 isotopomers
Authors: Alexander S. A. , Coldwell R. L.
Published: September 2008

Using variational Monte Carlo and simple explicitly correlated fully nonadiabatic wavefunctions we have computed the energy and 29 properties of the lowest rovibrational state of all the H2 isotopomers. Our results are in very good agreement with previous calculations on these systems.
Entropy production and fluctuation theorem along a stochastic limit cycle
Authors: Xiao Tie Jun , Hou Zhonghuai , Xin Houwen
Published: September 2008

Entropy production along a trajectory in the stochastic irreversible Brusselator model of chemical oscillating reactions is discussed. Particular attention is paid to a parameter region near the deterministic supercritical Hopf bifurcation. In the stationary state, detailed fluctuation theorem holds due to the reversibility in the state space, which is verified by direct simulations via Gillespie’s algorithm [J. Comput. Phys. 22, 403 (1976); J. Phys. Chem. 81, 2340 (1977)]. In addition, we have considered how the entropy production along a noisy limit cycle depends on the system size. Interestingly, in the large system size limit, the entropy production approaches a constant value when the control parameter stays at the deterministic steady state region, while it increases linearly in the deterministic oscillatory region. Such simulation results can be well understood by a stochastic normal form analysis.
Room temperature multiferroic behavior of Cr-doped ZnO films
Authors: Yang Y. C. , Zhong C. F. , Wang X. H. , He B. , Wei S. Q. , Zeng F. , Pan F.
Published: September 2008

Single-phase 9 at. % Cr-doped ZnO film has been prepared on Pt(111)/Ti/SiO2/Si(100) substrates by reactive sputtering method. The film is found to present ferroelectric and ferromagnetic behaviors simultaneously at room temperature, and it undergoes transitions to paraelectric and paramagnetic phases at ∼368–373 and ∼495 K, respectively. It is considered that the local electric dipoles induced by the distortions of CrO4 tetrahedra should be responsible for the ferroelectricity. On the other hand, the ferromagnetic ordering could be explained by the interaction of the localized spins with statically occupied polaron states. The multiferroic behavior adds a dimension to the multifunction of ZnO.
First-principles LDA+U studies of the In-doped ZnO transparent conductive oxide
Authors: Zhou X. H. , Hu Q.-H. , Fu Y.
Published: September 2008

Electronic energy band structure of In-doped ZnO transparent conducting oxide was investigated by density functional calculations using local density approximation+Hubbard U (LDA+U) scheme. By systematically calculating the formation energies and transition energy levels of In atom and In-related complex in ZnO, it has been shown that the substitutional In atom has a low formation energy and introduces a shallow donor level, which is 38 meV below the conduction-band minimum. Substitutional In atoms contribute significantly delocalized s orbitals in the conduction band states, which are expected to increase the mobility of the material. In p-type ZnO, interstitial In atom acts as a donor and has a low formation energy, making it a compensating center in the case of acceptor doping. Under O-rich growth conditions, however, interstitial In is energetically unfavorable. The modulated band structure of ZnO after In doping shows a total energy band gap widening effect due to a pronounced Burstein–Moss shift and a relatively small exchange-correlation-induced band gap narrowing.
Self-nucleation free and dimension dependent metal-induced lateral crystallization of amorphous germanium for single crystalline germanium growth on insulating substrate
Authors: Park Jin-Hong , Tada Munehiro , Kapur Pawan , Peng Hailin , Saraswat Krishna C.
Published: September 2008

In this work we have investigated Ni- or Au-induced crystallization and the lateral crystallization of planar amorphous germanium (α-Ge) on silicon dioxide at 360 °C without the deleterious effects of thermally induced self-nucleation. Subsequently, single crystalline Ge growth has been achieved on SiO2 by making dimension of α-Ge line to be smaller than the size of grains formed using Ni- and Au-induced lateral crystallizations at 360 °C. This method can be used to form the channel region of the MOS devices in upper layers of the three-dimensional integrated circuits at low temperatures.
Impact of channel constrictions on the formation of multiple tunnel junctions in heavily doped silicon single electron transistors
Authors: Manoharan M. , Oda Shunri , Mizuta Hiroshi
Published: September 2008

This paper reports the study of the uncontrolled multiple tunnel junctions (MTJs) induced by the random dopants in heavily doped silicon single electron transistors (SETs). The SETs are fabricated by making dual lateral constrictions in the narrow doped silicon channel formed on a silicon on insulator substrate. The doped SETs with relatively long constriction regions invariably exhibit the MTJ characteristics. The influence of the MTJs is suppressed by tuning the Fermi level in the constriction region. Finally, we show that the formation of uncontrolled MTJs can be avoided by making extremely sharp constrictions.
Nonvolatile memory effect based on gold nanoparticles doped ferroelectric liquid crystal
Authors: Prakash J. , Choudhary A. , Kumar A. , Mehta D. S. , Biradar A. M.
Published: September 2008

Nonvolatile memory effect based on gold nanoparticles (GNPs) doped deformed helix ferroelectric liquid crystal (DHFLC) has been observed. This observed memory effect has been attributed to electric field induced charge transfer from liquid crystal molecules to the GNPs and the stabilization of helix deformation of DHFLC material, which occurs on the application of electric field beyond a critical field. The memory effect has been analyzed by polarizing optical microscopy, high-resolution transmission electron microscopy, and dielectric spectroscopy. The observed memory effect combines two active research areas: nanotechnology and liquid crystal.
A composite photothermal technique for the measurement of thermal properties of solids
Authors: Astrath F. B. G. , Astrath N. G. C. , Shen J. , Zhou J. , Baesso M. L.
Published: September 2008

In this work, a composite photothermal technique combining open photoacoustic cell and photothermal deflection methods for thermal characterization of opaque solids was developed. An excitation laser was employed to concurrently generate both photoacoustic and mirage effects. Thermal diffusivity and thermal effusivity of carbon-based samples were measured, and the values of thermal conductivities and specific heat were then deduced. The experimental results were found to be in good agreement with the literature values. The photothermal technique developed in this work permits a convenient and precise measurement of thermal properties of solids.
Electron beam nanosculpting of suspended graphene sheets
Authors: Fischbein Michael D. , Drndić Marija
Published: September 2008

We demonstrate high-resolution modification of suspended multilayer graphene sheets by controlled exposure to the focused electron beam of a transmission electron microscope. We show that this technique can be used to realize, on time scales of a few seconds, a variety of features, including nanometer-scale pores, slits, and gaps that are stable and do not evolve over time. Despite the extreme thinness of the suspended graphene sheets, extensive removal of material to produce the desired feature geometries is found not to introduce long-range distortion of the suspended sheet structure.
Effects of the GaN and AlN nucleation layers on the crack-free AlGaN templates
Authors: Wang Tong-Wen , Chen Nie-Chuan , Lien Wei-Chieh , Wu Meng-Chyi , Shih Chuan-Feng
Published: September 2008

This paper reports the effects of GaN and AlN nucleation layers (NLs) on the characteristics of the subsequently grown AlGaN templates, which were grown by a two-step growth method on sapphire substrates using metal-organic chemical vapor deposition. The in situ monitored reflectance spectra reveal that the thickness variation in AlGaN templates grown on the GaN NL is much smaller than that on the AlN NL. X-ray diffraction patterns show that the AlGaN template with a GaN NL exhibits a better crystalline quality as compared to that with an AlN NL. Observed from the transmission electron microscopy, it is also shown that the dislocation density of the AlGaN template with a GaN NL can be substantially reduced. In addition, the fabricated light-emitting diodes from the AlGaN template with a GaN NL exhibit a lower forward voltage, a lower series resistance, a lower leakage current, and a narrower linewidth of electroluminescence peak than those with the AlN NL.
A constant-current electrospinning system for production of high quality nanofibers
Authors: Munir Muhammad Miftahul , Iskandar Ferry , Khairurrijal  , Okuyama Kikuo
Published: September 2008

A constant-current electrospinning system has been successfully developed to produce high quality nanofibers. In order to keep at a certain value of the electric current, a proportional-integral-derivative (PID) control action was employed, in which the PID parameters were manually tuned. The desired value of electric current was quickly achieved and no overshoot was observed in the system output. The restoration of the electric current due to a disturbance occurred rapidly. Poly(vinyl pyrrolidone) (PVP) nanofibers have been produced from a precursor solution prepared by dissolution of the PVP powder in a mixture of dimethyl formamide and ethanol using the constant-current electrospinning system. The cone jet shape observed at the end of the needle during the injection of the precursor solution became shorter with increasing electric current. The diameter of the PVP nanofibers was very uniform and reduced with increasing electric current, which is consistent with the model.
Entropy driven key-lock assembly
Authors: Odriozola G. , Jiménez-Ángeles F. , Lozada-Cassou M.
Published: September 2008

The effective interaction between a sphere with an open cavity (lock) and a spherical macroparticle (key), both immersed in a hard sphere fluid, is studied by means of Monte Carlo simulations. As a result, a two-dimensional map of the key-lock effective interaction potential is constructed, which leads to the proposal of a self-assembling mechanism: There exists trajectories through which the key-lock pair could assemble avoiding trespassing potential barriers. Hence, solely the entropic contribution can induce their self-assembling even in the absence of attractive forces. This study points out the solvent contribution within the underlying mechanisms of substrate-protein assembly∕disassembly processes, which are important steps of the enzyme catalysis and protein mediated transport.
Reduction of stacking fault density in m-plane GaN grown on SiC
Authors: Cho Y. S. , Sun Q. , Lee I.-H. , Ko T.-S. , Yerino C. D. , Han J. , Kong B. H. , Cho H. K. , Wang S.
Published: September 2008

We report the reduction in basal-plane stacking faults (BSFs) in m-plane GaN grown on m-plane SiC. The origin of BSFs is linked to heteronucleation of m-plane GaN and the presence of N-face basal-plane sidewalls of three-dimensional islands. Graded AlGaN layers help to alleviate mismatched nucleation and the generation of BSFs. Transmission electron microscopy shows that the density of BSFs is decreased to the low 105cm−1. Anisotropy in on-axis x-ray rocking curves, a salient feature in m-plane GaN heteroepitaxial layers, is greatly reduced. A possible mechanism of BSF generation, and the demonstration of improved InGaN∕GaN quantum well emission are presented.
How to Get Rid of W: A Latent Variables Approach to Modelling Spatially Lagged Variables
Authors: Folmer Henk , Oud Johan
Published: September 2008

In this paper we propose a structural equation model (SEM) with latent variables to model spatial dependence. Rather than using the spatial weights matrix W, we propose to use latent variables to represent spatial dependence and spillover effects, of which the observed spatially lagged variables are indicators. This approach allows us to incorporate and test more information on spatial dependence and offers more flexibility than the representation in terms of Wy or Wx. Furthermore, we adapt the ML estimator included in the software package Mx to estimate SEMs with spatial dependence. We present illustrations based on Anselin's Columbus, Ohio, crime dataset.
Possible early selection of short juvenile period olive plants based on seedling traits
Authors: Rallo Pilar , Jiménez Rocío , Ordovás José , Suárez M Paz
Published: September 2008

The relationship between the length of the juvenile period and nine olive seedling parameters (plant height, diameter, number of nodes, lateral shoots, internode length, leaf length, width, area, and shape index) was explored in 287 plants belonging to four different progeny. The traits were measured at two timepoints: after the plants had completed a forced growth cycle in the greenhouse/shadehouse (15 months after sowing) and after one growing season in the field (27 months after sowing). Strong linear tendencies of most vigour traits (mainly plant height and diameter) with the time of first flowering were observed. Leaf traits measured after one year in the field were also related to the length of the juvenile period, but not the same traits that were measured the previous year. Strong positive correlations were observed between the parameters studied. All results are discussed in terms of selecting the best seedling traits to be used as pre-selection criteria for short juvenile period during early stages.
The effects on grain quality traits of a grain serpin protein and the VPM1 segment in southern Australian wheat breeding
Authors: Cane Karen , Sharp P. J. , Eagles H. A. , Eastwood R. F. , Hollamby G. J. , Kuchel Haydn , Lu Meiqin , Martin P. J.
Published: September 2008

Production of wheat of sufficient quality to meet market demands is an ongoing agricultural challenge. Identification and evaluation of alleles of genes affecting quality parameters enables breeders to improve their germplasm by active selection towards specific allele combinations. Using a large dataset obtained from southern Australian wheat breeding programs, and including a relationship matrix in the analysis to minimise bias, we re-evaluated the effects of high- and low-molecular-weight glutenin alleles and puroindoline alleles on the grain quality parameters Rmax, dough extensibility, dough development time, flour water absorption, and milling yield and found that estimated effects were in close agreement with those from earlier analyses without a relationship matrix. We also evaluated, for the first time, the effects on the same quality parameters of 2 alleles (wild-type and null) of a defence grain protein, a serpin located on chromosome 5B. In addition, we assessed the effect of the VPM1 alien segment.
The serpin null allele significantly reduced milling yield by ~0.4 g of flour per 100 g of grain milled across different germplasm sources and flour protein levels. In Australian germplasm, the origin of this allele was traced to a 19th Century introduction from India by William Farrer; however other sources, of significance in international breeding programs, were also identified. Our analysis of the effect of the VPM1 segment on quality traits revealed no detrimental effects of its presence on the traits we measured.
Quantifying the response of crops to shelter in the agricultural regions of South Australia
Authors: Bennell M. R. , Verbyla A. P.
Published: September 2008

Integrating belts of woody perennials into Australian farms is proposed as a method of enhancing crop productivity through shelter benefits while addressing natural resource management issues including groundwater recharge. This paper presents yield data from cereal and pulse crops collected from windbreak sites through the eastern agricultural districts of South Australia, using a harvester equipped with a yield monitor. The crop response followed the expected pattern of a competition zone of reduced yield of 1–4 tree heights (H) adjacent to the windbreak followed by a shelter benefit zone of unchanged or improved yield extending out to a maximum of 20H. The yield response in the sheltered benefit zone is +3.7% for all cereals (2.2H–9.7H) and is +14.0% for all pulse crops (1.7H–10.4H). Wheat and barley have similar results, with gains in the shelter benefit zones of 4.1% and 2.1%, respectively, with windbreak competition effects resulting in net yields of 3.0% for wheat and –1.1% for barley in the sheltered zones. Faba bean (Vicia faba) shows a strong consistent response to wind shelter, with a yield increase of 19.6% in the shelter benefit zone (1.5H–19.6H) and net gain of 19.1% in the sheltered zone (crop edge at 1.0H and extending to 19.6H). The response of cereals to sheltered effects varied across the years of the survey, with net positive results in 1997 (7.4%) and 1999 (7.5%) and close to zero in 1998 and 2000. A theoretical prediction of potential crop yield based on climate for the years of the survey showed that 1997 and 1999 had lower yield potential than 2000 and 1998. This suggests that the climatic conditions occurring during the growing season also influence crop shelter responses. Where cereals are the predominant crop the net yield returns from windbreaks would be small, even if root pruning could be successfully undertaken.
Molecular and physiological adaptation to prolonged drought stress in the leaves of two Andean potato genotypes
Authors: Mane Shrinivasrao P. , Robinet Cecilia Vasquez , Ulanov Alexander , Schafleitner Roland , Tincopa Luz , Gaudin Amelie , Nomberto Giannina , Alvarado Carlos , Solis Christian , Bolivar Luis Avila , Blas Raul , Ortega Oscar , Solis Julio , Panta Ana , Rivera Cristina , Samolski Ilanit , Carbajulca Doris H. , Bonierbale Meredith , Pati Amrita , Heath Lenwood S. , Bohnert Hans J. , Grene Ruth
Published: September 2008

Responses to prolonged drought and recovery from drought of two South American potato (Solanum tuberosum L. ssp. andigena (Juz & Buk) Hawkes) landraces, Sullu and Ccompis were compared under field conditions. Physiological and biomass measurements, yield analysis, the results of hybridisation to a potato microarray platform (44 000 probes) and metabolite profiling were used to characterise responses to water deficit. Drought affected shoot and root biomass negatively in Ccompis but not in Sullu, whereas both genotypes maintained tuber yield under water stress. Ccompis showed stronger reduction in maximum quantum yield under stress than Sullu, and less decrease in stomatal resistance. Genes associated with PSII functions were activated during recovery in Sullu only. Evidence for sucrose accumulation in Sullu only during maximum stress and recovery was observed, in addition to increases in cell wall biosynthesis. A depression in the abundance of plastid superoxide dismutase transcripts was observed under maximum stress in Ccompis. Both sucrose and the regulatory molecule trehalose accumulated in the leaves of Sullu only. In contrast, in Ccompis, the raffinose oligosaccharide family pathway was activated, whereas low levels of sucrose and minor stress-mediated changes in trehalose were observed. Proline, and expression of the associated genes, rose in both genotypes under drought, with a 3-fold higher increase in Sullu than in Ccompis. The results demonstrate the presence of distinct molecular and biochemical drought responses in the two potato landraces leading to yield maintenance but differential biomass accumulation in vegetative tissues.
Leaf longevity and drought: avoidance of the costs and risks of early leaf abscission as inferred from the leaf carbon isotopic composition
Authors: Escudero Alfonso , Mediavilla Sonia , Heilmeier Hermann
Published: September 2008

Plant species with longer leaf longevity tend to maintain lower photosynthetic rates. Among other factors, differences in stomatal limitation have been proposed to explain the negative effects of leaf longevity on photosynthesis, although it is not yet clear why stomatal limitations should be stronger in species with longer leaf longevity. We measured carbon isotopic composition (δ13C) in the fresh leaf litter of several Mediterranean woody species to estimate the mean stomatal limitations during the photosynthetically active part of the leaf life. Interspecific differences in δ13C were best explained by a multiple regression including, as independent variables, the maximum leaf longevity and the annual water deficit. For a similar level of water availability, stomatal limitations were higher in species with longer leaf longevity. We hypothesise that stronger stomatal control of transpiration in longer-living leaves arose as a mechanism to reduce the risk of leaf desiccation and to avoid the high costs for the future C assimilation of anticipated leaf mortality in species with a long leaf life expectancy. This stronger sensitivity to drought should be added to the suite of traits accompanying long leaf longevity and contributes decisively to the overall limitations to C assimilation in long-lived leaves.
Network inference using informative priors
Authors: Mukherjee Sach , Speed Terence P.
Published: September 2008

Recent years have seen much interest in the study of systems characterized by multiple interacting components. A class of statistical models called graphical models, in which graphs are used to represent probabilistic relationships between variables, provides a framework for formal inference regarding such systems. In many settings, the object of inference is the network structure itself. This problem of “network inference” is well known to be a challenging one. However, in scientific settings there is very often existing information regarding network connectivity. A natural idea then is to take account of such information during inference. This article addresses the question of incorporating prior information into network inference. We focus on directed models called Bayesian networks, and use Markov chain Monte Carlo to draw samples from posterior distributions over network structures. We introduce prior distributions on graphs capable of capturing information regarding network features including edges, classes of edges, degree distributions, and sparsity. We illustrate our approach in the context of systems biology, applying our methods to network inference in cancer signaling.
The Parkinson's disease genes
pink1
and
parkin
promote mitochondrial fission and/or inhibit fusion in
Drosophila
Authors: Deng Hansong , Dodson Mark W. , Huang Haixia , Guo Ming
Published: September 2008

Mutations in
PTEN-induced kinase 1
(
pink1
) or
parkin
cause autosomal-recessive and some sporadic forms of Parkinson's disease.
pink1
acts upstream of
parkin
in a common genetic pathway to regulate mitochondrial integrity in
Drosophila
. Mitochondrial morphology is maintained by a dynamic balance between the opposing actions of mitochondrial fusion, controlled by
Mitofusin
(
mfn
) and
Optic atrophy 1
(
opa1
), and mitochondrial fission, controlled by
drp1
. Here, we explore interactions between
pink1
/
parkin
and the mitochondrial fusion/fission machinery. Muscle-specific knockdown of the fly homologue of
Mfn
(
Marf
) or
opa1
, or overexpression of
drp1
, results in significant mitochondrial fragmentation.
Mfn
-knockdown flies also display altered cristae morphology. Interestingly, knockdown of
Mfn
or
opa1
or overexpression of
drp1
, rescues the phenotypes of muscle degeneration, cell death, and mitochondrial abnormalities in
pink1
or
parkin
mutants. In the male germline, we also observe genetic interactions between
pink1
and the testes-specific
mfn
homologue
fuzzy onion
, and between
pink1
and
drp1
. Our data suggest that the
pink1
/
parkin
pathway promotes mitochondrial fission and/or inhibits fusion by negatively regulating
mfn
and
opa1
function, and/or positively regulating
drp1
. However,
pink1
and
parkin
mutant flies show distinct mitochondrial phenotypes from
drp1
mutant flies, and flies carrying a heterozygous mutation in
drp1
enhance the
pink1
-null phenotype, resulting in lethality. These results suggest that
pink1
and
parkin
are likely not core components of the
drp1
-mediated mitochondrial fission machinery. Modification of fusion and fission may represent a novel therapeutic strategy for Parkinson's disease.
The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTICCINO2 is essential and limiting for plant development
Authors: Bach Liên , Michaelson Louise V. , Haslam Richard , Bellec Yannick , Gissot Lionel , Marion Jessica , Da Costa Marco , Boutin Jean-Pierre , Miquel Martine , Tellier Frédérique , Domergue Frederic , Markham Jennifer E. , Beaudoin Frederic , Napier Johnathan A. , Faure Jean-Denis
Published: September 2008

Very-long-chain fatty acids (VLCFAs) are synthesized as acyl-CoAs by the endoplasmic reticulum-localized elongase multiprotein complex. Two
Arabidopsis
genes are putative homologues of the recently identified yeast 3-hydroxy-acyl-CoA dehydratase (
PHS1
), the third enzyme of the elongase complex. We showed that
Arabidopsis PASTICCINO2
(
PAS2
) was able to restore
phs1
cytokinesis defects and sphingolipid long chain base overaccumulation. Conversely, the expression of
PHS1
was able to complement the developmental defects and the accumulation of long chain bases of the
pas2–1
mutant. The
pas2–1
mutant was characterized by a general reduction of VLCFA pools in seed storage triacylglycerols, cuticular waxes, and complex sphingolipids. Most strikingly, the defective elongation cycle resulted in the accumulation of 3-hydroxy-acyl-CoA intermediates, indicating premature termination of fatty acid elongation and confirming the role of PAS2 in this process. We demonstrated by
in vivo
bimolecular fluorescence complementation that PAS2 was specifically associated in the endoplasmic reticulum with the enoyl-CoA reductase CER10, the fourth enzyme of the elongase complex. Finally, complete loss of PAS2 function is embryo lethal, and the ectopic expression of
PHS1
led to enhanced levels of VLCFAs associated with severe developmental defects. Altogether these results demonstrate that the plant 3-hydroxy-acyl-CoA dehydratase PASTICCINO2 is an essential and limiting enzyme in VLCFA synthesis but also that PAS2-derived VLCFA homeostasis is required for specific developmental processes.
The BK-mediated fAHP is modulated by learning a hippocampus-dependent task
Authors: Matthews Elizabeth A. , Weible Aldis P. , Shah Samit , Disterhoft John F.
Published: September 2008

Intrinsic excitability is a plastic property of cells that, along with synaptic changes, can be modulated by learning. Action potential (AP) height, width, and frequency are intrinsically controlled properties which rely on the activation of Na+, Ca2+, and K+channels in the dendritic, somatic, and axonal membranes. The fast after-hyperpolarization (fAHP) after an AP is partially responsible for determining the half-width and duration of the AP and thus Ca2+influx during the depolarization. In CA1 hippocampal pyramidal cells, the fAHP is carried by the voltage- and Ca2+-dependent BK channel. In addition to modulating the duration of the AP, the BK-mediated potassium current exerts control over the frequency of AP generation in response to a depolarizing input. These facts position BK-mediated effects to not only modulate immediate intraneuronal communication, but also to control longer-term Ca2+-dependent changes in the neuron, such as kinase activation, gene transcription, and synaptic plasticity. We examined how the BK-mediated fAHP was altered in hippocampal neurons after learning trace eyeblink conditioning. By using current clamp methods, it was found that the fAHP is reduced and the AP duration is increased in cells from conditioned animals. Additionally,in vitroandin vivomeasures of firing frequency show that BK-channel blockade increases both evoked (in vitro) and spontaneous (in vivo) firing frequency of CA1 neurons, implicating the BK channel in the control of intrinsic excitability. These data indicate that the reduction of the BK-mediated fAHP is an essential part of the total increase of neuronal excitability known to accompany hippocampus-dependent learning.
The
Saccharomyces cerevisiae
linker histone Hho1p is essential for chromatin compaction in stationary phase and is displaced by transcription
Authors: Schäfer Georgia , McEvoy Christopher R. E. , Patterton Hugh-G.
Published: September 2008

The importance of core histones in the regulation of DNA function by chromatin is clear. However, little is known about the role of the linker histone. We investigated the role of H1 in
Saccharomyces cerevisiae
during extensive transcriptional reprogramming in stationary phase. Although the levels of linker histone Hho1p remained constant during growth to semiquiescence, there was a genome-wide increase in binding to chromatin. Hho1p was essential for compaction of chromatin in stationary phase, but not for general transcriptional repression. A clear, genome-wide anticorrelation was seen between the level of bound Hho1p and gene expression. Surprisingly, the rank order of gene activity was maintained even in the absence of Hho1p. Based on these findings, we suggest that linker histone Hho1p has a limited role in transcriptional regulation and that the dynamically exchanging linker histone may be evicted from chromatin by transcriptional activity.
The structure of a complete phytochrome sensory module in the Pr ground state
Authors: Essen Lars-Oliver , Mailliet Jo , Hughes Jon
Published: September 2008

Phytochromes are red/far-red photochromic biliprotein photoreceptors, which in plants regulate seed germination, stem extension, flowering time, and many other light effects. However, the structure/functional basis of the phytochrome photoswitch is still unclear. Here, we report the ground state structure of the complete sensory module of Cph1 phytochrome from the cyanobacterium
Synechocystis
6803. Although the phycocyanobilin (PCB) chromophore is attached to Cys-259 as expected, paralleling the situation in plant phytochromes but contrasting to that in bacteriophytochromes, the
ZZZssa
conformation does not correspond to that expected from Raman spectroscopy. We show that the PHY domain, previously considered unique to phytochromes, is structurally a member of the GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) family. Indeed, the tandem-GAF dumbbell revealed for phytochrome sensory modules is remarkably similar to the regulatory domains of cyclic nucleotide (cNMP) phosphodiesterases and adenylyl cyclases. A unique feature of the phytochrome structure is a long, tongue-like protrusion from the PHY domain that seals the chromophore pocket and stabilizes the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue. The structure that we present provides a framework for light-driven signal transmission in phytochromes.
Crystal structure of
Pseudomonas aeruginosa
bacteriophytochrome: Photoconversion and signal transduction
Authors: Yang Xiaojing , Kuk Jane , Moffat Keith
Published: September 2008

Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 Å resolution of a bacteriophytochrome from
Pseudomonas aeruginosa
with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an “arm” structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.
Blood-stage
Plasmodium
infection induces CD8
+
T lymphocytes to parasite-expressed antigens, largely regulated by CD8α
+
dendritic cells
Authors: Lundie Rachel J. , de Koning-Ward Tania F. , Davey Gayle M. , Nie Catherine Q. , Hansen Diana S. , Lau Lei Shong , Mintern Justine D. , Belz Gabrielle T. , Schofield Louis , Carbone Francis R. , Villadangos Jose A. , Crabb Brendan S. , Heath William R.
Published: September 2008

Although CD8
+
T cells do not contribute to protection against the blood stage of
Plasmodium
infection, there is mounting evidence that they are principal mediators of murine experimental cerebral malaria (ECM). At present, there is no direct evidence that the CD8
+
T cells mediating ECM are parasite-specific or, for that matter, whether parasite-specific CD8
+
T cells are generated in response to blood-stage infection. To resolve this and to define the cellular requirements for such priming, we generated transgenic
P. berghei
parasites expressing model T cell epitopes. This approach was necessary as MHC class I-restricted antigens to blood-stage infection have not been defined. Here, we show that blood-stage infection leads to parasite-specific CD8
+
and CD4
+
T cell responses. Furthermore, we show that
P. berghei
-expressed antigens are cross-presented by the CD8α
+
subset of dendritic cells (DC), and that this induces pathogen-specific cytotoxic T lymphocytes (CTL) capable of lysing cells presenting antigens expressed by blood-stage parasites. Finally, using three different experimental approaches, we provide evidence that CTL specific for parasite-expressed antigens contribute to ECM.
Determination of hierarchical relationship of Src and Rac at subcellular locations with FRET biosensors
Authors: Ouyang Mingxing , Sun Jie , Chien Shu , Wang Yingxiao
Published: September 2008

Genetically encoded biosensors based on FRET have enabled the visualization of signaling events in live cells with high spatiotemporal resolution. However, the limited sensitivity of these biosensors has hindered their broad application in biological studies. We have paired enhanced CFP (ECFP) with YPet, a variant of YFP. This ECFP/YPet FRET pair markedly enhanced the sensitivity of biosensors (several folds enhancement without the need of tailored optimization for each individual biosensor) for a variety of signaling molecules, including tyrosine kinase Src, small GTPase Rac, calcium, and a membrane-bound matrix metalloproteinase MT1-MMP. The application of these improved biosensors revealed that the activations of Src and Rac by PDGF displayed distinct subcellular patterns during directional cell migration on micropatterned surface. The activity of Rac is highly polarized and concentrated at the leading edge, whereas Src activity is relatively uniform. These FRET biosensors also led to the discovery that Src and Rac mutually regulate each other. Our findings indicate that molecules within the same signaling feedback loop can be differentially regulated at different subcellular locations. In summary, ECFP/YPet may serve as a general FRET pair for the development of highly sensitive biosensors to allow the determination of molecular hierarchies at subcellular locations in live cells.