bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating regional cloud‐permitting simulations of the WRF model for the Tropical Warm Pool International Cloud Experiment (TWP‐ICE), Darwin, 2006
Authors: Wang Yi , Long C. N. , Leung L. R. , Dudhia J. , McFarlane S. A. , Mather J. H. , Ghan S. J. , Liu X.
Published: November 2009

Data from the Tropical Warm Pool International Cloud Experiment (TWP‐ICE) were used to evaluate Weather Research and Forecasting (WRF) model simulations with foci on the performance of three six‐class bulk microphysical parameterizations (BMPs). Before the comparison with data from TWP‐ICE, a suite of WRF simulations were carried out under an idealized condition, in which the other physical parameterizations were turned off. The idealized simulations were intended to examine the interaction of BMP at a “cloud‐resolving” scale (250 m) with the nonhydrostatic dynamic core of the WRF model. The other suite of nested WRF simulations was targeted on the objective analysis of TWP‐ICE at a “cloud‐permitting” scale (quasi‐convective resolving, 4 km). Wide ranges of discrepancies exist among the three BMPs when compared with ground‐based and satellite remote sensing retrievals for TWP‐ICE. Although many processes and associated parameters may influence clouds, it is strongly believed that atmospheric processes fundamentally govern the cloud feedbacks through the interactions between the atmospheric circulations, cloudiness, and the radiative and latent heating of the atmosphere. Based on the idealized experiments, we suggest that the discrepancy is a result of the different treatment of ice‐phase microphysical processes (e.g., cloud ice, snow, and graupel). Because of the turn‐off of the radiation and other physical parameterizations, the cloud radiation feedback is not studied in idealized experiments. On the other hand, the “cloud‐permitting” experiments engage all physical parameterizations in the WRF model so that the radiative heating processes are considered together with other physical processes. Common features between these two experiment suites indicate that the major discrepancies among the three BMPs are similar. This strongly suggests the importance of ice‐phase microphysics. To isolate the influence of cloud radiation feedback, we further carried out an additional suite of simulations, which turns off the interactions between cloud and radiation schemes. It is found that the cloud radiation feedback plays a secondary, but nonnegligible role in contributing to the wide range of discrepancies among the three BMPs.
Continuous measurements of discharge from a horizontal acoustic Doppler current profiler in a tidal river
Authors: Hoitink A. J. F. , Buschman F. A. , Vermeulen B.
Published: November 2009

Acoustic Doppler current profilers (ADCPs) can be mounted horizontally at a river bank, yielding single‐depth horizontal array observations of velocity across the river. This paper presents a semideterministic, semistochastic method to obtain continuous measurements of discharge from horizontal ADCP (HADCP) data in a tidal river. In the deterministic part, single‐depth velocity data are converted to specific discharge by applying the law of the wall, which requires knowledge of local values of the bed roughness length (z0). A new filtration technique was developed to infer cross‐river profiles of z0 from moving boat ADCP measurements. Width‐averaged values of z0 were shown to be predominantly constant in time but differed between ebb and flood. In the stochastic part of the method, specific discharge was converted to total discharge on the basis of a model that accounts for the time lag between flow variation in the central part of the river and flow variation near the banks. Model coefficients were derived using moving boat ADCP data. The consistency of mutually independent discharge estimates from HADCP measurements was investigated to validate the method, analyzing river discharge and tidal discharge separately. Inaccuracy of the method is attributed primarily to mechanisms controlling transverse exchange of momentum, which produce temporal variation in the discharge distribution over the cross section. Specifically, development of river dunes may influence the portion of the discharge concentrated within the range of the HADCP.
The Energy Use Associated with Neural Computation in the Cerebellum
Authors: Howarth Clare , Peppiatt-Wildman Claire M , Attwell David
Published: November 2009

The brain's energy supply determines its information processing power, and generates functional imaging signals, which are often assumed to reflect principal neuron spiking. Using measured cellular properties, we analysed how energy expenditure relates to neural computation in the cerebellar cortex. Most energy is used on information processing by non-principal neurons: Purkinje cells use only 18% of the signalling energy. Excitatory neurons use 73% and inhibitory neurons 27% of the energy. Despite markedly different computational architectures, the granular and molecular layers consume approximately the same energy. The blood vessel area supplying glucose and O2 is spatially matched to energy consumption. The energy cost of storing motor information in the cerebellum was also estimated.
Effects of Administration Route on Migration and Distribution of Neural Progenitor Cells Transplanted into Rats with Focal Cerebral Ischemia, an MRI Study
Authors: Li Lian , Jiang Quan , Ding Guangliang , Zhang Li , Zhang Zheng Gang , Li Qingjiang , Panda Swayamprava , Lu Mei , Ewing James R , Chopp Michael
Published: November 2009

We tested the hypotheses that administration routes affect the migration and distribution of grafted neural progenitor cells (NPCs) in the ischemic brain and that the ischemic lesion plays a role in mediating the grafting process. Male Wistar rats ( n=41) were subjected to 2-h middle cerebral artery occlusion (MCAo), followed 1 day later by administration of magnetically labeled NPCs. Rats with MCAo were assigned to one of three treatment groups targeted for cell transplantation intra-arterially (IA), intracisternally (IC), or intravenously (IV). MRI measurements consisting of T2-weighted imaging and three-dimensional (3D) gradient echo imaging were performed 24 h after MCAo, 4 h after cell injection, and once a day for 4 days. Prussian blue staining was used to identify the labeled cells, 3D MRI to detect cell migration and distribution, and T2 map to assess lesion volumes. Intra-arterial (IA) administration showed significantly increased migration, a far more diffuse distribution pattern, and a larger number of transplanted NPCs in the target brain than IC or IV administration. However, high mortality with IA delivery (IA: 41%; IC: 17%; IV: 8%) poses a serious concern for using this route of administration. Animals with smaller lesions at the time of transplantation have fewer grafted cells in the parenchyma.
Ecophysiological traits of grasses: resolving the effects of photosynthetic pathway and phylogeny
Authors: Taylor Samuel , Rees Mark , Hulme Stephen , Freckleton Rob , Ripley Brad , Woodward F. , Osborne Colin
Published: November 2009

C4 photosynthesis is an important example of convergent evolution in plants, having arisen in eudicots, monocots and diatoms. Comparisons between such diverse groups are confounded by phylogenetic and ecological differences, so that only broad generalisations can be made about the role of C4 photosynthesis indetermining ecophysiological traits. However, 60% of C4 species occur in the grasses (Poaceae) and molecular phylogenetic techniques confirm that there are between 8 and 17 independent origins of C4 photosynthesis in the Poaceae. In a screening experiment, we compared leaf physiology and growth traits across several majorindependent C3 & C4 groups within the Poaceae, asking 1) which traits differ consistently between photosynthetictypes and 2) which traits differ consistently between clades within each photosynthetic type.
TLRR (lrrc67) interacts with PP1 and is associated with a cytoskeletal complex in the testis
Authors: Wang Rong , Kaul Aseem , Sperry Ann O.
Published: November 2009

Background information. Spermatozoa are formed via a complex series of cellular transformations, including acrosome and flagellum formation, nuclear condensation and elongation and removal of residual cytoplasm. Nuclear elongation is accompanied by the formation of a unique cytoskeletal structure, the manchette. We have previously identified a leucine‐rich repeat protein that we have named TLRR (testis leucine‐rich repeat), associated with the manchette that contains a PP1 (protein phosphatase‐1)‐binding site. Leucine‐rich repeat proteins often mediate protein–protein interactions; therefore, we hypothesize that TLRR acts as a scaffold to link signalling molecules, including PP1, to the manchette near potential substrate proteins important for spermatogenesis.

Results. TLRR and PP1 interact with one another as demonstrated by co‐immunoprecipitation and the yeast two‐hybrid assay. TLRR binds more strongly to PP1γ2 than it does to PP1α. Anti‐phosphoserine antibodies immunoprecipitate TLRR from testis lysate, indicating that TLRR is a phosphoprotein. TLRR is part of a complex in testis that includes cytoskeletal proteins and constituents of the ubiquitin–proteasome pathway. The TLRR complex purified from 3T3 cells contains similar proteins, co‐localizes with microtubules and is enriched at the microtubule‐organizing centre. TLRR is also detected near the centrosome of elongated, but not mid‐stage, spermatids.

Conclusion. We demonstrate here that TLRR interacts with PP1, particularly the testis‐specific isoform, PP1γ2. Immunoaffinity purification confirms that TLRR is associated with the spermatid cytoskeleton. In addition, proteins involved in protein stability are part of the TLRR complex. These results support our hypothesis that TLRR links signalling molecules to the spermatid cytoskeleton in order to regulate important substrates involved in spermatid transformation. The translocation of TLRR from the manchette to the centrosome region suggests a possible role for this protein in tail formation. Our finding that TLRR is associated with microtubules in cultured cells suggests that TLRR may play a common role in modulating the cytoskeleton in other cell types besides male germ cells.
Structural insights into the catalytic mechanism of Trypanosoma cruzi GPXI (glutathione peroxidase-like enzyme I)
Authors: Patel Shreenal , Hussain Syeed , Harris Richard , Sardiwal Sunita , Kelly John M. , Wilkinson Shane R. , Driscoll Paul C. , Djordjevic Snezana
Published: November 2009

Current drug therapies against Trypanosoma cruzi, the causative agent of Chagas disease, have limited effectiveness and are highly toxic. T. cruzi-specific metabolic pathways that utilize trypanothione for the reduction of peroxides are being explored as potential novel therapeutic targets. In the present study we solved the X-ray crystal structure of one of the T. cruzi enzymes involved in peroxide reduction, the glutathione peroxidase-like enzyme TcGPXI (T. cruzi glutathione peroxidase-like enzyme I). We also characterized the wild-type, C48G and C96G variants of TcGPXI by NMR spectroscopy and biochemical assays. Our results show that residues Cys48 and Cys96 are required for catalytic activity. In solution, the TcGPXI molecule readily forms a Cys48–Cys96 disulfide bridge and the polypeptide segment containing Cys96 lacks regular secondary structure. NMR spectra of the reduced TcGPXI are indicative of a protein that undergoes widespread conformational exchange on an intermediate time scale. Despite the absence of the disulfide bond, the active site mutant proteins acquired an oxidized-like conformation as judged from their NMR spectra. The protein that was used for crystallization was pre-oxidized by t-butyl hydroperoxide; however, the electron density maps clearly showed that the active site cysteine residues are in the reduced thiol form, indicative of X-ray-induced reduction. Our crystallographic and solution studies suggest a level of structural plasticity in TcGPXI consistent with the requirement of the atypical two-cysteine (2-Cys) peroxiredoxin-like mechanism implied by the behaviour of the Cys48 and Cys96 mutant proteins.
Regulation of cellular polyamine levels and cellular proliferation by antizyme and antizyme inhibitor
Authors: Kahana Chaim
Published: November 2009

Polyamines are small aliphatic polycations present in all living cells. Polyamines are essential for cellular viability and are involved in regulating fundamental cellular processes, most notably cellular growth and proliferation. Being such central regulators of fundamental cellular functions, the intracellular polyamine concentration is tightly regulated at the levels of synthesis, uptake, excretion and catabolism. ODC (ornithine decarboxylase) is the first key enzyme in the polyamine biosynthesis pathway. ODC is characterized by an extremely rapid intracellular turnover rate, a trait that is central to the regulation of cellular polyamine homoeostasis. The degradation rate of ODC is regulated by its end-products, the polyamines, via a unique autoregulatory circuit. At the centre of this circuit is a small protein called Az (antizyme), whose synthesis is stimulated by polyamines. Az inactivates ODC and targets it to ubiquitin-independent degradation by the 26S proteasome. In addition, Az inhibits uptake of polyamines. Az itself is regulated by another ODC-related protein termed AzI (antizyme inhibitor). AzI is highly homologous with ODC, but it lacks ornithine-decarboxylating activity. Its ability to serve as a regulator is based on its high affinity to Az, which is greater than the affinity Az has to ODC. As a result, it interferes with the binding of Az to ODC, thus rescuing ODC from degradation and permitting uptake of polyamines.
Design of polyamine-based therapeutic agents: new targets and new directions
Authors: Senanayake M.D. Thulani , Amunugama Hemali , Boncher Tracey D. , Casero Robert A. , Woster Patrick M.
Published: November 2009

Enzymes in the biosynthetic and catabolic polyamine pathway have long been considered targets for drug development, and early drug discovery efforts in the polyamine area focused on the design and development of specific inhibitors of the biosynthetic pathway, or polyamine analogues that specifically bind DNA. More recently, it has become clear that the natural polyamines are involved in numerous known and unknown cellular processes, and disruption of polyamine functions at their effector sites can potentially produce beneficial therapeutic effects. As new targets for polyamine drug discovery continue to evolve, the rational design of polyamine analogues will result in more structurally diverse agents. In addition, the physical linkage of polyamine-like structures to putative drug molecules can have beneficial effects resulting from increases in DNA affinity and selective cellular uptake. The present chapter will summarize recent advances in the development of alkylpolyamine analogues as antitumour agents, and describe subsequent advances that have resulted from incorporating polyamine character into more diverse drug molecules. Specifically, new polyamine analogues, and the role of polyamine fragments in the design of antiparasitic agents, antitumour metal complexes, histone deacetylase inhibitors and lysine-specific demethylase 1 inhibitors, will be described.
Polyamines as mediators of APC-dependent intestinal carcinogenesis and cancer chemoprevention
Authors: Rial Nathaniel S. , Meyskens Frank L. , Gerner Eugene W.
Published: November 2009

Combination chemoprevention for cancer was proposed a quarter of a century ago, but has not been implemented in standard medical practice owing to limited efficacy and toxicity. Recent trials have targeted inflammation and polyamine biosynthesis, both of which are increased in carcinogenesis. Preclinical studies have demonstrated that DFMO (difluoromethylornithine), an irreversible inhibitor of ODC (ornithine decarboxylase) which is the first enzyme in polyamine biosynthesis, combined with NSAIDs (non-steroidal anti-inflammatory drugs) suppresses colorectal carcinogenesis in murine models. The preclinical rationale for combination chemoprevention with DFMO and the NSAID sulindac, was strengthened by the observation that a SNP (single nucleotide polymorphism) in the ODC promoter was prognostic for adenoma recurrence in patients with prior sporadic colon polyps and predicted reduced risk of adenoma in those patients taking aspirin. Recent results from a phase III clinical trial showed a dramatic reduction in metachronous adenoma number, size and grade. Combination chemoprevention with DFMO and sulindac was not associated with any serious toxicity. A non-significant trend in subclinical ototoxicity was detected by quantitative audiology in a subset of patients identified by a genetic marker. These preclinical, translational and clinical data provide compelling evidence for the efficacy of combination chemoprevention. DFMO and sulindac is a rational strategy for the prevention of metachronous adenomas, especially in patients with significant risk for colorectal cancer. Toxicities from this combination may be limited to subsets of patients identified by either past medical history or clinical tests.
Transgenic animals modelling polyamine metabolism-related diseases
Authors: Alhonen Leena , Uimari Anne , Pietilä Marko , Hyvönen Mervi T. , Pirinen Eija , Keinänen Tuomo A.
Published: November 2009

Cloning of genes related to polyamine metabolism has enabled the generation of genetically modified mice and rats overproducing or devoid of proteins encoded by these genes. Our first transgenic mice overexpressing ODC (ornithine decarboxylase) were generated in 1991 and, thereafter, most genes involved in polyamine metabolism have been used for overproduction of the respective proteins, either ubiquitously or in a tissue-specific fashion in transgenic animals. Phenotypic characterization of these animals has revealed a multitude of changes, many of which could not have been predicted based on the previous knowledge of the polyamine requirements and functions. Animals that overexpress the genes encoding the inducible key enzymes of biosynthesis and catabolism, ODC and SSAT (spermidine/spermine N1-acetyltransferase) respectively, appear to possess the most pleiotropic phenotypes. Mice overexpressing ODC have particularly been used as cancer research models. Transgenic mice and rats with enhanced polyamine catabolism have revealed an association of rapidly depleted polyamine pools and accelerated metabolic cycle with development of acute pancreatitis and a fatless phenotype respectively. The latter phenotype with improved glucose tolerance and insulin sensitivity is useful in uncovering the mechanisms that lead to the opposite phenotype in humans, Type 2 diabetes. Disruption of the ODC or AdoMetDC [AdoMet (S-adenosylmethionine) decarboxylase] gene is not compatible with mouse embryogenesis, whereas mice with a disrupted SSAT gene are viable and show no harmful phenotypic changes, except insulin resistance at a late age. Ultimately, the mice with genetically altered polyamine metabolism can be used to develop targeted means to treat human disease conditions that they relevantly model.
Structure and electrical properties of double perovskite Sr(Ni1∕2Mo1∕2)O3 ceramics
Authors: Prasatkhetragarn Anurak , Ketsuwan Piyachon , Maensiri Santi , Yimnirun Rattikorn , Huang Chien-Chih , Cann David P.
Published: November 2009

The double perovskite Sr(Ni1∕2Mo1∕2)O3 has been prepared with solid-state reaction and was characterized by x-ray diffraction technique. It has been indicated that the single phase is formed at 1300°C in air. The compound undergoes a phase transition at 280°C, where the structure of the ordered perovskite type changes from tetragonal (I4∕m) to cubic (Fm3¯m). Dielectric constant (εr) and dielectric loss (tanδ) are observed at the transition point. The conductivity of the sample has been studied, and the slope of dc conductivity versus the inverse of temperature corresponds to an Arrhenius activation energy in the range of 0.34–0.46eV. This range of activation is nearly double ionized oxygen vacancies VO⋅⋅ in the resistivity transition of other perovskite oxides.
Barrier width dependence of the donor binding energy of hydrogenic impurity in wurtzite InGaN/GaN quantum dot
Authors: Xia Congxin , Zeng Zaiping , Wei Shuyi
Published: November 2009

Within the framework of the effective-mass approximation, the barrier width dependence of the donor binding energy of hydrogenic impurity in a cylindrical wurtzite (WZ) InGaN/GaN strained quantum dot (QD) is calculated by means of a variational procedure, considering the strong built-in electric field effect due to the spontaneous and piezoelectric polarizations. Numerical results show that the built-in electric field and the donor binding energy of the impurity located at any growth direction position are obviously dependent on the barrier width in WZ In0.1Ga0.9N/GaN strained QD with a small barrier width (<8 nm). However, the built-in electric field and the donor binding energy of the impurity located at any growth direction position are insensitive to the barrier width in WZ In0.1Ga0.9N/GaN strained QD with a large barrier width (>8 nm). Moreover, the donor binding energy of the impurity located at the right boundary of the QD is independent of the barrier width with any dot height and indium composition when the barrier width is large (>8 nm).
Design and evaluation of a fast Fourier transform-based nonlinear dielectric spectrometer
Authors: Treo Ernesto F. , Felice Carmelo J.
Published: November 2009

Nonlinear dielectric spectroscopy of micro-organism is carried out by applying a moderate electrical field to an aqueous sample through two metal electrodes. Several ad hoc nonlinear spectrometers were proposed in the literature. However, these designs barely compensated the nonlinear distortion derived from the electrode-electrolyte interfaces (EEI). Moreover, the contribution of the suspension is masked by the effect of the nonlinearity introduced by the electrode contacts. Conversely, the nonlinear capability of a commercial tetrapolar analyzer has not been fully investigated. In this paper a new nonlinear tetrapolar spectrometer is proposed based on a commercial linear apparatus and ad hoc control and signal processing software. The system was evaluated with discrete electronic phantoms and showed that it can measure nonlinear properties of aqueous suspension independently of the presence of EEI (ANOVA test, p>0.001). It was also tested with real aqueous samples. The harmonics observed in the current that circulates through the sample reveals useful information about the transfer function of the sample. The total harmonic distortion was computed for linear mediums. Values lower than −60 dB suggest that the system has enough capability to perform nonlinear microbiological analysis. Design specifications, sources of interference, and equipment’s limitations are discussed.
Anomalous thermoelectric power of overdoped Bi2Sr2CaCu2O8 superconductor
Authors: Awana V. P. S. , Bains Jagdish Kumar , Okram G. S. , Soni Ajay , Ahluwalia P. K. , Kishan H.
Published: November 2009

All the samples possess single-phase character and their superconducting transition temperatures (TcR=0) are 85, 90, and 72 K, respectively for Bi2212-MQ, Bi2212-N2, and Bi2212-O2. Though the Bi2212-MQ and Bi2212-N2 samples are in near optimum doping regime, the Bi2212-O2 is an overdoped sample. TcS=0 values obtained through S(T) data are also in line with those determined from the temperature dependence of resistance (TcR=0) and dc magnetization (Tcdia). Interestingly, S(T) behavior of the optimally doped Bi2212-MQ and Bi2212-N2 samples is seen to be positive in whole temperature range, the same is found negative for the overdoped Bi2212-O2 sample above TcS=0. This anomalous S(T) behavior is seen in the light of the recent band structure calculations and the ensuing split Fermi surface as determined by angle-resolved photoelectron spectroscopy.
The interaction of Al atoms with water molecules: A theoretical study
Authors: Álvarez-Barcia S. , Flores J. R.
Published: November 2009

The interaction of individual Al atoms with water molecules has been studied from the point of view of the energy by means of ab initio and DFT calculations in order to find the pathways for the generation of HAlOH⋅(H2O)n or AlOH⋅(H2O)n+H. The potential energy surface of the Al(H2O)n+1 (n=0–3) systems has been explored for local minima and the relevant saddle points. The interaction of Al and several water molecules tends to produce low-lying local minima in which (for n=2–3) Al is “inserted” into relatively compact structures of water molecules, so typically a ring is formed containing an Al⋅OH2 moiety. Isomerization of such moiety into HAlOH⋅(H2O)n may take place through saddle points of the “relay” type; however those saddle points lie very close to Al⋅OH2⋅(H2O)n−1+H2O, which means that such isomerization process has to compete with a water-elimination process. Larger systems Al(H2O)n+1 (n=4–7) have also been computed by means of a DFT method, as a first step to predict the behavior of isolated Al atoms in even larger clusters or in the bulk. Finally, an effective fragment potential method has been employed to simulate those large clusters together with a polarizable continuum model to take into account the effect of the bulk. Our results suggest that the reaction should take place in inert matrices and in the bulk. We also conclude that HAlOH⋅(H2O)n and AlOH⋅(H2O)n could be the intermediates involved in the generation of hydrogen by the interaction of Al atoms with water, so their production would be the critical step of such process.
Universal perturbative explicitly correlated basis set incompleteness correction
Authors: Torheyden Martin , Valeev Edward F.
Published: November 2009

Basis set incompleteness error for an arbitrary approximate electronic wave function is robustly reduced using a second-order perturbative correction into a basis of explicitly correlated, internally contracted geminal functions. The Hylleraas functional for the second-order energy correction is evaluated algebraically involving at most a four-electron reduced density matrix and four-electron integrals. By using the R12 technology in combination with screening approximations such a correction only requires a two-electron reduced density matrix and two-electron integrals. Preliminary investigations of potential energy surfaces of hydrogen fluoride and nitrogen molecules at the multireference configuration interaction singles and doubles indicate that with the perturbative correction only an aug-cc-pVDZ basis is necessary to compute correlation energies of an aug-cc-pVQZ quality, or better. The proposed correction, dubbed [2]R12, can in principle be combined with any single reference and multireference method in use today.
Controlling the spectrum of x-rays generated in a laser-plasma accelerator by tailoring the laser wavefront
Authors: Mangles S. P. D. , Genoud G. , Kneip S. , Burza M. , Cassou K. , Cros B. , Dover N. P. , Kamperidis C. , Najmudin Z. , Persson A. , Schreiber J. , Wojda F. , Wahlström C.-G.
Published: November 2009

By tailoring the wavefront of the laser pulse used in a laser-wakefield accelerator, we show that the properties of the x-rays produced due to the electron beam’s betatron oscillations in the plasma can be controlled. By creating a wavefront with coma, we find that the critical energy of the synchrotronlike x-ray spectrum can be significantly increased. The coma does not substantially change the energy of the electron beam, but does increase its divergence and produces an energy-dependent exit angle, indicating that changes in the x-ray spectrum are due to an increase in the electron beam's oscillation amplitude within the wakefield.
Ca impurity in small mixed H4e–H3e clusters
Authors: Guardiola R. , Navarro J. , Mateo D. , Barranco M.
Published: November 2009

The structure of small mixed helium clusters doped with one calcium atom has been determined within the diffusion Monte Carlo framework. The results show that the calcium atom sits at the H4e–H3e interface. This is in agreement with previous studies, both experimental and theoretical, performed for large clusters. A comparison between the results obtained for the largest cluster we have considered for each isotope shows a clear tendency of the Ca atom to reside in a deep dimple at the surface of the cluster for H4e clusters, and to become fully solvated for H3e clusters. We have calculated the absorption spectrum of Ca around the 4s4p←4s2 transition and have found that it is blueshifted from that of the free-atom transition by an amount that depends on the size and composition of the cluster.
First-principles study on the enhancement of lithium storage capacity in boron doped graphene
Authors: Wang Xianlong , Zeng Zhi , Ahn Hyojun , Wang Guoxiu
Published: November 2009

The adsorption of Li ions on boron doped graphene was investigated using a first-principles method. Our results show that, as boron doping turns graphene into an electron-deficient system, more Li ions can be captured around boron doped centers than in pristine graphene. One boron atom doped into graphene (6C ring unit) can adsorb six Li ions, which indicates that boron doped graphene is an efficient Li-ion storage material for lithium batteries. Further investigations show that, under limited conditions, boron doped graphene (BC5) can form Li6BC5 compound after Li-ion adsorption, corresponding to a lithium storage capacity of 2271 mAh/g which is six times that of graphite.
Precise Positions of Methanol Masers
Authors: Caswell J. L.
Published: November 2009

The Australia Telescope Compact Array (ATCA) has been used to determine positions for many southern methanol maser sites, with accuracy better than 1 arcsec. The results are presented here as a catalogue of more than 350 distinct sites, some of them new discoveries, and many others with positional precision 10-times better than existing published values. Clusters of 2 or 3 sites are occasionally found to account for single previously listed sources. This in turn reveals that the velocity range for each individual site is sometimes smaller than that of the originally tabulated (blended) source. Only a handful of examples then remain with a velocity range of more than 16 km s−1 at a single compact (less than 2 arcsec) site. The precise methanol positions now allow apparent coincidences with OH masers to be confidently accepted or rejected; this has led to the important conclusion that, where a 1665-MHz OH maser lies in a massive star formation region, at more than 80 percent of the OH sites there is a precisely coincident methanol maser. The methanol precision achieved here will also allow clear comparisons with likely associated IR sources when the next generation of far-IR surveys produce precise positions.
Feedback limitation of photosynthesis at high CO2 acts by modulating the activity of the chloroplast ATP synthase
Authors: Kiirats Olavi , Cruz Jeffrey A. , Edwards Gerald E. , Kramer David M.
Published: November 2009

It was previously shown that photosynthetic electron transfer is controlled under low CO2 via regulation of the chloroplast ATP synthase. In the current work, we studied the regulation of photosynthesis under feedback limiting conditions, where photosynthesis is limited by the capacity to utilise triose-phosphate for synthesis of end products (starch or sucrose), in a starch-deficient mutant of Nicotiana sylvestris Speg. & Comes. At high CO2, we observed feedback control that was progressively reversed by increasing O2 levels from 2 to 40%. The activity of the ATP synthase, probed in vivo by the dark-interval relaxation kinetics of the electrochromic shift, was proportional to the O2-induced increases in O2 evolution from PSII (JO2), as well as the sum of Rubisco oxygenation (vo) and carboxylation (vc) rates. The altered ATP synthase activity led to changes in the light-driven proton motive force, resulting in regulation of the rate of plastoquinol oxidation at the cytochrome b6f complex, quantitatively accounting for the observed control of photosynthetic electron transfer. The ATP content of the cell decreases under feedback limitation, suggesting that the ATP synthesis was downregulated to a larger extent than ATP consumption. This likely resulted in slowing of ribulose bisphosphate regeneration and JO2). Overall, our results indicate that, just as at low CO2, feedback limitations control the light reactions of photosynthesis via regulation of the ATP synthase, and can be reconciled with regulation via stromal Pi, or an unknown allosteric affector.
Chlorophyll fluorescence imaging as tool for understanding the impact of fungal diseases on plant performance: a phenomics perspective
Authors: Scholes Julie D. , Rolfe Stephen A.
Published: November 2009

Chlorophyll fluorescence imaging is a non-invasive, non-destructive means with which to examine the impact of fungal pathogens on the photosynthetic metabolism of host plants. As such, it has great potential for screening purposes in high-throughput phenomics environments. However, there is great diversity in the responses of plants to different plant-fungal pathogens and the choice of suitable experimental conditions and protocols and interpretation of the results requires both preliminary laboratory experiments and an understanding of the biology of the specific plant-pathogen interaction. In this review, we examine the interaction between biotrophic, hemi-biotrophic and necrotrophic fungal pathogens and their hosts to illustrate the extent to which chlorophyll fluorescence imaging can be used to detect the presence of disease before the appearance of visible symptoms, distinguish between compatible and incompatible fungal interactions, identify heterogeneity in photosynthetic performance within the infected leaf and provide insights into the underlying mechanisms. The limitations and challenges of using chlorophyll fluorescence imaging in high throughput screens is discussed.
C4 rice: a challenge for plant phenomics
Authors: Furbank Robert T. , von Caemmerer Susanne , Sheehy John , Edwards Gerry
Published: November 2009

There is now strong evidence that yield potential in rice (Oryza sativa L.) is becoming limited by ‘source’ capacity, i.e. photosynthetic capacity or efficiency, and hence the ability to fill the large number of grain ‘sinks’ produced in modern varieties. One solution to this problem is to introduce a more efficient, higher capacity photosynthetic mechanism to rice, the C4 pathway. A major challenge is identifying and engineering the genes necessary to install C4 photosynthesis in rice. Recently, an international research consortium was established to achieve this aim. Central to the aims of this project is phenotyping large populations of rice and sorghum (Sorghum bicolor L.) mutants for ‘C4-ness’ to identify C3 plants that have acquired C4 characteristics or revertant C4 plants that have lost them. This paper describes a variety of plant phenomics approaches to identify these plants and the genes responsible, based on our detailed physiological knowledge of C4 photosynthesis. Strategies to asses the physiological effects of the installation of components of the C4 pathway in rice are also presented.
Chlorophyll fluorescence screening of Arabidopsis thaliana for CO2 sensitive photorespiration and photoinhibition mutants
Authors: Badger Murray R. , Fallahi Hossein , Kaines Sarah , Takahashi Shunichi
Published: November 2009

Exposure of Arabidopsis thaliana (L.) photorespiration mutants to air leads to a rapid decline in the Fv/Fm chlorophyll fluorescence parameter, reflecting a decline in PSII function and an onset of photoinhibition. This paper demonstrates that chlorophyll fluorescence imaging of Fv/Fm can be used as an easy and efficient means of detecting Arabidopsis mutants that are impaired in various aspects of photorespiration. This screen was developed to be sensitive and high throughput by the use of exposure to zero CO2 conditions and the use of array grids of 1-week-old Arabidopsis seedlings as the starting material for imaging. Using this procedure, we screened ~25 000 chemically mutagenised M2 Arabidopsis seeds and recovered photorespiration phenotypes (reduction in Fv/Fm at low CO2) at a frequency of ~4 per 1000 seeds. In addition, we also recovered mutants that showed reduced Fv/Fm at high CO2. Of this group, we detected a novel ‘reverse photorespiration’ phenotype that showed a high CO2 dependent reduction in Fv/Fm. This chlorophyll fluorescence screening technique promises to reveal novel mutants associated with photorespiration and photoinhibition.
Non-destructive measurement of chlorophyll b:a ratios and identification of photosynthetic pathways in grasses by reflectance spectroscopy
Authors: Siebke Katharina , Ball Marilyn C.
Published: November 2009

Equations for non-destructive determination of chlorophyll b : a ratios in grasses were developed from reflectance spectra of intact leaves of barley (Hordeum vulgare L.) and two barley mutants: clorina f2, which lacks chlorophyll b and clorina f104, which has a low chlorophyll b content. These plants enabled separation of effects of chlorophyll composition on reflectance spectra due to differential light absorption by chlorophylls a and b and to measure the effects of chlorophyll b on the contribution of fluorescence emitted by chlorophyll a to the reflectance spectra. Indices developed from these data were then tested on growth chamber-grown leaves from six C3 and 17 C4 grass species (7 NAD-ME and 10 NADP-ME subtypes). We used the chlorophyll b : a ratio because the data were less skewed than the chlorophyll a : b ratio. The best index for determination of the chlorophyll b : a ratio utilised wavelengths affected by chlorophyll absorbance: [R626 – 0.5 (R603 + R647)]/[R552– R626]. The chlorophyll b : a ratio was significantly lower in the C4 than C3 grasses, but was not sufficient in itself to separate these two functional groups. However, because of differences in fluorescence characteristics, C3 and C4 species could be distinguished by an index based on wavelengths affected by chlorophyll fluorescence: [R696 to 709/R545 to 567].
The shoot and root growth of Brachypodium and its potential as a model for wheat and other cereal crops
Authors: Watt Michelle , Schneebeli Katharina , Dong Pan , Wilson Iain W.
Published: November 2009

The grass genetic model Brachypodium (Brachypodium distachyon (L.) Beauv., sequenced line Bd 21) was studied from germination to seed production to assess its potential as a phenotypic model for wheat (Triticum aestivum L.) and other cereal crops. Brachypodium and wheat shoot and root development and anatomy were highly similar. Main stem leaves and tillers (side shoots) emerged at the same time in both grasses in four temperature and light environments. Both developed primary and nodal axile roots at similar leaf stages with the same number and arrangement of vascular xylem tracheary elements (XTEs). Brachypodium, unlike wheat, had an elongated a mesocotyl above the seed and developed only one fine primary axile root from the base of the embryo, while wheat generally has three to five. Roots of both grasses could develop first, second and third order branches that emerged from phloem poles. Both developed up to two nodal axile roots from the coleoptile node at leaf 3, more than eight nodal axile roots from stem nodes after leaf 4, and most (97%) of the deepest roots at flowering were branches. In long days Brachypodium flowered 30 days after emergence, and root systems ceased descent 42 cm from the soil surface, such that mature roots can be studied readily in much smaller soil volumes than wheat. Brachypodium has the overwhelming advantage of a small size, fast life cycle and small genome, and is an excellent model to study cereal root system genetics and function, as well as genes for resource partitioning in whole plants.
Reconstruction of the climate envelopes of salamanders and their evolution through time
Authors: Vieites David R. , Nieto-Román Sandra , Wake David B.
Published: November 2009

Ecological niches evolve through time, but at different rates and to different degrees. An integrated approach using diverse databases, methods, and analytical tools is used to estimate climate envelopes for species of salamanders (family Salamandridae). These species, which range widely across the Holarctic and have a rich and long fossil record, are used to probe the evolutionary dynamics of niches studied in a phylogenetic context through time and across space. Climate data and statistical methods are used to estimate niche dimensions related to precipitation and temperature, in both a phylogenetic and ecogeographic context. Using phylogenetic methods, climate envelopes are estimated for segments of a time-calibrated phylogenetic tree of salamandrids, to explore how far back in time it is reasonable to make such estimates. Our research strategy illuminates some of the challenges and limitations of the available data and methods and identifies potential solutions, such as the need for physiological and behavioral data that may help to better define species' niches or the development of novel evolutionary models that account for paleoclimatic data. We explore and analyze limits to the application of currently available methodologies. Organisms known to have evolved slowly and conservatively, and which are ectotherms and likely to be profoundly affected by climatic variables, may be the most useful for studies of this kind.
Role of dysbindin in dopamine receptor trafficking and cortical GABA function
Authors: Ji Yuanyuan , Yang Feng , Papaleo Francesco , Wang Huai-Xing , Gao Wen-Jun , Weinberger Daniel R. , Lu Bai
Published: November 2009

Dysbindin has been implicated in the pathogenesis of schizophrenia, but little is known about how dysbindin affects neuronal function in the circuitry underlying psychosis and related behaviors. Using a
dysbindin
knockout line (dys
−/−
) derived from the natural
dysbindin
mutant Sandy mice, we have explored the role of dysbindin in dopamine signaling and neuronal function in the prefrontal cortex (PFC). Combined cell imaging and biochemical experiments revealed a robust increase in the dopamine receptor D2, but not D1, on cell surface of neurons from dys
−/−
cortex. This was due to an enhanced recycling and insertion, rather than reduced endocytosis, of D2. Disruption of
dysbindin
gene resulted in a marked decrease in the excitability of fast-spiking (FS) GABAergic interneurons in both PFC and striatum. Dys
−/−
mice also exhibited a decreased inhibitory input to pyramidal neurons in layer V of PFC. The increased D2 signaling in dys
−/−
FS interneurons was associated with a more pronounced increase in neuronal firing in response to D2 agonist, compared to that in wild-type interneurons. Taken together, these results suggest that dysbindin regulates PFC function by facilitating D2-mediated modulation of GABAergic function.
A nonsense mutation in cGMP-dependent type II protein kinase (
PRKG2
) causes dwarfism in American Angus cattle
Authors: Koltes James E. , Mishra Bishnu P. , Kumar Dinesh , Kataria Ranjit S. , Totir Liviu R. , Fernando Rohan L. , Cobbold Rowland , Steffen David , Coppieters Wouter , Georges Michel , Reecy James M.
Published: November 2009

Historically, dwarfism was the major genetic defect in U.S. beef cattle. Aggressive culling and sire testing were used to minimize its prevalence; however, neither of these practices can eliminate a recessive genetic defect. We assembled a 4-generation pedigree to identify the mutation underlying dwarfism in American Angus cattle. An adaptation of the Elston-Steward algorithm was used to overcome small pedigree size and missing genotypes. The dwarfism locus was fine-mapped to BTA6 between markers
AFR227
and
BM4311
. Four candidate genes were sequenced, revealing a nonsense mutation in exon 15 of cGMP-dependant type II protein kinase (
PRKG2
). This C/T transition introduced a stop codon (R678X) that truncated 85 C-terminal amino acids, including a large portion of the kinase domain. Of the 75 mutations discovered in this region, only this mutation was 100% concordant with the recessive pattern of inheritance in affected and carrier individuals (log of odds score = 6.63). Previous research has shown that PRKG2 regulates SRY (sex-determining region Y) box 9 (SOX9)-mediated transcription of collagen 2 (
COL2
). We evaluated the ability of wild-type (WT) or R678X PRKG2 to regulate
COL2
expression in cell culture. Real-time PCR results confirmed that
COL2
is overexpressed in cells that overexpressed
R678X PRKG2
as compared with WT
PRKG2
. Furthermore,
COL2
and
COL10
mRNA expression was increased in dwarf cattle compared with unaffected cattle. These experiments indicate that the
R678X
mutation is functional, resulting in a loss of PRKG2 regulation of
COL2
and
COL10
mRNA expression. Therefore, we present
PRKG2 R678X
as a causative mutation for dwarfism cattle.
Shape-specific preparatory activity mediates attention to targets in human visual cortex
Authors: Stokes Mark , Thompson Russell , Nobre Anna C. , Duncan John
Published: November 2009

The mechanisms of attention prioritize sensory input for efficient perceptual processing. Influential theories suggest that attentional biases are mediated via preparatory activation of task-relevant perceptual representations in visual cortex, but the neural evidence for a preparatory coding model of attention remains incomplete. In this experiment, we tested core assumptions underlying a preparatory coding model for attentional bias. Exploiting multivoxel pattern analysis of functional neuroimaging data obtained during a non-spatial attention task, we examined the locus, time-course, and functional significance of shape-specific preparatory attention in the human brain. Following an attentional cue, yet before the onset of a visual target, we observed selective activation of target-specific neural subpopulations within shape-processing visual cortex (lateral occipital complex). Target-specific modulation of baseline activity was sustained throughout the duration of the attention trial and the degree of target specificity that characterized preparatory activation patterns correlated with perceptual performance. We conclude that top-down attention selectively activates target-specific neural codes, providing a competitive bias favoring task-relevant representations over competing representations distributed within the same subregion of visual cortex.
Cell cycle deregulation by a poxvirus partial mimic of anaphase-promoting complex subunit 11
Authors: Mo Min , Fleming Stephen B. , Mercer Andrew A.
Published: November 2009

The anaphase-promoting complex (APC), or cyclosome, is a ubiquitin ligase with major roles in cell cycle regulation. It is required for mitotic exit, but must be deactivated for the G
1
/S phase transition to occur. APC consists of at least 12 subunits with the catalytic core formed by a scaffold protein, APC2, and a RING-H2 protein, APC11. APC11 facilitates ubiquitin chain formation by recruiting ubiquitin-charged conjugating enzymes through its RING-H2 domain. We report that a small number of poxviruses encode RING-H2 proteins with sequence similarities to APC11. We show that a representative of these viral proteins mimics APC11 in its interactions with APC, but unlike APC11, the viral protein fails to promote ubiquitin chain formation. This absence of ubiquitin ligase activity is linked to a distinctive sequence variation within its RING-H2 domain. Expression of the viral protein led to cell cycle deregulation and the accumulation of APC substrates in a manner consistent with impaired APC function. Our data characterize this protein as a regulator of APC activity, and consequently, we have called it PACR (poxvirus APC/cyclosome regulator). Deletion of the PACR gene substantially reduced viral replication. Here, we report a viral mimic of an APC component and reveal an intriguing mechanism by which viruses can manipulate cell cycle progression and, thereby, promote their own replication.