bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling springtime shallow frontal clouds with cloud‐resolving and single‐column models
Authors: Xu Kuan‐Man , Zhang Minghua , Eitzen Zachary A. , Ghan Steven J. , Klein Stephen A. , Wu Xiaoqing , Xie Shaocheng , Branson Mark , Del Genio Anthony D. , Iacobellis Sam F. , Khairoutdinov Marat , Lin Wuyin , Lohmann Ulrike , Randall David A. , Somerville Richard C. J. , Sud Yogesh C. , Walker Gregory K. , Wolf Audrey , Yio J. John , Zhang Junhua
Published: April 2005

This modeling study compares the performance of eight single‐column models (SCMs) and four cloud‐resolving models (CRMs) in simulating shallow frontal cloud systems observed during a short period of the March 2000 Atmospheric Radiation Measurement (ARM) intensive operational period. Except for the passage of a cold front at the beginning of this period, frontal cloud systems are under the influence of an upper tropospheric ridge and are driven by a persistent frontogenesis over the Southern Great Plains and moisture transport from the northwestern part of the Gulf of Mexico. This study emphasizes quantitative comparisons among the model simulations and with the ARM data, focusing on a 27‐hour period when only shallow frontal clouds were observed. All CRMs and SCMs simulate clouds in the observed shallow cloud layer. Most SCMs also produce clouds in the middle and upper troposphere, while none of the CRMs produce any clouds there. One possible cause for this is the decoupling between cloud condensate and cloud fraction in nearly all SCM parameterizations. Another possible cause is the weak upper tropospheric subsidence that has been averaged over both descending and ascending regions. Significantly different cloud amounts and cloud microphysical properties are found in the model simulations. All CRMs and most SCMs underestimate shallow clouds in the lowest 125 hPa near the surface, but most SCMs overestimate the cloud amount above this layer. These results are related to the detailed formulations of cloud microphysical processes and fractional cloud parameterizations in the SCMs, and possibly to the dynamical framework and two‐dimensional configuration of the CRMs. Although two of the CRMs with anelastic dynamical frameworks simulate the shallow frontal clouds much better than the SCMs, the CRMs do not necessarily perform much better than the SCMs for the entire period when deep and shallow frontal clouds are present.
Functional Recovery of Neuronal Activity in Rat Whisker-Barrel Cortex Sensory Pathway from Freezing Injury after Transplantation of Adult Bone Marrow Stromal Cells
Authors: Mori Kentaro , Iwata Junko , Miyazaki Masahiro , Nakao Yasuaki , Maeda Minoru
Published: April 2005

The effect of transplantation of adult bone marrow stromal cells (MSCs) into the freeze-lesioned left barrel field cortex in the rat was investigated by measurement of local cerebral glucose utilization (lCMRglc) in the anatomic structures of the whisker-to-barrel cortex sensory pathway. Bone marrow stromal cells or phosphate-buffered saline (PBS) were injected intracerebrally into the boundary zone 1 h after induction of the freezing cortical lesion. Three weeks after surgery, the 2-[14C]deoxyglucose method was used to measure lCMRglc during right whisker stimulation. The volume of the primary necrotic freezing lesion was significantly reduced ( P<0.05), and secondary retrograde degeneration in the left ventral posteromedial (VPM) thalamic nucleus was diminished in the MSC-treated group. Local cerebral glucose utilization measurements showed that the freezing cortical lesion did not alter the metabolic responses to stimulation in the brain stem trigeminal nuclei, but eliminated the responses in the left VPM nucleus and periphery of the barrel cortex in the PBS-treated group. The left/right (stimulated/unstimulated) lCMRglc ratios were significantly improved in both the VPM nucleus and periphery of the barrel cortex in the MSC-treated group compared with the PBS-treated group ( P<0.05). These results indicate that MSC transplantation in adults may stimulate metabolic and functional recovery in injured neuronal pathways.
Elimination of translational and rotational motions in nuclear orbital plus molecular orbital theory
Authors: Nakai Hiromi , Hoshino Minoru , Miyamoto Kaito , Hyodo Shiaki
Published: April 2005

The nuclear orbital plus molecular orbital (NOMO) theory was developed in order to determine the nonadiabatic nuclear and electronic wave functions. This study presents a formulation to remove the contamination of rotational motion as well as translational motion in the NOMO theory. We have formulated the translation- and rotation-free (TRF)-NOMO theory by introducing the TRF Hamiltonian. The principal moment of inertia, which is the denominator in the rotational Hamiltonian, is expanded in a Taylor series. The zeroth-order of the Taylor expansion corresponds to a rigid-body rotator. The first-order terms contribute the coupling between the vibration and the rotation. Hartree–Fock equations have been derived in the framework of the TRF-NOMO theory. Numerical assessments, which were preformed for H2, D2, T2, μ2 (muon dimmer), and H2O, confirmed the importance of the TRF treatment.
A pulsed-field ionization photoelectron secondary ion coincidence study of the H2+(X,υ+=–15,N+=1)+He proton transfer reaction
Authors: Tang X. N. , Xu H. , Zhang T. , Hou Y. , Chang C. , Ng C. Y. , Chiu Y. , Dressler R. A. , Levandier D. J.
Published: April 2005

The endothermic proton transfer reaction, H2+(υ+)+He→HeH++H(ΔE=0.806eV), is investigated over a broad range of reactant vibrational levels using high-resolution vacuum ultraviolet to prepare reactant ions either through excitation of autoionization resonances, or using the pulsed-field ionization-photoelectron-secondary ion coincidence (PFI-PESICO) approach. In the former case, the translational energy dependence of the integral reaction cross sections are measured for υ+=0–3 with high signal-to-noise using the guided-ion beam technique. PFI-PESICO cross sections are reported for υ+=1–15 and υ+=0–12 at center-of-mass collision energies of 0.6 and 3.1eV, respectively. All ion reactant states selected by the PFI-PESICO scheme are in the N+=1 rotational level. The experimental cross sections are complemented with quasiclassical trajectory (QCT) calculations performed on the ab initio potential energy surface provided by Palmieri et al. [Mol. Phys. 98, 1839 (2000)]. The QCT cross sections are significantly lower than the experimental results near threshold, consistent with important contributions due to resonances observed in quantum scattering studies. At total energies above 2eV, the QCT calculations are in excellent agreement with the present results. PFI-PESICO time-of-flight (TOF) measurements are also reported for υ+=3 and 4 at a collision energy of 0.6eV. The velocity inverted TOF spectra are consistent with the prevalence of a spectator-stripping mechanism.
Colloidal electroconvection in a thin horizontal cell. I. Microscopic cooperative patterns at low voltage
Authors: Han Yilong , Grier David G.
Published: April 2005

Applying an electric field to an aqueous colloidal dispersion establishes a complex interplay of forces among the highly mobile simple ions, the more highly charged but less mobile colloidal spheres, and the surrounding water. This interplay can induce a wide variety of visually striking dynamical instabilities even when the applied field is constant. This paper reports on the highly organized patterns that emerge when electrohydrodynamic forces compete with gravity in thin layers of charge-stabilized colloidal spheres subjected to low voltages between parallel-plate electrodes. Depending on the conditions, these spheres can form levitating clusters with morphologies ranging from tumbling clouds to toroidal vortex rings and to writhing labyrinths.
Non-Born–Oppenheimer variational calculations of HT+ bound states with zero angular momentum
Authors: Bednarz Eugeniusz , Bubin Sergiy , Adamowicz Ludwik
Published: April 2005

We report fully nonadiabatic calculations of all rotationless bound states of HT+ molecular ion (t+p+e−) carried out in the framework of the variational method. We show that, in all the states, except the two highest ones, the bond in the system can be described as covalent. In the highest two states the bond becomes essentially ionic and HT+ can be described as a T+H+ complex. The wave function of the system was expanded in terms of spherically symmetric, explicitly correlated Gaussian functions with preexponential multipliers consisting of powers of the internuclear distance. Apart from the total energies of the states, we have calculated the expectation values of the t-p, t-e, and p-e interparticle distances, their squares, and the nucleus-nucleus correlation functions.
Magnetic properties of the Co–C60 and Fe–C60 nanocrystalline magnetic thin films
Authors: Zheng Lingyi A. , Barrera Enrique V. , Shull Robert D.
Published: April 2005

The basic magnetic properties of Co–C60 and Fe–C60 nanocrystalline magnetic thin films and the temperature effects on these properties have been investigated. Experimental results show that the Co–C60 films possess an in-plane magnetic anisotropy, but such an anisotropy is not found in the Fe–C60 films. At room temperature, the magnetic coercivity decreases with increasing C60 concentration in the Co–C60 films while it increases with increasing C60 concentration in the Fe–C60 film. Strong temperature-dependent remanence and saturation magnetization are found in both the Co–C60 and Fe–C60 films with high C60 concentration due to the nanosize grain effects. The effects of temperature on the coercivity of the Co–C60 and Fe–C60 films are different and determined by the intrinsic magnetocrystalline anisotropy energy of Co and Fe, respectively.
Probing liquation cracking and solidification through modeling of momentum, heat, and solute transport during welding of aluminum alloys
Authors: Mishra S. , Chakraborty S. , DebRoy T.
Published: April 2005

A transport phenomena-based mathematical model is developed to understand liquation cracking in weldments during fusion welding. Equations of conservation of mass, momentum, heat, and solute transport are numerically solved considering nonequilibrium solidification and filler metal addition to determine the solid and liquid phase fractions in the solidifying region and the solute distribution in the weld pool. An effective partition coefficient that considers the local interface velocity and the undercooling is used to simulate solidification during welding. The calculations show that convection plays a dominant role in the solute transport inside the weld pool. The predicted weld-metal solute content agreed well with the independent experimental observations. The liquation cracking susceptibility in Al–Cu alloy weldments could be reliably predicted by the model based on the computed solidifying weld-metal composition and solid fraction considering nonequilibrium solidification.
Microstructural comparisons of ultrathin Cu films deposited by ion-beam and dc-magnetron sputtering
Authors: Prater W. L. , Allen E. L. , Lee W.-Y. , Toney M. F. , Kellock A. , Daniels J. S. , Hedstrom J. A. , Harrell T.
Published: April 2005

We report and contrast both the electrical resistance and the microstructure of copper thin films deposited in an oxygen-containing atmosphere by ion-beam and dc-magnetron sputtering. For films with thicknesses of 5 nm or less, the resistivity of the Cu films is minimized at oxygen concentrations ranging from 0.2% to 1% for dc-magnetron sputtering and 6%–10% for ion-beam sputtering. Films sputtered under both conditions show a similar decrease of interface roughness with increasing oxygen concentration, although the magnetron-deposited films are smoother. The dc-magnetron-produced films have higher resistivity, have smaller Cu grains, and contain a higher concentration of cuprous oxide particles. We discuss the mechanisms leading to the grain refinement and the consequent reduced resistivity in both types of films.
Guided elastic waves in porous materials saturated by air under Lamb conditions
Authors: Boeckx L. , Leclaire P. , Khurana P. , Glorieux C. , Lauriks W. , Allard J. F.
Published: April 2005

The propagation of guided elastic waves in porous materials saturated by air under Lamb conditions is studied theoretically and experimentally. The modes are derived from expressing the boundary conditions on the normal and tangential stresses and the displacements at the interfaces between the porous layer and the surrounding fluid. The stresses and the fluid pressure inside the porous medium are obtained from Biot’s equations of poroelasticity. Symmetrical and antisymmetrical modes are found when the porous layer is loaded by the same fluid on both sides. Damping mechanisms include viscous and thermal exchanges between the solid and the fluid, in addition to the classical structural damping. Using an experimental setup based on the generation of standing waves in the layer and taking the spatial Fourier transform of the displacement profile, the phase velocities of three modes were measured for two porous materials in a frequency range between 80 Hz and 4 kHz. The measurements confirm the theoretical predictions and provide information on the shear modulus of a sound-absorbing material in a wide frequency range.
Plasma-nitrided silicon-rich oxide as an extension to ultrathin nitrided oxide gate dielectrics
Authors: Cubaynes F. N. , Venezia V. C. , van der Marel C. , Snijders J. H. M. , Everaert J. L. , Shi X. , Rothschild A. , Schaekers M.
Published: April 2005

We have investigated the mechanism of N incorporation, during plasma nitridation, in thermally grown ultrathin (<2nm)SiO2 films and deposited silicon-rich oxide films. X-ray photoelectron spectroscopy analysis indicates that N atoms exchange mainly with O to bond with Si atoms in ultrathin plasma-nitrided oxides. Based on this understanding, we were able to increase the amount of N that can be incorporated in plasma-nitrided silicon oxides by increasing the silicon content in these films. This was achieved by depositing ultrathin substoichiometric silicon-rich oxide films. We demonstrate an increase of almost twice as much N in these ultrathin plasma-nitrided silicon-rich oxide films yielding lower gate leakage current for a given thickness.
Surface-charge lithography for GaN microstructuring based on photoelectrochemical etching techniques
Authors: Tiginyanu I. M. , Popa V. , Volciuc O.
Published: April 2005

We show that host defects introduced at the surface of GaN epilayers by mechanical means (e.g., using needles, microscribers), or 2-keV-argon ion beam are resistant to photoelectrochemical etching in aqueous solution of KOH, presumably due to trapped negative charge. The spatial distribution of surface defects and related negative charge can be designed as lithographic mask for the purpose of GaN microstructuring. The possibility to fabricate GaN mesostructures using the approach involved is demonstrated.
Scanning the human proteome for calmodulin-binding proteins
Authors: Shen Xinchun , Valencia C. Alexander , Szostak Jack , Dong Biao , Liu Rihe
Published: April 2005

The calcium ion (Ca
2+
) is a ubiquitous second messenger that is crucial for the regulation of a wide variety of cellular processes. The diverse transient signals transduced by Ca
2+
are mediated by intracellular Ca
2+
-binding proteins, also known as Ca
2+
sensors. A key obstacle to studying many Ca
2+
-sensing proteins is the difficulty in identifying the numerous downstream target interactions that respond to Ca
2+
-induced conformational changes. Among a number of Ca
2+
sensors in the eukaryotic cell, calmodulin (CaM) is the most widespread and the best studied. Employing the mRNA display technique, we have scanned the human proteome for CaM-binding proteins and have identified and characterized a large number of both known and previously uncharacterized proteins that interact with CaM in a Ca
2+
-dependent manner. The interactions of several identified proteins with Ca
2+
/CaM were confirmed by using pull-down assays and coimmunoprecipitation. Many of the CaM-binding proteins identified belong to protein families such as the DEAD/H box proteins, ribosomal proteins, proteasome 26S subunits, and deubiquitinating enzymes, suggesting the possible involvement of Ca
2+
/CaM in different signaling pathways. The selection method described herein could be used to identify the binding partners of other calcium sensors on the proteome-wide scale.
Nanoscale visualization and characterization of
Myxococcus xanthus
cells with atomic force microscopy
Authors: Pelling Andrew E. , Li Yinuo , Shi Wenyuan , Gimzewski James K.
Published: April 2005

Multicellular microbial communities are the predominant form of existence for microorganisms in nature. As one of the most primitive social organisms,
Myxococcus xanthus
has been an ideal model bacterium for studying intercellular interaction and multicellular organization. Through previous genetic and EM studies, various extracellular appendages and matrix components have been found to be involved in the social behavior of
M. xanthus
, but none of them was directly visualized and analyzed under native conditions. Here, we used atomic force microscopy (AFM) imaging and
in vivo
force spectroscopy to characterize these cellular structures under native conditions. AFM imaging revealed morphological details on the extracellular ultrastructures at an unprecedented resolution, and
in vivo
force spectroscopy of live cells in fluid allowed us to nanomechanically characterize extracellular polymeric substances. The findings provide the basis for AFM as a useful tool for investigating microbial-surface ultrastructures and nanomechanical properties under native conditions.
Reversible redox-dependent modulation of mitochondrial aconitase and proteolytic activity during
in vivo
cardiac ischemia/reperfusion
Authors: Bulteau Anne-Laure , Lundberg Kathleen C. , Ikeda-Saito Masao , Isaya Grazia , Szweda Luke I.
Published: April 2005

Prooxidents can induce reversible inhibition or irreversible inactivation and degradation of the mitochondrial enzyme aconitase. Cardiac ischemia/reperfusion is associated with an increase in mitochondrial free radical production. In the current study, the effects of reperfusion-induced production of prooxidants on mitochondrial aconitase and proteolytic activity were determined to assess whether alterations represented a regulated response to changes in redox status or oxidative damage. Evidence is provided that ATP-dependent proteolytic activity increased during early reperfusion followed by a time-dependent reduction in activity to control levels. These alterations in proteolytic activity paralleled an increase and subsequent decrease in the level of oxidatively modified protein.
In vitro
data supports a role for prooxidants in the activation of ATP-dependent proteolytic activity. Despite inhibition during early periods of reperfusion, aconitase was not degraded under the conditions of these experiments. Aconitase activity exhibited a decline in activity followed by reactivation during cardiac reperfusion. Loss and regain in activity involved reversible sulfhydryl modification. Aconitase was found to associate with the iron binding protein frataxin exclusively during reperfusion.
In vitro
, frataxin has been shown to protect aconitase from [4Fe-4S]
2+
cluster disassembly, irreversible inactivation, and, potentially, degradation. Thus, the response of mitochondrial aconitase and ATP-dependent proteolytic activity to reperfusion-induced prooxidant production appears to be a regulated event that would be expected to reduce irreparable damage to the mitochondria.
Gelation-driven component selection in the generation of constitutional dynamic hydrogels based on guanine-quartet formation
Authors: Sreenivasachary Nampally , Lehn Jean-Marie
Published: April 2005

The guanosine hydrazide 1 yields a stable supramolecular hydrogel based on the formation of a guanine quartet (G-quartet) in presence of metal cations. The effect of various parameters (concentration, nature of metal ion, and temperature) on the properties of this gel has been studied. Proton NMR spectroscopy is shown to allow a molecular characterization of the gelation process. Hydrazide 1 and its assemblies can be reversibly decorated by acylhydrazone formation with various aldehydes, resulting in formation of highly viscous dynamic hydrogels. When a mixture of aldehydes is used, the dynamic system selects the aldehyde that leads to the most stable gel. Mixing hydrazides 1, 9 and aldehydes 6, 8 in 1:1:1:1 ratio generated a constitutional dynamic library containing the four acylhydrazone derivatives A, B, C, and D. The library constitution displayed preferential formation of the acylhydrazone B that yields the strongest gel. Thus, gelation redirects the acylhydrazone distribution in the dynamic library as guanosine hydrazide 1 scavenges preferentially aldehyde 8, under the pressure of gelation because of the collective interactions in the assemblies of G-quartets B, despite the strong preference of the competing hydrazide 9 for 8. Gel formation and component selection are thermoreversible. The process amounts to gelation-driven self-organization with component selection and amplification in constitutional dynamic hydrogels based on G-quartet formation and reversible covalent connections. The observed self-organization and component selection occur by means of a multilevel self-assembly involving three dynamic processes, two of supramolecular and one of reversible covalent nature. They extend constitutional dynamic chemistry to phase-organization and phase-transition events.
Mast cells enhance T cell activation: Importance of mast cell-derived TNF
Authors: Nakae Susumu , Suto Hajime , Kakurai Maki , Sedgwick Jonathon D. , Tsai Mindy , Galli Stephen J.
Published: April 2005

Mast cells are not only important effector cells in immediate hypersensitivity reactions and immune responses to pathogens but also can contribute to T cell-mediated disorders. However, the mechanisms by which mast cells might influence T cells in such settings are not fully understood. We find that mast cells can enhance proliferation and cytokine production in multiple T cell subsets. Mast cell-dependent enhancement of T cell activation can be promoted by FcεRI-dependent mast cell activation, TNF production by both mast cells and T cells, and mast cell-T cell contact. However, at high concentrations of cells, mast cells can promote T cell activation independent of IgE or TNF. Finally, mast cells also can promote T cell activation by means of soluble factors. These findings identify multiple mechanisms by which mast cells can influence T cell proliferation and cytokine production.
A brain detoxifying enzyme for organophosphorus nerve poisons
Authors: Nomura Daniel K. , Leung Donmienne , Chiang Kyle P. , Quistad Gary B. , Cravatt Benjamin F. , Casida John E.
Published: April 2005

Organophosphorus (OP) insecticides and chemical warfare agents act primarily by inhibiting acetylcholinesterase. There are many secondary targets for OP toxicants as observed for example with the major insecticide chlorpyrifos and its bioactivated metabolite chlorpyrifos oxon (CPO). Therefore, it was surprising that the predominant mouse brain protein labeled
in vitro
by [
3
H-ethyl]CPO (1 nM) (designated CPO-binding protein or CPO-BP) is not one of these known OP toxicant targets. CPO-BP is a 50-kDa membrane-bound serine hydrolase measured by derivatization with [
3
H]CPO and SDS/PAGE or filtration binding assay. It appears to undergo rapid diethylphosphorylation by [
3
H]CPO followed by either dephosphorylation and reactivation or aging on loss of an ethyl group. CPO and several other OP toxicants potently inhibit CPO-BP
in vivo
(i.p., 2 h) (50% inhibition at 2-25 mg/kg) and
in vitro
(50% inhibition at 8-68 nM). Using three chemical labeling reagents, i.e., [
3
H]CPO and the activity-based proteomic probes fluorophosphonate-biotin and fluorophosphonate-rhodamine, mouse brain CPO-BP is identified as serine hydrolase KIAA1363 of unknown function. Brains from
KIAA1363
-/-
mice show greatly reduced levels of CPO labeling and hydrolytic metabolism compared to brains from wild-type mice. KIAA1363 therefore is the principal enzyme for metabolizing low levels of CPO in brain and may play a more general role in detoxification of OP nerve poisons.
Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution
Authors: Pagani Franco , Raponi Michela , Baralle Francisco E.
Published: April 2005

It is well established that exonic sequences contain regulatory elements of splicing that overlap with coding capacity. However, the conflict between ensuring splicing efficiency and preserving the coding capacity for an optimal protein during evolution has not been specifically analyzed. In fact, studies on genomic variability in fields as diverse as clinical genetics and molecular evolution mainly focus on the effect of mutations on protein function. Synonymous variations, in particular, are assumed to be functionally neutral both in clinical diagnosis and when measuring evolutionary distances between species. Using the cystic fibrosis transmembrane conductance regulator (CFTR) exon 12 splicing as a model, we have established that about one quarter of synonymous variations result in exon skipping and, hence, in an inactive CFTR protein. Furthermore, comparative splicing evaluation of mammalian sequence divergences showed that artificial combinations of CFTR exon 12 synonymous and nonsynonymous substitutions are incompatible with normal RNA processing. In particular, the combination of the mouse synonymous with the human missense variations causes exon skipping. It follows that there are two sequential levels at which evolutionary selection of genomic variants take place: splicing control and protein function optimization.
Sex and sugar in yeast: two distinct GPCR systems
Authors: Versele Matthias , Lemaire Katleen , Thevelein Johan M
Published: April 2005

Although eukaryotic G‐protein coupled receptor (GPCR) systems are well known for their ability to detect and mediate rapid responses to extracellular signals, the full range of stimuli to which they respond may not yet have been identified. Activation of GPCRs by hormones, pheromones, odorants, neurotransmitters, light and different taste compounds is well established. However, the recent discovery of a glucose‐sensing GPCR system in Saccharomyces cerevisiae has unexpectedly added common nutrients to this list of stimuli. This GPCR system mediates glucose activation of adenylate cyclase during the switch from respirative/gluconeogenic metabolism to fermentation. The GPCR system involved in pheromone signalling in S. cerevisiae has already served as an important model and tool for the study of GPCR systems in higher eukaryotic cell types. Here, we highlight the similarities and differences between these two signalling systems. We also indicate how the new glucose‐sensing system can serve as a model for GPCR function and as a tool with which to screen for heterologous components of signalling pathways as well as for novel ligands in high‐throughput assays.
A genetic look at the active site of RNA polymerase III
Authors: Rozenfeld Sophie , Thuriaux Pierre
Published: April 2005

rpc160‐112, a mutant of the RNA polymerase III active site, is corrected in vivo by six second‐site mutants obtained by random mutagenesis. These mutants introduce single‐site amino acid replacements at the two large subunits of the enzyme. The mutated motifs are conserved in RNA polymerases I and II and, for some of them, in the bacterial enzyme, thus delineating key elements of the active site in eukaryotic RNA polymerases.
Structure–function relationships in HIV‐1 Nef
Authors: Geyer Matthias , Fackler Oliver T , Peterlin B Matija
Published: April 2005

The accessory Nef protein of HIV and SIV is essential for viral pathogenesis, yet it is perplexing in its multitude of molecular functions. In this review we analyse the structure–function relationships of motifs recently proposed to play roles in aspects of Nef modification, signalling and trafficking, and thereby to impinge on the ability of the virus to survive in, and to manipulate, its cellular host. Based on the full‐length structure assembly of HIV Nef, we correlate surface accessibility with secondary structure elements and sequence conservation. Motifs involved in Nef‐mediated CD4 and MHC I downregulation are located in flexible regions of Nef, suggesting that the formation of the transient trafficking complexes involved in these processes depends on the recognition of primary sequences. In contrast, the interaction sites for signalling molecules that contain SH3 domains or the p21‐activated kinases are associated with the well folded core domain, suggesting the recognition of highly structured protein surfaces.
A UK Test of an Inflation‐Adjusted Ohlson Model
Authors: Gregory Alan , Saleh Walid , Tucker Jon
Published: April 2005

Abstract:  This paper conducts a UK test of a version of the Ohlson (1995) model. We should only expect abnormal earnings to revert to zero if the book value of assets is economically meaningful. In this paper we make use of the property revaluations common in UK accounts, but estimate other asset values and earnings in inflation‐adjusted terms. This, we argue, gives rise to estimates of abnormal earnings that can reasonably be expected to revert to zero. We then test this modified model on UK data using the Dechow, Hutton and Sloan (1999) method. In line with the predictions of the Ohlson model, we find that these modified abnormal earnings appear to mean revert, and that a first order autoregressive process is sufficient to capture the persistence of UK real abnormal earnings. The modified abnormal earnings model in general predicts one year ahead earnings more successfully than an unmodified model. Furthermore, for much of the sample period, one year ahead predictions of abnormal earnings are better for the real model during periods of higher inflation. The undervaluation problem found in prior studies appears to be replaced with an overvaluation problem in the real model which is more acute during periods of high inflation. Last, we show that an estimate of the model based upon an industry level specification appears to perform no better than a market‐wide specification of the model.
Multiplicity of different cell‐ and organ‐specific import routes for the NADPH‐protochlorophyllide oxidoreductases A and B in plastids of Arabidopsis seedlings
Authors: Kim Chanhong , Ham Hyemin , Apel Klaus
Published: April 2005

The NADPH‐dependent protochlorophyllide (Pchlide) oxidoreductase (POR) is a photoenzyme that requires light for its catalytic activity and uses Pchlide itself as a photoreceptor. In Arabidopsis there are three PORs denoted PORA, PORB and PORC. The PORA and PORB genes are strongly expressed early in seedling development. In contrast to PORB the import of PORA into plastids of cotyledons is substrate‐dependent and organ‐specific. These differences in the import reactions between PORA and PORB most likely are due to different import mechanisms that are responsible for the uptake of these proteins. The two major core constituents of the translocon of the outer plastid envelope, Toc159 and Toc34, have been implicated in the binding and recognition of precursors of nuclear‐encoded plastid proteins. Their involvement in conferring substrate dependency and organ specificity of PORA import was analyzed in intact Arabidopsis seedlings of wild type and the three mutants ppi3, ppi1 and ppi2 that are deficient in atToc34, atToc33, a closely related isoform of atToc34, and atToc159. Whereas none of these three Toc constituents is required for maintaining the organ specificity and substrate dependency of PORA import, atToc33 is indispensable for the import of PORB in cotyledons and true leaves suggesting that in these parts of the plant translocation of PORA and PORB occurs via two distinct import pathways. The analysis of PORA and PORB import into plastids of intact seedlings revealed an unexpected multiplicity of import routes that differed by their substrate, cell, tissue and organ specificities. This versatility of pathways for protein targeting to plastids suggests that in intact seedlings not only the constituents of the core complex of import channels but also other factors are involved in mediating the import of nuclear‐encoded plastid proteins.
Stylar glycoproteins bind to S‐RNase in vitro
Authors: Cruz‐Garcia Felipe , Nathan Hancock C. , Kim Donggiun , McClure Bruce
Published: April 2005

S‐RNases determine the specificity of S‐specific pollen rejection in self‐incompatible plants of the Solanaceae, Rosaceae, and Scrophulariaceae. They are also implicated in at least two distinct types of unilateral interspecific incompatibility in Nicotiana. However, S‐RNase itself is not sufficient for most types of pollen rejection, and evidence for its direct interaction with pollen tubes is limited. Thus, non‐S‐RNase factors also are required for pollen rejection. As one approach to identifying such factors, we tested whether SC10‐RNase from Nicotiana alata would bind to other stylar proteins in vitro. SC10‐RNase was immobilized on Affi‐gel, and binding proteins were analyzed by SDS‐PAGE and immunoblotting. In addition to SC10‐RNase and a small protein similar to lily chemocyanin, the most prominent binding proteins include NaTTS, 120K, and NaPELPIII, these latter three being arabinogalactan proteins previously shown to interact directly with pollen tubes. We also show that SC10‐RNase and these glycoproteins migrate as a complex in a native PAGE system. Our hypothesis is that S‐RNase forms a complex with these glycoproteins in the stylar ECM, that the glycoproteins interact directly with the pollen tubes and thus that the initial interaction between the pollen tube and S‐RNase is indirect.
A nuclear gene of Chlamydomonas reinhardtii, Tba1, encodes a putative oxidoreductase required for translation of the chloroplast psbA mRNA
Authors: Somanchi Aravind , Barnes Dwight , Mayfield Stephen P.
Published: April 2005

Biosynthesis of chloroplast proteins is to a large extent regulated post‐transcriptionally, and a number of nuclear‐encoded genes have been identified that are required for translation or stability of specific chloroplast mRNAs. A nuclear mutant of Chlamydomonas reinhardtii, hf261, deficient in the translation of the psbA mRNA, has reduced association of the psbA mRNA with ribosomes and is deficient in binding of the chloroplast localized poly (A) binding protein (cPAB1) to the psbA mRNA. Cloning of the hf261 locus and complementation of hf261 using a wt genomic clone has identified a novel gene, Tba1, for translational affector of psbA. Strains complemented with the wt Tba1 gene restore the ability of the psbA mRNA to associate with ribosomes, and restores RNA binding activity of cPAB1 for the psbA mRNA. Analysis of the Tba1 gene identified a protein with significant homology to oxidoreductases. The effect of Tba1 expression on the RNA binding activity of cPAB1, and on the association of psbA mRNA with ribosomes, implies that Tba1 functions as a redox regulator of cPAB1 RNA binding activity to indirectly promote psbA mRNA translation initiation. A model of chloroplast translation incorporating Tba1 and other members of the psbA mRNA binding complex is presented.
EDS1 in tomato is required for resistance mediated by TIR‐class R genes and the receptor‐like R gene Ve
Authors: Hu Gongshe , DeHart Amy K.A. , Li Yansu , Ustach Carolyn , Handley Vanessa , Navarre Roy , Hwang Chin‐Feng , Aegerter Brenna J. , Williamson Valerie M. , Baker Barbara
Published: April 2005

In tobacco and other Solanaceae species, the tobacco N gene confers resistance to tobacco mosaic virus (TMV), and leads to induction of standard defense and resistance responses. Here, we report the use of N‐transgenic tomato to identify a fast‐neutron mutant, sun1‐1 (suppressor of N), that is defective in N‐mediated resistance. Induction of salicylic acid (SA) and expression of pathogenesis‐related (PR) genes, each signatures of systemic acquired resistance, are both dramatically suppressed in sun1‐1 plants after TMV treatment compared to wild‐type plants. Application of exogenous SA restores PR gene expression, indicating that SUN1 acts upstream of SA. Upon challenge with additional pathogens, we found that the sun1‐1 mutation impairs resistance mediated by certain resistance (R) genes, (Bs4, I, and Ve), but not others (Mi‐1). In addition, sun1‐1 plants exhibit enhanced susceptibility to TMV, as well as to virulent pathogens. sun1‐1 has been identified as an EDS1 homolog present on chromosome 6 of tomato. The discovery of enhanced susceptibility in the sun1‐1 (Le_eds1‐1) mutant plant, which contrasts to reports in Nicotiana benthamiana using virus‐induced gene silencing, provides evidence that the intersection of R gene‐mediated pathways with general resistance pathways is conserved in a Solanaceous species. In tomato, EDS1 is important for mediating resistance to a broad range of pathogens (viral, bacterial, and fungal pathogens), yet shows specificity in the class of R genes that it affects (TIR‐NBS‐LRR as opposed to CC‐NBS‐LRR). In addition, a requirement for EDS1 for Ve‐mediated resistance in tomato exposes that the receptor‐like R gene class may also require EDS1.
The pvr1 locus in Capsicum encodes a translation initiation factor eIF4E that interacts with Tobacco etch virus VPg
Authors: Kang Byoung‐Cheorl , Yeam Inhwa , Frantz James D. , Murphy John F. , Jahn Molly M.
Published: April 2005

Mutations in the eIF4E homolog encoded at the pvr1 locus in Capsicum result in broad‐spectrum potyvirus resistance attributed to the pvr1 resistance allele, a gene widely deployed in agriculture for more than 50 years. We show that two other resistance genes, previously known to be eIF4E with narrower resistance spectra, pvr21 and pvr22, are alleles at the pvr1 locus. Based on these data and current nomenclature guidelines, we have re‐designated these alleles, pvr11 and pvr12, respectively. Point mutations in pvr1, pvr11, and pvr12 grouped to similar regions of eIF4E and were predicted by protein homology models to cause conformational shifts in the encoded proteins. The avirulence determinant in this potyvirus system has previously been identified as VPg, therefore yeast two‐hybrid and GST pull‐down assays were carried out with proteins encoded by the pvr1 alleles and VPg from two different strains of Tobacco etch virus (TEV) that differentially infected Capsicum lines carrying these genes. While the protein encoded by the susceptible allele pvr1+ interacted strongly, proteins translated from all three resistance alleles (pvr1, pvr11, and pvr12) failed to bind VPg from either strain of TEV. This failure to bind correlated with resistance or reduced susceptibility, suggesting that interruption of the interaction between VPg and this eIF4E paralog may be necessary, but is not sufficient for potyvirus resistance in vivo. Among the three resistance alleles, only the pvr1 gene product failed to bind m7‐GTP cap‐analog columns, suggesting that disrupted cap binding is not required for potyvirus resistance.
SIPK signaling controls multiple components of harpin‐induced cell death in tobacco
Authors: Samuel Marcus A. , Hall Hardy , Krzymowska Magdalena , Drzewiecka Kinga , Hennig Jacek , Ellis Brian E.
Published: April 2005

Harpin from Pseudomonas syringae pv. phaseolicola (HrpZ) elicits a rapid cell death response in tobacco plants. Multiple signaling components, including mitogen‐activated protein kinase (MAPK), reactive oxygen species (ROS) and salicylic acid (SA), have been reported to be involved in this cell death process, but the interaction between these molecules is poorly understood. Here we show through utilizing plants manipulated in SIPK expression levels that lack of SIPK results in increased sensitivity to harpin with concomitant accumulation of higher levels of ROS. Conversely, SIPK‐overexpressing plants show reduced sensitivity to harpin relative to wild‐type plants, and display reduced ROS accumulation. Harpin‐induced cell death was found to be conditional on the ability of the plant to accumulate SA, whereas harpin induction of MAPK activation and ROS accumulation are not. However, harpin‐induced ROS accumulation is required for activation of SIPK and wound‐induced protein kinase. Transcriptional profiling revealed that suppression of SIPK signaling also affects early expression of a range of pathogen‐ and stress‐responsive genes during harpin challenge.
Staphylococcus aureus pathogenicity on Arabidopsis thaliana is mediated either by a direct effect of salicylic acid on the pathogen or by SA‐dependent, NPR1‐independent host responses
Authors: Prithiviraj Balakrishnan , Bais Harsh P. , Jha Ajay K. , Vivanco Jorge M.
Published: April 2005

Staphylococcus aureus is a ubiquitous gram‐positive bacterium that can cause superficial to serious systemic infections in animals and humans. Here we report the development of a plant infection model to study the pathogenesis of this bacterium. Three global regulatory mutants, RN6911 (agr−), ALC 488 (sarA−) ALC 842 (sarA−/agr−) and an alpha‐toxin mutant defective in biofilm formation (DU1090) which are attenuated in animal pathogenesis, were also attenuated in their ability to infect plants, suggesting that these regulators that mediate synthesis of virulence factors essential for animal pathogenesis are also required for plant pathogenesis. Further, using Arabidopsis plants altered in defense responses such as the transgenic lines NahG [defective in salicylic acid (SA) accumulation], and 35S‐LOX2(−) (defective in jasmonic acid production and hyper‐accumulator of SA), and mutants ics1 (depleted in SA accumulation), and npr1‐1 (non‐expressor of pathogenesis‐related protein) we show that resistance of Arabidopsis to typical plant pathogens and the animal pathogen S. aureus is conserved and is mediated by SA. The data presented here suggest that Arabidopsis thaliana resistance to S. aureus is mediated either by a direct effect of SA on the pathogen, specifically one that affects the attachment/aggregate formation on the root surface and reduces the pathogen's virulence, or by SA‐dependent, NPR1‐independent host responses.
Marking cell lineages in living tissues
Authors: Kurup Smita , Runions John , Köhler Uwe , Laplaze Laurent , Hodge Sarah , Haseloff Jim
Published: April 2005

We have generated a novel genetic system to visualize cell lineages in living tissues at high resolution. Heat shock was used to trigger the excision of a specific transposon and activation of a fluorescent marker gene. A histone‐YFP marker was used to allow identification of cell lineages and easy counting of cells. Constitutive expression of a green fluorescent membrane protein was used to provide a precise outline of all surrounding cells. Marked lineages can be induced from specific cells within the organism by targeted laser irradiation, and the fate of the marked cells can be followed non‐invasively. We have used the system to map cell lineages originating from the initials of primary and lateral roots in Arabidopsis. The lineage marking technique enabled us to measure the differential contribution of primary root pericycle cell files to developing lateral root primordia. The majority of cells in an emerging lateral root primordium derive from the central file of pericycle founder cells while off‐centre founder cells contribute only a minor proliferation of tissue near the base of the root. The system shows great promise for the detailed study of cell division during morphogenesis.
Corridors in Real Landscapes: A Reply to Simberloff and Cox
Authors: NOSS REED F.
Published: April 2005

Abstract: Habitat corridors have become popular in land‐use plans and conservation strategies, yet few data are available to either support or refute their value. Simberloff and Cox (1987) have criticized what they consider an uncritical acceptance of corridors in conservation planning.

Any reasonable conservation strategy must address the overwhelming problem of habitat fragmentation. Although Simberloff and Cox use island analogies to illustrate advantages of isolation, these analogies do not apply directly to problems in landscape planning. Genetics also does not offer unequivocal advice, but the life histories of wide‐ranging animals (eg., the Florida panther) suggest that the maintenance or restoration of connectivity in the landscape is a prudent strategy. Translocation of individuals among reserves—considered by Simberloff and Cox a viable alternative to natural dispersal—is impractical for whole communities of species that are likely to suffer from problems related to fragmentation.

Many of the potential disadvantages of corridors could be avoided or mitigated by enlatging cowidor width or by applying ecologically sound zoning regulations. Corridors are not the solution to all of our conservation problems, nor should they be used as a justification for small reserves. But corridors can be a cost‐effective complement to the strategy of large and multiple reserves in real‐life landscapes.
How Dams and Wildlife Can Coexist: Natural Habitats, Agriculture, and Major Water Resource Development Projects in Tropical Asia
Authors: McNEELY JEFFREY A.
Published: April 2005

Abstract: Tropical Asia is densely populated, yet is selfsufficient in food (at least in the good years). Major investments have been made in water resources development, aimed at expanding the area of land under irrigated agriculture and thereby increasing agricultural production. Such investments are often considered highly destructive of natural habitats, but destruction is not always a necessary companion of dam construction. This paper examines three examples—at international, national, and local levels—where governments and various development agencies have determined that the success of their investments depended on controlling deforestation in the watershed areas of major water resources development projects: the massive Mekong development program in Indochina, Sri Lanka's Mahaweli scheme, and Indonesia's Dumoga project in northern Sulawesi. In each situation, national parks and other sorts of reserves were found essential to the success of the overall effort, with diyferent sorts of land‐use problems requiring different sorts of solutions. Each case has experienced, for different reasons, some difficulty in converting ecological science to on‐the‐ground solutions to development problems. Suggestions are made on bow ecological science can help water resources development projects yield maximum benefits, within the limits imposed by politics and economics, for the conservation of biological diversity. Watershed protection can be used to justify reserves that otherwise might not be established, and irrigation agencies can make powerful potential allies for protected areas that protect watersheds In many cases, the total costs of establishing and managing reserves that protect catchment areas can be met and justified as part of the hydrological investment.