bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermodynamics of G⋅A mispairs in DNA: Continuum electrostatic model
Authors: Berashevich Julia , Chakraborty Tapash
Published: January 2009

An analysis of the stability of a duplex containing G⋅A mispairs or G⋅A/A⋅G tandem during the DNA melting has shown that the duplex stability depends on both DNA sequences and the conformations of the G⋅A mispairs. The thermodynamics of single pair opening for the G(anti)⋅A(syn) and G(anti)⋅A(anti) conformations adopted by a G⋅A mispair is found to strongly correlate with that of the canonical base pairs, while for the sheared conformation a significant difference is observed.
Enhanced identification and exploitation of time scales for model reduction in stochastic chemical kinetics
Authors: Gómez-Uribe Carlos A. , Verghese George C. , Tzafriri Abraham R.
Published: January 2009

Widely different time scales are common in systems of chemical reactions and can be exploited to obtain reduced models applicable to the time scales of interest. These reduced models enable more efficient computation and simplify analysis. A classic example is the irreversible enzymatic reaction, for which separation of time scales in a deterministic mass action kinetics model results in approximate rate laws for the slow dynamics, such as that of Michaelis–Menten. Recently, several methods have been developed for separation of slow and fast time scales in chemical master equation (CME) descriptions of stochastic chemical kinetics, yielding separate reduced CMEs for the slow variables and the fast variables. The paper begins by systematizing the preliminary step of identifying slow and fast variables in a chemical system from a specification of the slow and fast reactions in the system. The authors then present an enhanced time-scale-separation method that can extend the validity and improve the accuracy of existing methods by better accounting for slow reactions when equilibrating the fast subsystem. The resulting method is particularly accurate in systems such as enzymatic and protein interaction networks, where the rates of the slow reactions that modify the slow variables are not a function of the slow variables. The authors apply their methodology to the case of an irreversible enzymatic reaction and show that the resulting improvements in accuracy and validity are analogous to those obtained in the deterministic case by using the total quasi-steady-state approximation rather than the classical Michaelis–Menten. The other main contribution of this paper is to show how mass fluctuation kinetics models, which give approximate evolution equations for the means, variances, and covariances of the concentrations in a chemical system, can feed into time-scale-separation methods at a variety of stages.
Bianalyte mass detection with a single resonant microcantilever
Authors: Yu Haitao , Li Xinxin
Published: January 2009

Mass-loading detection of multiple kinds of analyte with a single resonant microcantilever is proposed and experimentally validated. By exciting the cantilever in different resonance modes and adsorbing the different analytes at different locations of the cantilever, the specific mass of either kind of analyte can be independently detected. The proposed micromechanical resonant cantilever sensor is designed and fabricated using silicon micromachining techniques. Used as simulant adsorbates, Au and Cr thin films are selectively implemented on the cantilever to verify the bianalyte detecting function. The testing results are consistent with the theoretical analysis, with the detection error being an order of magnitude lower than the analyzed mass.
Structural changes and ferroelectric properties of BiFeO3–PbTiO3 thin films grown via a chemical multilayer deposition method
Authors: Gupta Shashaank , Garg Ashish , Agrawal Dinesh Chandra , Bhattacharjee Shuvrajyoti , Pandey Dhananjai
Published: January 2009

Thin films of (1−x)BiFeO3–xPbTiO3 (BF-xPT) with x≈0.60 were fabricated on Pt/Si substrates by chemical solution deposition of precursor BF and PT layers alternately in three different multilayer configurations. These multilayer deposited precursor films upon annealing at 700 °C in nitrogen show pure perovskite phase formation. In contrast with the equilibrium tetragonal structure for the overall molar composition of BF:PT::40:60, we find monoclinic structured BF-xPT phase of MA type. Piezoforce microscopy confirmed ferroelectric switching in the films and revealed different normal and lateral domain distributions in the samples. Room temperature electrical measurements show good quality ferroelectric hysteresis loops with remanent polarization Pr of up to 18 μC/cm2 and leakage currents as low as 10−7 A/cm2.
Streaming potential generated by a small charged drop in Poiseuille flow
Authors: Sherwood J. D.
Published: January 2009

The streaming potential generated by a charged spherical drop of viscosity αμe suspended in fluid of viscosity μe flowing through a circular capillary is considered. The spherical drop is neutrally buoyant and has radius a much smaller than the capillary radius R0. The drop viscosity is arbitrary, and the drop becomes a rigid sphere in the limit α→∞. The drop is assumed to be a perfect conductor, with no exchange of charge between the drop and the external fluid. This model has been used in the past to study the electrophoresis of a charged mercury drop suspended in water, and may perhaps offer insight into the streaming potential caused by a water droplet immersed in oil. When the electrical potential ζd at the surface of the drop is small, the streaming potential is determined for charge cloud thicknesses κ−1 that are small compared to the capillary radius R0, but are arbitrary compared to the drop radius a. A second analysis is given for thin double layers (aκ⪢1) at higher potentials. Streaming potentials generated by a viscous charged drop are predicted to be larger than for a rigid particle. The effect of a rigid sphere at potential ζd in a charged capillary with surface potential ζc is also considered. When potentials are small and the charge clouds are thin, the change in streaming potential caused by the presence of the sphere is proportional to ζc−ζd.
γ
-Fe
2
O
3
nanoparticles dispersed in porous Vycor glass: A magnetically diluted integrated system
Authors: Cangussu Danielle , Nunes Wallace Castro , Corrêa Heberton Luis da Silva , Macedo Waldemar Augusto de Almeida , Knobel Marcelo , Alves Oswaldo Luiz , Filho Antônio Gomes Souza , Mazali Italo Odone
Published: January 2009

An investigation of the effect of interparticle interaction and particle size distribution has been carried out on iron oxide nanoparticles dispersed into porous Vycor glass. γ-Fe2O3 nanoparticles dispersed into monoliths of Vycor glass were obtained using impregnation-decomposition cycles through the single-source metallo-organic decomposition process. Magnetic properties were investigated by ac magnetic susceptibility measurements, as a function of temperature at different frequencies, by measuring zero-field-cooled and field-cooled magnetization curves and by constructing hysteresis loops at different temperatures. A log-normal size distribution of monodomain nanoparticles has been deduced from the analysis of the magnetization curves. F57e Mössbauer spectroscopy was also employed for investigating the magnetic behavior as a function of nanoparticle size. The systems exhibit typical superparamagnetic behaviors with a wide particle size distribution that can be changed without significantly affecting the interparticle interaction. The experimental data are discussed in terms of the evolution of the particle size distribution with the number of impregnation-decomposition cycles used for preparing the nanoparticles.
Behaviors of neutral and charged silicon self-interstitials during transient enhanced diffusion in silicon investigated by isotope superlattices
Authors: Shimizu Yasuo , Uematsu Masashi , Itoh Kohei M. , Takano Akio , Sawano Kentarou , Shiraki Yasuhiro
Published: January 2009

We investigated the contributions of neutral and charged silicon self-interstitials to self- and boron diffusion during transient enhanced diffusion in silicon. We simultaneously observed self- and boron diffusion in silicon using Snati/S28i isotope superlattices. A calculation based on diffusion equations involving {311} defects and boron-interstitial cluster models was employed to reproduce the diffusion profiles in silicon-implanted (intrinsic) and boron-implanted (extrinsic) silicon isotope superlattices, followed by annealing. To investigate the diffusion processes, the time evolution of the silicon self-interstitial profiles during the transient diffusion was simulated. The results directly demonstrate that excess neutral self-interstitials dominantly enhance the self-diffusion during the transient process in the intrinsic conditions, while doubly positively charged self-interstitials dominate the self-diffusion in the extrinsic conditions.
Electrical transport and percolation in structural phase-separated manganites La1−xBaxMnO3
Authors: Li Pai , Yuan Songliu , Ying Shiyan , Wang Chuanhui , Liu Kuili , Tian Zhaoming , Yuan Shijun , He Jinghua
Published: January 2009

Microstructural studies show that manganites La1−xBaxMnO3 (0.33≤x≤0.95) begin structural phase separation into La0.67Ba0.33MnO3 and BaMnO3 for x>0.33. These composites form a cellularlike structure when the volume faction of La0.67Ba0.33MnO3 (fLBMO) is near the percolation threshold (fC). The percolation threshold (fC) for our composites is 0.18. This result is not consistent with the previous results, which prefer smaller percolation threshold value. This could be attributed to the contribution of grain boundaries. This grain-boundary contribution also induces the large low-temperature bump in electrical transport. The critical exponents t gained from the good fitting for the experimental data are 1.6 at 150 K and 1.7 at 300 K, which are in good agreement with the previous universal result: t=1.6–2.0 for the three dimensional space.
Two modes of oscillatory instability in the flow between a pair of corotating disks
Authors: Mizushima Jiro , Sugihara Genki , Miura Tomohito
Published: January 2009

The mechanism of pattern formation in the flow between two corotating disks in a stationary enclosure and its transition are investigated experimentally, and the experimental results are confirmed by numerical simulation. Particle image velocimetry and laser-Doppler-velocimetry measurements are achieved in the experiment, and the data acquired are examined by using Fourier decomposition analyses and applying the bifurcation theory. Two distinct modes of oscillatory instability are identified as origins that break the axisymmetry of the flow; one originates from the detached shear layer and the other from the outer boundary layer along the enclosure. The former instability is found to lead to the polygonal patterns, which have been reported in previous papers, while the latter instability induces a flow with a shift-and-reflect symmetry, having small spiral vortices along the outer boundary. A mixed-mode polygonal flow, which is surrounded by small vortices is observed at large Reynolds numbers. We identify two transition routes to the mixed-mode flow by adopting two different driving processes of the disk rotation.
Direct measurements of the frequency-dependent dielectrophoresis force
Authors: Wei Ming-Tzo , Junio Joseph , Ou-Yang H. Daniel
Published: January 2009

Dielectrophoresis (DEP), the phenomenon of directed motion of electrically polarizable particles in a nonuniform electric field, is promising for applications in biochemical separation and filtration. For colloidal particles in suspension, the relaxation of the ionic species in the shear layer gives rise to a frequency-dependent, bidirectional DEP force in the radio frequency range. However, quantification methods of the DEP force on individual particles with the pico-Newton resolution required for the development of theories and design of device applications are lacking. We report the use of optical tweezers as a force sensor and a lock-in phase-sensitive technique for analysis of the particle motion in an amplitude modulated DEP force. The coherent detection and sensing scheme yielded not only unprecedented sensitivity for DEP force measurements, but also provided a selectivity that clearly distinguishes the pure DEP force from all the other forces in the system, including electrophoresis, electro-osmosis, heat-induced convection, and Brownian forces, all of which can hamper accurate measurements through other existing methods. Using optical tweezers-based force transducers already developed in our laboratory, we have results that quantify the frequency-dependent DEP force and the crossover frequency of individual particles with this new experimental method.
Transferring cold atoms in double magneto-optical trap by a continuous-wave transfer laser beam with large red detuning
Authors: Wang Junmin , Wang Jing , Yan Shubin , Geng Tao , Zhang Tiancai
Published: January 2009

A novel scheme of transferring cold atoms in a double magneto-optical trap (MOT) system has been experimentally demonstrated. Cold cesium atoms trapped in a vapor-cell MOT are efficiently transferred to an ultrahigh-vacuum (UHV) MOT by a continuous-wave divergent Gaussian transfer laser beam. When large red detuning and moderate intensity are adopted for the transfer laser beam, enhancement of the recapturing of atoms in the UHV MOT is clearly observed. Using the divergent transfer laser beam (diameter of ~1.60 mm in the vapor-cell MOT region) with typical power of ~20.2 mW, up to ~85% of transfer efficiency is obtained when the frequency detuning is set to around −1.2 GHz, and it is not sensitive to small detuning variation. This transfer is much efficient compared with that in the case of continuous-wave near-resonance weak transfer laser beam (typical power of order of ∼100 μW and typical frequency detuning of ~−10 MHz) which is normally used in double-MOT experiment. The enhancement is ascribed to the guiding effect on cold atomic flux by transverse dipole potential of the large red-detuned transfer laser beam.
Irreversibility in cooling and heating processes in the magnetocaloric MnAs and alloys
Authors: Lima Sharma A. L. , Gama S. , Coelho A. A. , de Campos A.
Published: January 2009

Irreversibility of adiabatic processes in the magnetocaloric MnAs and alloys is presented here. We used a differential scanning calorimeter to record the heat flux as a function of the temperature and applied field for MnAs (Mn,X)As, where X stands for Fe or Cu in 0.6% of doping. We extracted the latent heat and entropy in a cycle. In the cooling process, we observed that SMnc>SFec>SCuc, and for the heating process, SFeh≈SMnh>SCuh. The difference in the entropy obtained between processes was found to be as high as 37%.
A new spin-polarized photoemission spectrometer with very high efficiency and energy resolution
Authors: Okuda Taichi , Takeichi Yasuo , Maeda Yuuki , Harasawa Ayumi , Matsuda Iwao , Kinoshita Toyohiko , Kakizaki Akito
Published: January 2009

A new spin- and angle-resolved photoemission spectrometer was developed adopting the very-low-energy-electron-diffraction (VLEED)-type spin polarimeter. The Fe(001)p(1×1)–O film grown on MgO(001) crystal for the VLEED target yields significantly high spin-resolving power, the effective Sherman function of 0.40±0.02, with long lifetime and stability compared to the conventional Fe(001) target. Under the favor of high resolving power, approximately 100 times higher efficiency than that of conventional Mott-type spin polarimeter, the figure of merit of 1.9±0.2×10−2 was achieved. Owing to this high efficiency, high-energy resolution can be realized with this new spin-polarized photoemission spectrometer. The simplified ways of target preparation and revitalization make the VLEED spin polarimeter much more convenient and feasible for the spin-polarized photoemission spectroscopy.
The advanced ion-milling method for preparation of thin film using ion slicer: Application to a sample recovered from diamond-anvil cell
Authors: Tateno Shigehiko , Sinmyo Ryosuke , Hirose Kei , Nishioka Hideo
Published: January 2009

The advanced argon ion-milling technique using a new instrument called ion slicer was newly developed for preparation of thin foil. Compared to the conventional ion-milling methods, this technique facilitates very wide area to be homogeneously thinned by rocking the ion beam source with low angle and the specimen during milling. Here we applied this technique to a sample recovered from a laser-heated diamond-anvil cell (DAC). We obtained the thin film of almost entire cross section of the DAC sample along the compression axis, which possesses of ∼(10×50) μm2. The laser-heated sample is often heterogeneous due to a large temperature gradient. However the chemical analyses are obtained from the whole hot spot under the transmission electron microscope by preparing the thin foil using the ion slicer.
Single nanopore transport of synthetic and biological polyelectrolytes in three-dimensional hybrid microfluidic/nanofluidic devices
Authors: King Travis L. , Gatimu Enid N. , Bohn Paul W.
Published: January 2009

This paper presents a study of electrokinetic transport in single nanopores integrated into vertically stacked three-dimensional hybrid microfluidic/nanofluidic structures. In these devices, single nanopores, created by focused ion beam (FIB) milling in thin polymer films, provide fluidic connection between two vertically separated, perpendicular microfluidic channels. Experiments address both systems in which the nanoporous membrane is composed of the same (homojunction) or different (heterojunction) polymer as the microfluidic channels. These devices are then used to study the electrokinetic transport properties of synthetic (i.e., polystyrene sulfonate and polyallylamine) and biological (i.e., DNA) polyelectrolytes across these nanopores using both electrical current measurements and confocal microscopy. Both optical and electrical measurements indicate that electro-osmotic transport is predominant over electrophoresis in single nanopores with d>180nm, consistent with results obtained under similar conditions for nanocapillary array membranes.
Abnormal domain switching in Pb(Zr,Ti)O3 thin film capacitors
Authors: Wu Aiying , Vilarinho Paula M. , Wu Dong , Gruverman Alexei
Published: January 2009

Observation of abnormal (against the applied electric field) domain switching in Pb(ZrxTi1−x)O3 films by piezoresponse force microscopy is reported. In some grains polarization orients opposite to the external field in the presence of the applied field, while the rest of the film volume switches in a normal way. This effect is observed in thin film capacitors which excludes charge injection effect and spontaneous backswitching due the built-in field, which is the possible reason for this behavior. The abnormal switching behavior is attributed to the charge compensation effect at the boundaries of the grains with rhombohedral structure.
Time and spectrally resolved enhanced fluorescence using silver nanoparticle impregnated polycarbonate substrates
Authors: Lagonigro Laura , Peacock Anna C. , Rohrmoser Stefan , Hasell Tom , Howdle Steven M. , Sazio Pier J. A. , Lagoudakis Pavlos G.
Published: January 2009

Silver nanoparticle impregnated polycarbonate strips have been investigated as substrates for metal-enhanced photoluminescence of a blue emitting dye molecule (coumarin 102). By considering simultaneous time and spectrally resolved photoluminescence we observed fluorescence enhancement resulting from plasmon coupling with an increase in the emission by a factor of ∼8.5 with an associated reduction in the photon lifetime. We relate the fast and slow components of the observed emission decay to the presence of both monomers and aggregates in the films and we discuss their different responses to the plasmon coupling.
Nanolubrication of poly(methyl methacrylate) films on Si for microelectromechanical systems applications
Authors: Satyanarayana N. , Lau K. H. , Sinha S. K.
Published: January 2009

Polymers, such as poly(methyl methacrylate) (PMMA), are important structural materials for microsystems because of their excellent mechanical properties; however, they suffer from severe problems of adhesion, friction, and wear [B. Bhushan, J. N. Israelachvili, and U. Landman, Nature (London) 374, 607 (1995)]. We report a simple process of O2 plasma treatment on a PMMA film, followed by overcoating with an ultrathin layer of perfluoropolyether (PFPE) which improved tribological performance of the film. O2 plasma on PMMA film has formed unique wavy nanotextured surface and increased the hardness and the elastic modulus of the film, which, together with the nanolurbication by PFPE, has increased the wear life of PMMA film by more than five orders of magnitude.
Enhancing and tuning absorption properties of microwave absorbing materials using metamaterials
Authors: Zou Yanhong , Jiang Leyong , Wen Shuangchun , Shu Weixing , Qing Yongjun , Tang Zhixiang , Luo Hailu , Fan Dianyuan
Published: January 2009

We proposed and demonstrated a scheme to enhance and tune absorption properties of conventional microwave absorbing materials (MAMs) by metamaterials (MMs). By covering a MAM, say, carbonyl iron powder coating, with MMs composed of split ring resonators (SRRs) and wires, we show both by experiments and by simulations that the maximum reflection loss (RL) is increased significantly and the frequency region for absorption is shifted to lower frequency. The frequency region in which the maximum RL is less than −10 dB shifts from 5–7 to 4.2–6.2 GHz for perpendicular polarization electromagnetic waves and to 4–9 GHz for parallel polarization waves. Simulation results reveal that the magnetic resonance obtained by SRRs and the electric resonance obtained by copper wires are the main factors in enhancing and tuning microwave absorption properties.
High domain wall velocities induced by current in ultrathin Pt/Co/AlOx wires with perpendicular magnetic anisotropy
Authors: Moore T. A. , Miron I. M. , Gaudin G. , Serret G. , Auffret S. , Rodmacq B. , Schuhl A. , Pizzini S. , Vogel J. , Bonfim M.
Published: January 2009

Current-induced domain wall (DW) displacements in an array of ultrathin Pt/Co/AlOx wires with perpendicular magnetic anisotropy have been directly observed by wide field Kerr microscopy. DWs in all wires in the array were driven simultaneously and their displacement on the micrometer scale was controlled by the current pulse amplitude and duration. At the lower current densities where DW displacements were observed (j≤1.5×1012 A/m2), the DW motion obeys a creep law. At higher current density (j=1.8×1012 A/m2), zero-field average DW velocities up to 130±10 m/s were recorded.
Probing and modulating surface electron accumulation in InN by the electrolyte gated Hall effect
Authors: Brown G. F. , Ager J. W. , Walukiewicz W. , Schaff W. J. , Wu J.
Published: January 2009

The surface contribution to the electrical transport properties of InN was directly measured and modulated by the electrolyte gated Hall effect. Undoped and Mg-doped films show different behaviors that can be effectively described by a multilayer model, taking into account the conduction contribution from both the surface and interface with the buffer layer. Gated photoluminescence experiments further show the surface accumulation layer enhances radiative electron-hole recombination in undoped InN.
Poly(phenylene ethynylene)-coated aligned ZnO nanorod arrays for 2,4,6-trinitrotoluene detection
Authors: Zhu Defeng , He Qingguo , Cao Huimin , Cheng Jiangong , Feng Songlin , Xu Yuansen , Lin Tong
Published: January 2009

The structure of ZnO nanorods coated with fluorescent polymer poly(phenylene ethynylene) (PPE) have been fabricated for 2,4,6-trinitrotoluene (TNT) detection. In this structure, hydrothermally synthesized crystalline ZnO nanorod arrays were used as waveguides and supporting materials for the TNT sensitive polymer, PPE. The evanescent-wave guiding property of the ZnO nanorod waveguide considerably increased fluorescence intensity. The space between the adjacent nanorods and the larger surface-to-volume ratio of the nanorods enhanced the fluorescence response (quenching) to TNT vapor. This work will contribute to design of combining ZnO nanorod arrays with a functional polymer for sensor applications.
Effects of donor doping on Ga1−xMnxAs
Authors: Cho Y. J. , Yu K. M. , Liu X. , Walukiewicz W. , Furdyna J. K.
Published: January 2009

We investigate the effect compensating Mn acceptors in Ga1−xMnxAs films by doping with Si donors. For Ga1−xMnxAs with low Mn content (e.g., x<0.033), doping by Si decreases the Curie temperature TC compared to undoped Ga1−xMnxAs. At high values of x, however (e.g., x>0.10), Si doping is found to increase TC. We ascribe this to an increase in the hole mobility in high x samples due to changes in the relative occupancy of the hole impurity band associated with compensation by the Si donors.
Different arbuscular mycorrhizal fungi induce differences in cellular responses and fungal activity in a mycorrhiza-defective mutant of tomato (rmc)
Authors: Manjarrez Maria , Wallwork Meredith , Smith Sally E. , Smith F. Andrew , Dickson Sandy
Published: January 2009

The reduced mycorrhizal colonisation (rmc) mutant of tomato forms different phenotypes with different arbuscular mycorrhizal (AM) fungi. Our aim was to characterise microscopically the cellular responses in plant and fungus in order to reveal how these varied when colonisation was blocked at different stages. Synchronised colonisation coupled with vital staining, autofluorescence and laser scanning confocal microscopy (LSCM) were used to determine how long the AM fungi stay alive during the interactions with rmc, whether nuclear repositioning occurred in the same way as in wild-type interactions and whether there was evidence for deployment of defence responses. The results showed that (1) all the AM fungi tested were attracted to roots of rmc, on which they developed active external mycelium and appressoria, the latter sometimes in higher numbers than on the wild type; (2) plant cellular responses, such as nuclear movement, occurred only when the AM fungus was able to penetrate the epidermal cells of rmc; and (3) plant defence responses such as autofluorescence were observed only transiently and callose deposition was not involved in blocking AM fungi in rmc. The results demonstrate that multi-step AM colonisation is not only an outcome of cellular processes influenced by both plant and fungus, but is also modified by the capacity of different AM fungi to respond to the plant phenotype induced by the rmc mutation.
Self-organisation at the whole-plant level: a modelling study
Authors: Yang Zongjian , Midmore David J.
Published: January 2009

Within-plant light and nutrient environments are spatially and temporally heterogeneous. The development of different parts of a plant is highly coordinated, which enables the efficient capture and use of resources in such heterogeneous environments. The physiological mechanisms underlying the correlative control of distantly located plant tissues and organs are still not fully understood. In this study, a mathematical model based on a self-organisation mechanism for resource allocation mediated by polar auxin transport is proposed to explain the origin of correlative effects among shoot branches. In the model, the shoot system of an individual plant is treated as a collection of relatively independent modular subunits competing for root-derived resources. The allocation of root-derived resources to different parts of the shoot is determined by their relative vascular contacts with the root system. The development of the vascular network is specified by the polar transport of auxin produced by various parts of the shoot in response to their immediate internal and external environments. The simulation results show that, by altering the amount of auxin they release individually in response to the local environment and modifying their relative vascular contact with the root system, subunits of a shoot are able to coordinate without a central controller and self-organise into functional and structural patterns such as light foraging and correlative dominance. This modelling study suggests that morphological dynamics at the whole-plant level can be understood as the sum of all modular responses to their local environments. The concept of self-organisation holds great promise for an in-depth understanding of the organisational laws that generate overall plant structure and functions.
Environmental stress and genetics influence night-time leaf conductance in the C4 grass Distichlis spicata
Authors: Christman Mairgareth A. , James Jeremy J. , Drenovsky Rebecca E. , Richards James H.
Published: January 2009

Growing awareness of night-time leaf conductance (gnight) in many species, as well as genetic variation in gnight within several species, has raised questions about how genetic variation and environmental stress interact to influence the magnitude of gnight. The objective of this study was to investigate how genotype salt tolerance and salinity stress affect gnight for saltgrass [Distichlis spicata (L.) Greene]. Across genotypes and treatments, night-time water loss rates were 5–20% of daytime rates. Despite growth declining 37–87% in the high salinity treatments (300 mm and 600 mm NaCl), neither treatment had any effect on gnight in four of the six genotypes compared with the control treatment (7 mm NaCl). Daytime leaf conductance (gday) also was not affected by salinity treatment in three of the six genotypes. There was no evidence that more salt tolerant genotypes (assessed as ability to maintain growth with increasing salinity) had a greater capacity to maintain gnight or gday at high salinity. In addition, gnight as a percentage of gday was unaffected by treatment in the three most salt tolerant genotypes. Although gnight in the 7 mm treatment was always highest or not different compared with the 300 mm and 600 mm treatments, gday was generally highest in the 300 mm treatment, indicating separate regulation of gnight and gday in response to an environmental stress. Thus, it is clear that genetics and environment both influence the magnitude of gnight for this species. Combined effects of genetic and environmental factors are likely to impact our interpretation of variation of gnight in natural populations.
Ebf1-mediated down-regulation of Id2 and Id3 is essential for specification of the B cell lineage
Authors: Thal Melissa A. , Carvalho Thiago L. , He Ti , Kim Hyung-Gyoon , Gao Hua , Hagman James , Klug Christopher A.
Published: January 2009

Gene knockout experiments in mice have suggested a hierarchical model of early B cell commitment wherein E2A proteins (E47 and E12) activate early B cell factor (Ebf1), which in turn activates expression of the B cell commitment factor, Pax5. In IL-7 receptor alpha (IL-7Rα) knockout mice, B cell development is blocked before B-lineage commitment at the prepro-B cell stage in adult animals. In
IL-7R
α
−/−
prepro-B cells, E47 is expressed and yet is insufficient to transcriptionally activate the putative downstream target gene,
Ebf1
. In this study, we show that further increases of E47 expression in
IL-7R
α
−/−
prepro-B cells fails to activate
Ebf1
, but rather leads to a dramatic induction of the E2A inhibitory factors,
Id2
and
Id3
. In contrast, enforced expression of Ebf1 in
IL-7R
α
−/−
bone marrow potently down-regulates
Id2
and
Id3
mRNA expression and restores B cell differentiation in vivo. Down-regulation of both Id2 and Id3 during B cell specification is essential in that overexpression of either Id2 or Id3 in wild-type bone marrow blocks B cell specification at the prepro-B cell stage. Collectively, these studies suggest a model where Ebf1 induction specifies the B cell fate by dramatically increasing activity of E47 at the posttranslational level.
Microtubule plus-end tracking by CLIP-170 requires EB1
Authors: Dixit Ram , Barnett Brian , Lazarus Jacob E. , Tokito Mariko , Goldman Yale E. , Holzbaur Erika L. F.
Published: January 2009

Microtubules are polarized polymers that exhibit dynamic instability, with alternating phases of elongation and shortening, particularly at the more dynamic plus-end. Microtubule plus-end tracking proteins (+TIPs) localize to and track with growing microtubule plus-ends in the cell. +TIPs regulate microtubule dynamics and mediate interactions with other cellular components. The molecular mechanisms responsible for the +TIP tracking activity are not well understood, however. We reconstituted the +TIP tracking of mammalian proteins EB1 and CLIP-170 in vitro at single-molecule resolution using time-lapse total internal reflection fluorescence microscopy. We found that EB1 is capable of dynamically tracking growing microtubule plus-ends. Our single-molecule studies demonstrate that EB1 exchanges rapidly at microtubule plus-ends with a dwell time of <1 s, indicating that single EB1 molecules go through multiple rounds of binding and dissociation during microtubule polymerization. CLIP-170 exhibits lattice diffusion and fails to selectively track microtubule ends in the absence of EB1; the addition of EB1 is both necessary and sufficient to mediate plus-end tracking by CLIP-170. Single-molecule analysis of the CLIP-170–EB1 complex also indicates a short dwell time at growing plus-ends, an observation inconsistent with the copolymerization of this complex with tubulin for plus-end-specific localization. GTP hydrolysis is required for +TIP tracking, because end-specificity is lost when tubulin is polymerized in the presence of guanosine 5′-[α,β-methylene]triphosphate (GMPCPP). Together, our data provide insight into the mechanisms driving plus-end tracking by mammalian +TIPs and suggest that EB1 specifically recognizes the distinct lattice structure at the growing microtubule end.
Consumers indirectly increase infection risk in grassland food webs
Authors: Borer Elizabeth T. , Mitchell Charles E. , Power Alison G. , Seabloom Eric W.
Published: January 2009

Most pathogens exist within complicated food webs of interacting hosts, vectors, competitors, and predators. Although theory has demonstrated a variety of mechanisms by which predation and competition in food webs can indirectly control infection risk in hosts, there have until now been no experimental tests of this theory. We sampled the effect of long-term exclusion of large vertebrate herbivores on the prevalence of infection by a group of aphid-vectored viruses that infect grasses (barley and cereal yellow dwarf viruses) in an oak savannah in central California. We found that pathogen prevalence was ≈4-fold higher in the presence of consumers than in areas where they were excluded. Vertebrate consumers did not directly alter infection rates by this aphid-vectored pathogen group, but rather increased infection risk by increasing the relative abundance of highly-competent hosts in the grassland community. This large-scale experiment, measuring changes in host abundance and infection risk in response to altered consumption rates, confirms theoretical predictions that consumers can indirectly increase infection risk by altering the composition of whole communities. Most importantly, these results demonstrate that, even in complex natural communities, alterations to food web composition such as consumer invasion or extinction can lead to significant impacts that cascade throughout entire communities, including changes in infection risk.
Inferring biological mechanisms from spatial analysis: Prediction of a local inhibitor in the ovary
Authors: Da Silva-Buttkus P. , Marcelli G. , Franks S. , Stark J. , Hardy K.
Published: January 2009

Female mammals are born with a lifetime's supply of oocytes individually enveloped in flattened epithelial cells to form primordial follicles. It is not clear how sufficient primordial follicles are maintained to sustain the reproductive lifespan, while providing an adequate supply of mature oocytes for ovulation. Locally produced growth factors are thought to be critical regulators of early follicle growth, but knowledge of their identity and source remains incomplete. Here, we have used a simple approach of spatial analysis of structures in histological tissue sections to identify likely sources of such regulatory molecules, narrowing the field for future screening for candidate growth factors or antagonists. We have quantified the relative spatial positions of primordial (resting) follicles and growing follicles in mice on days 4, 8, and 12 after birth, and calculated interfollicular distances. Follicles were significantly less likely to have started growing if they had 1 or more primordial follicles close by (within 10 μm), predicting that primordial follicles inhibit each other. This approach allows us to hypothesize that primordial follicles produce a diffusible inhibitor that prevents neighboring primordial follicles from growing. Such an approach has wide applicability within many branches of developmental and cell biology for studying spatial signaling within tissues and cells.
Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis
Authors: Villa Elizabeth , Sengupta Jayati , Trabuco Leonardo G. , LeBarron Jamie , Baxter William T. , Shaikh Tanvir R. , Grassucci Robert A. , Nissen Poul , Ehrenberg Måns , Schulten Klaus , Frank Joachim
Published: January 2009

In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-Å cryo-electron microscopy map of the aminoacyl-tRNA·EF-Tu·GDP·kirromycin-bound
Escherichia coli
ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic gate mechanism.
Low-barrier hydrogen bond in photoactive yellow protein
Authors: Yamaguchi Shigeo , Kamikubo Hironari , Kurihara Kazuo , Kuroki Ryota , Niimura Nobuo , Shimizu Nobutaka , Yamazaki Yoichi , Kataoka Mikio
Published: January 2009

Low-barrier hydrogen bonds (LBHBs) have been proposed to play roles in protein functions, including enzymatic catalysis and proton transfer. Transient formation of LBHBs is expected to stabilize specific reaction intermediates. However, based on experimental results and theoretical considerations, arguments against the importance of LBHB in proteins have been raised. The discrepancy is caused by the absence of direct identification of the hydrogen atom position. Here, we show by high-resolution neutron crystallography of photoactive yellow protein (PYP) that a LBHB exists in a protein, even in the ground state. We identified ≈87% (819/942) of the hydrogen positions in PYP and demonstrated that the hydrogen bond between the chromophore and E46 is a LBHB. This LBHB stabilizes an isolated electric charge buried in the hydrophobic environment of the protein interior. We propose that in the excited state the fast relaxation of the LBHB into a normal hydrogen bond is the trigger for photo-signal propagation to the protein moiety. These results give insights into the novel roles of LBHBs and the mechanism of the formation of LBHBs.
Evolution of F-box genes in plants: Different modes of sequence divergence and their relationships with functional diversification
Authors: Xu Guixia , Ma Hong , Nei Masatoshi , Kong Hongzhi
Published: January 2009

F-box proteins are substrate-recognition components of the
S
kp1-Rbx1-
C
ul1-
F
-box protein (SCF) ubiquitin ligases. In plants, F-box genes form one of the largest multigene superfamilies and control many important biological functions. However, it is unclear how and why plants have acquired a large number of F-box genes. Here we identified 692, 337, and 779 F-box genes in
Arabidopsis
, poplar and rice, respectively, and studied their phylogenetic relationships and evolutionary patterns. We found that the plant F-box superfamily can be divided into 42 families, each of which has a distinct domain organization. We also estimated the number of ancestral genes for each family and identified highly conservative versus divergent families. In conservative families, there has been little or no change in the number of genes since the divergence between eudicots and monocots ≈145 million years ago. In divergent families, however, the numbers have increased dramatically during the same period. In two cases, the numbers of genes in extant species are >100 times greater than that in the most recent common ancestor (MRCA) of the three species. Proteins encoded by highly conservative genes always have the same domain organization, suggesting that they interact with the same or similar substrates. In contrast, proteins of rapidly duplicating genes sometimes have quite different domain structures, mainly caused by unusually frequent shifts of exon-intron boundaries and/or frameshift mutations. Our results indicate that different F-box families, or different clusters of the same family, have experienced dramatically different modes of sequence divergence, apparently having resulted in adaptive changes in function.
Quantifying the global cellular thiol–disulfide status
Authors: Hansen Rosa E. , Roth Doris , Winther Jakob R.
Published: January 2009

It is widely accepted that the redox status of protein thiols is of central importance to protein structure and folding and that glutathione is an important low-molecular-mass redox regulator. However, the total cellular pools of thiols and disulfides and their relative abundance have never been determined. In this study, we have assembled a global picture of the cellular thiol–disulfide status in cultured mammalian cells. We have quantified the absolute levels of protein thiols, protein disulfides, and glutathionylated protein (PSSG) in all cellular protein, including membrane proteins. These data were combined with quantification of reduced and oxidized glutathione in the same cells. Of the total protein cysteines, 6% and 9.6% are engaged in disulfide bond formation in HEK and HeLa cells, respectively. Furthermore, the steady-state level of PSSG is <0.1% of the total protein cysteines in both cell types. However, when cells are exposed to a sublethal dose of the thiol-specific oxidant diamide, PSSG levels increase to >15% of all protein cysteine. Glutathione is typically characterized as the “cellular redox buffer”; nevertheless, our data show that protein thiols represent a larger active redox pool than glutathione. Accordingly, protein thiols are likely to be directly involved in the cellular defense against oxidative stress.
Recent advances in cause-effect research on oak decline in Europe.
Authors: Thomas F. M.
Published: January 2009

This review attempts to assess the causal factors and their interrelations that cause decline of widespread European oak (
Quercus
) species. In particular, it provides an overview of recent advances in cause-effect research since 2000. The first recorded outbreak of oak decline took place in 1739-1748, and was followed by several other decline episodes, most of them occurring in the twentieth century. The mortality rates differ substantially among the European regions and decline episodes; however, the decline of entire stands is a rare event. The principal causes of oak decline are the following site-unspecific factors: severe (in particular, repeated) defoliation by insect larvae, especially in combination with infection by powdery mildew and weather extremes (summer drought, winter frost and spring frost); and the following site-specific factors: the root pathogen
Phytophthora quercina
(which is virulent in soils with a pH[CaCl
2
] value ≥3.5 and certain fractions of exchangeable calcium), and a distinct decrease in the groundwater level. At hydromorphic sites, intermittent soil moisture can intensify the impact of drought. At least in the temperate regions, two or more of these factors have to act in combination to cause major outbreaks of decline. Other biotic factors such as the root pathogen
Collybia fusipes
and the borers
Agrilus biguttatus
or
Platypus cylindrus
can contribute to the damage in later stages of decline. In the Mediterranean region, the aggressive root pathogen
Phytophthora cinnamomi
as well as prolonged periods of intense drought probably are capable of causing oak decline without any contribution of additional factors. Other possible causal factors, whose importance still has to be corroborated, are the decrease in chemical defence compounds against leaf herbivores due to eutrophication with nitrogen, and increased ozone concentrations.
Nanotechnology and food safety: potential benefits, possible risks?
Authors: Powell M. , Colin M.
Published: January 2009

Nanotechnology is the new frontier in food science. A purported 150-500 nano-based food and food-related products are already on the market worldwide, and the nanotechnology food industry is expected to grow to over $20 billion by 2010-2015. Food safety applications are expected to be a key focus of food nanotechnology research, development and commercialization in the near future. Recent
Escherichia coli
,
Salmonella
and other food-borne pathogen scares have made preventing and tracking of pathogens in food products and agricultural and industrial food systems a top priority. Nanotechnology-based applications could prevent food-borne pathogens from causing public illness and disease via improved packaging, sensing, tracking and more effective antibiotics, and many nanotechnology applications intended to make food safer are already on the market. At the same time, some scientists, regulators and non-governmental organizations are raising concerns about potential risks related to the increasing use of nanomaterials and nanotechnologies in foods and other products. In this review, we broadly review what nanotechnology is and provide a brief overview of some of the food-related applications on the market and in development. In the bulk of the review, we describe applications of nanotechnologies and nanomaterials for food safety in particular. In conclusion, we discuss some of the potential health risks and unknowns related to the use of nanomaterials in foods and food packaging.
Land use decisions in smallholder rural communities in developing countries.
Authors: Mertz O. , Reenberg A. , Bruun T. B. , Birch-Thomsen T.
Published: January 2009

Land use change has become increasingly acknowledged as an important issue in terms of understanding the processes of global change. Hence, land use decision-making by smallholder communities in developing countries become a vital part of the broader comprehension of environmental and social change that are related to the change processes at the global scale. A wide range of analytical and conceptual frameworks has been developed to facilitate and sharpen such analyses, ranging from very theoretical to directly operational approaches. Five regional cases are used to illustrate the diversity of land use decisions and drivers of decisions. These range from political decisions on land tenure and development (Tanzania, Vietnam and Borneo) to the global effects of climate change (Sahel), and represent a diversity of contexts from the agricultural frontiers of humid tropical sites in Amazonia and Borneo to the more intensively farmed and long-settled tropical dryland areas of the Sahel. We conclude that although there are specific issues in all areas, the multiplicity of drivers for land use change is always important and necessary to capture if adequate understanding and development is to be achieved. The analytical and conceptual frameworks presented are useful for ensuring this.