OsGERLP: A novel aluminum tolerance rice gene isolated from a local cultivar in Indonesia.

There is a decrease in the land available for rice cultivation due to the rapid conversion to urban uses. Subsequently, acid soil could be an alternative land cultivating rice, but will require the use of aluminum (Al)-tolerant rice varieties. This Al tolerance trait is genetically controlled, and there is a need to discover more genes needed to develop Al-tolerant rice. Therefore, the objective of this study was to clone and characterize a novel Al tolerance gene isolated from a local cultivar of Indonesian rice. The gene cloning was conducted based on the rye/rice microsynteny relationship. In addition, the root growth and gene expression analyses were performed to verify the role of the gene on Al tolerance in gene-silenced rice and in overexpressed transgenic tobacco. The results showed an Al tolerance candidate gene, OsGERLP, was successfully cloned from rice cv. Hawara Bunar, with its gene encoding a protein similar to a bacterial ribosomal L32 protein. Additionally, the analysis showed that low gene expression caused the gene-silenced rice to be sensitive to Al, while high expression induced the Al tolerance in transgenic tobacco. Furthermore, it was discovered that the gene expression level in both plants was in line with the lower expression of the OsFRDL4 gene in the silenced rice and the high expression of the MATE gene in transgenic tobacco also with the higher citrate secretion from transgenic tobacco roots. In conclusion, the OsGERLP gene could act as a regulator for other Al tolerance genes, with the potential to develop Al-tolerant rice varieties.

Combining high-energy X-ray diffraction with Surface Optical Reflectance and Planar Laser Induced Fluorescence for operando catalyst surface characterization.

We have combined three techniques, High Energy Surface X-Ray Diffraction (HESXRD), Surface Optical Reflectance, and Planar Laser Induced Fluorescence in an operando study of CO oxidation over a Pd(100) catalyst. We show that these techniques provide useful new insights such as the ability to verify that the finite region being probed by techniques such as HESXRD is representative of the sample surface as a whole. The combination is also suitable to determine when changes in gas composition or surface structure and/or morphology occur and to subsequently correlate them with high temporal resolution. In the study, we confirm previous results which show that the Pd(100) surface reaches high activity before an oxide can be detected. Furthermore, we show that the single crystal catalyst surface does not behave homogeneously, which we attribute to the surface being exposed to inhomogeneous gas conditions in mass transfer limited scenarios.

Search for Boosted Dark Matter Interacting with Electrons in Super-Kamiokande.

A search for boosted dark matter using 161.9 kt yr of Super-Kamiokande IV data is presented. We search for an excess of elastically scattered electrons above the atmospheric neutrino background, with a visible energy between 100 MeV and 1 TeV, pointing back to the Galactic center or the Sun. No such excess is observed. Limits on boosted dark matter event rates in multiple angular cones around the Galactic center and Sun are calculated. Limits are also calculated for a baseline model of boosted dark matter produced from cold dark matter annihilation or decay. This is the first experimental search for boosted dark matter from the Galactic center or the Sun interacting in a terrestrial detector.

Oxidation and Reduction of TiOx Thin Films on Pd(111) and Pd(100).

Thin films of TiOx on Pd(100) and Pd(111) have been investigated with respect to their properties after oxidation and reduction cycles. High-resolution photoemission spectroscopy (HRPES) and low energy electron diffraction (LEED) have been applied to characterize the thin film oxidation states and structure before and after oxidation and reduction under ultrahigh vacuum conditions. Fully oxidized TiO2 films were formed on both surfaces. These structures display Moiré patterns in LEED, in one dimension for Pd(100) and in two dimensions for Pd(111), and they have previously not been reported for TiO2/Pd. The oxidation process causes strong reduction in the interaction between the oxide thin film and the Pd substrate, most significantly for Pd(111). Reversible oxidation/reduction cycling of TiOx thin films on Pd(111) and Pd(100) was possible.

Search for Nucleon and Dinucleon Decays with an Invisible Particle and a Charged Lepton in the Final State at the Super-Kamiokande Experiment.

Search results for nucleon decays p→e^{+}X, p→µ^{+}X, n→νγ (where X is an invisible, massless particle) as well as dinucleon decays np→e^{+}ν, np→µ^{+}ν, and np→τ^{+}ν in the Super-Kamiokande experiment are presented. Using single-ring data from an exposure of 273.4 kton·yr, a search for these decays yields a result consistent with no signal. Accordingly, lower limits on the partial lifetimes of τ_{p→e^{+}X}>7.9×10^{32} yr, τ_{p→µ^{+}X}>4.1×10^{32} yr, τ_{n→νγ}>5.5×10^{32} yr, τ_{np→e^{+}ν}>2.6×10^{32} yr, τ_{np→µ^{+}ν}>2.2×10^{32} yr, and τ_{np→τ^{+}ν}>2.9×10^{31} yr at a 90% confidence level are obtained. Some of these searches are novel.

Search for trilepton nucleon decay via p→e+νν and p→µ+νν in the Super-Kamiokande experiment.

The trilepton nucleon decay modes p→e+νν and p→µ+νν violate |Δ(B-L)| by two units. Using data from a 273.4 kt yr exposure of Super-Kamiokande a search for these decays yields a fit consistent with no signal. Accordingly, lower limits on the partial lifetimes of τp→e+νν>1.7×10(32) years and τp→µ+νν>2.2×10(32) years at a 90% confidence level are obtained. These limits can constrain Grand Unified Theories which allow for such processes.

Effects of non-local exchange on core level shifts for gas-phase and adsorbed molecules.

Density functional theory calculations are often used to interpret experimental shifts in core level binding energies. Calculations based on gradient-corrected (GC) exchange-correlation functionals are known to reproduce measured core level shifts (CLS) of isolated molecules and metal surfaces with reasonable accuracy. In the present study, we discuss a series of examples where the shifts calculated within a GC-functional significantly deviate from the experimental values, namely the CLS of C 1s in ethyl trifluoroacetate, Pd 3d in PdO and the O 1s shift for CO adsorbed on PdO(101). The deviations are traced to effects of the electronic self-interaction error with GC-functionals and substantially better agreements between calculated and measured CLS are obtained when a fraction of exact exchange is used in the exchange-correlation functional.

Carriage of methicillin-resistant staphylococci by healthy companion animals in the US.

UNLABELLED: Antimicrobial-resistant staphylococci have been associated with wounded or ill companion animals, but little is known about the prevalence of resistant staphylococci among healthy animals. In this study, 276 healthy dogs and cats from veterinary clinics were tested for the presence of antimicrobial-resistant Staphylococcus spp. Isolates were tested for antimicrobial susceptibility and the presence of select resistance genes, and typed using Pulsed-Field Gel Electrophoresis (PFGE). Staphylococcus aureus and Staphylococcus pseudintermedius were also characterized using multilocus sequence typing (MLST), spa typing and SCCmec typing. Approximately 5% (14/276) of the animals were positive by enrichment for five species of staphylococci [Staph. aureus (n = 11), Staph. pseudintermedius (n = 4), Staphylococcus sciuri (n = 6), Staphylococcus simulans (n = 1) and Staphylococcus warneri (n = 1)]. Seventy-eight per cent (18/23) of staphylococci were resistant to oxacillin and also multidrug resistant (resistance to ≥ 2 antimicrobials). All Staph. aureus isolates were mecA+ and blaZ+, SCCmec type II, spa type t002, ST5 and clonal using PFGE. Staphylococcus pseudintermedius were SCCmec type IV or V, spa type t06 and ST170; two of the isolates were pvl(+) . These results suggest that healthy companion animals may be a reservoir of multidrug-resistant staphylococci, which may be transferred to owners and others who handle companion animals. SIGNIFICANCE AND IMPACT OF THE STUDY: In this study, antimicrobial-resistant coagulase-negative and coagulase-positive staphylococci were isolated from various body sites on healthy dogs and cats. Resistance to 14 antimicrobials was observed including resistance to oxacillin; the majority of staphylococci were also multidrug resistant. Results from this study suggest that healthy dogs and cats may act as reservoirs of antimicrobial-resistant bacteria that may be transferred to people by simple interaction with the animals. Such carriage poses an underlying risk of infection, which should be considered during handling of healthy dogs and cats by pet owners and veterinary personnel.

High-energy surface X-ray diffraction for fast surface structure determination.

Understanding the interaction between surfaces and their surroundings is crucial in many materials-science fields, such as catalysis, corrosion, and thin-film electronics, but existing characterization methods have not been capable of fully determining the structure of surfaces during dynamic processes, such as catalytic reactions, in a reasonable time frame. We demonstrate an x-ray-diffraction-based characterization method that uses high-energy photons (85 kiloelectron volts) to provide unexpected gains in data acquisition speed by several orders of magnitude and enables structural determinations of surfaces on time scales suitable for in situ studies. We illustrate the potential of high-energy surface x-ray diffraction by determining the structure of a palladium surface in situ during catalytic carbon monoxide oxidation and follow dynamic restructuring of the surface with subsecond time resolution.

A high pressure x-ray photoelectron spectroscopy study of CO oxidation over Rh(100).

We have studied the oxidation of CO over Rh(100) using high pressure x-ray photoelectron spectroscopy under CO and O2 pressures ranging from 0.01 to 1 mbar. The results show a very low or no conversion for the CO covered surface found at low temperatures, while the activity rises slightly when the temperature is high enough for some CO to desorb, exposing surface sites for dissociative O2 adsorption. As the temperature is increased further, more CO desorbs and oxygen replaces CO as the dominating species at the surface. At the same time we find a sudden increase in the reactivity, such that all CO that reaches the surface is instantly transformed into CO2. We find that the O coverage in the active state is highly dependent on the total pressure and, although we do not detect any presence of a surface oxide as in previous surface x-ray diffraction studies, the highest O coverage indicates that the surface is close to being oxidized.

Isolation and characterization of Staphylococcus aureus strains from a Paso del Norte dairy.

The primary purpose of this study was to determine if methicillin-resistant Staphylococcus aureus (MRSA) strains could be identified in the milk of dairy cattle in a Paso del Norte region dairy of the United States. Using physiological and PCR-based identification schemes, a total of 40 Staph. aureus strains were isolated from 29 raw milk samples of 133 total samples analyzed. Pulsed-field gel electrophoresis after digestion with the SmaI enzyme revealed that the 40 confirmed strains were represented by 5 pulsed-field types, which each contained 3 or more strains. Of 7 hospital strains isolated from cows undergoing antibiotic therapy, 3 demonstrated resistance to 3 or more antimicrobial classes and displayed similar pulsed-field gel electrophoresis patterns. A secondary purpose of this study was to elucidate the evolutionary relationships of strains isolated in this study to genomically characterized Staph. aureus strains. Therefore, Roche 454 GS (Roche Diagnostics Corp., Dallas, TX) pyrosequencing was used to produce draft genome sequences of an MRSA raw milk isolate (H29) and a methicillin-susceptible Staph. aureus (PB32). Analysis using the BLASTn database (http://blast.ncbi.nlm.nih.gov/) demonstrated that the H29 draft genome was highly homologous to the human MRSA strain JH1, yet the ß-lactamase plasmid carried by H29 was different from that carried by JH1. Genomic analysis of H29 also clearly explained the multidrug resistance phenotype of this raw milk isolate. Analysis of the PB32 draft genome (using BLASTn) demonstrated that this raw milk isolate was most related to human MRSA strain 04-02981. Although PB32 is not a MRSA, the PB32 draft genome did reveal the presence of a unique staphylococcal cassette mec (SCCmec) remnant. In addition, the PB32 draft genome revealed the presence of a novel bovine staphylococcal pathogenicity island, SaPIbovPB32. This study demonstrates the presence of clones closely related to human and (or) bovine Staph. aureus strains circulating in a dairy herd.

In situ x-ray photoelectron spectroscopy of model catalysts: at the edge of the gap.

We present high-pressure x-ray photoelectron spectroscopy (HP-XPS) and first-principles kinetic Monte Carlo study addressing the nature of the active surface in CO oxidation over Pd(100). Simultaneously measuring the chemical composition at the surface and in the near-surface gas phase, we reveal both O-covered pristine Pd(100) and a surface oxide as stable, highly active phases in the near-ambient regime accessible to HP-XPS. Surprisingly, no adsorbed CO can be detected during high CO(2) production rates, which can be explained by a combination of a remarkably short residence time of the CO molecule on the surface and mass-transfer limitations in the present setup.

An in situ set up for the detection of CO2 from catalytic CO oxidation by using planar laser-induced fluorescence.

We report the first experiment carried out on an in situ setup, which allows for detection of CO(2) from catalytic CO oxidation close to a model catalyst under realistic reaction conditions by the means of planar laser-induced fluorescence (PLIF) in the mid-infrared spectral range. The onset of the catalytic reaction as a function of temperature was followed by PLIF in a steady state flow reactor. After taking into account the self-absorption of CO(2), a good agreement between the detected CO(2) fluorescence signal and the CO(2) mass spectrometry signal was shown. The observed difference to previously measured onset temperatures for the catalytic ignition is discussed and the potential impact of IR-PLIF as a detection technique in catalysis is outlined.

The Rh(100)-(3 × 1)-2O structure.

The O adsorption on Rh(100) has been studied using high resolution core level spectroscopy, low energy electron diffraction and scanning tunnelling microscopy. In addition to the well known (2 × 2), (2 × 2)-pg and c(8 × 2) structures at coverages of 0.25, 0.5 and 1.75 ML respectively, an intermediate (3 × 1) structure with a coverage of 2/3 ML is identified.

The Active Phase of Palladium during Methane Oxidation.

The active phase of Pd during methane oxidation is a long-standing puzzle, which, if solved, could provide routes for design of improved catalysts. Here, density functional theory and in situ surface X-ray diffraction are used to identify and characterize atomic sites yielding high methane conversion. Calculations are performed for methane dissociation over a range of Pd and PdOx surfaces and reveal facile dissociation on either under-coordinated Pd sites in PdO(101) or metallic surfaces. The experiments show unambiguously that high methane conversion requires sufficiently thick PdO(101) films or metallic Pd, in full agreement with the calculations. The established link between high activity and atomic structure enables rational design of improved catalysts.

Reconstruction of the synthetic W7984 x Opata M85 wheat reference population.

Reference populations are valuable resources in genetics studies for determining marker order, marker selection, trait mapping, construction of large-insert libraries, cross-referencing marker platforms, and genome sequencing. Reference populations can be propagated indefinitely, they are polymorphic and have normal segregation. Described are two new reference populations who share the same parents of the original wheat reference population Synthetic W7984 (Altar84/ Aegilops tauschii (219) CIGM86.940) x Opata M85, an F(1)-derived doubled haploid population (SynOpDH) of 215 inbred lines and a recombinant inbred population (SynOpRIL) of 2039 F(6) lines derived by single-plant self-pollinations. A linkage map was constructed for the SynOpDH population using 1446 markers. In addition, a core set of 42 SSR markers was genotyped on SynOpRIL. A new approach to identifying a core set of markers used a step-wise selection protocol based on polymorphism, uniform chromosome distribution, and reliability to create nested sets starting with one marker per chromosome, followed by two, four, and six. It is suggested that researchers use these markers as anchors for all future mapping projects to facilitate cross-referencing markers and chromosome locations. To enhance this public resource, researchers are strongly urged to validate line identities and deposit their data in GrainGenes so that others can benefit from the accumulated information.

Surface structure and reactivity of Pd(100) during CO oxidation near ambient pressures.

The surface structure of Pd(100) during CO oxidation was measured using a combination of a flow reactor and in situ surface X-ray diffraction coupled to a large-area 2-dimensional detector. The surface structure was measured for P(O(2))/P(CO) ratios between 0.6 and 10 at a fixed total gas pressure of 200 mbar and a fixed CO pressure of 10 ± 1 mbar. In conjunction with the surface structure the reactivity of the surface was also determined. For all P(O(2))/P(CO) ratios the surface was found to oxidize above a certain temperature. Three different types of oxides were observed: the surface oxide, an epitaxial layer of bulk-like PdO, and a non-epitaxial layer of bulk-like PdO. As soon as an oxide was present the reactivity of the surface was found to be mass transfer limited by the flux of CO molecules reaching the surface.

Size matters in Triticeae polyploids: larger genomes have higher remodeling.

Polyploidization is one of the major driving forces in plant evolution and is extremely relevant to speciation and diversity creation. Polyploidization leads to a myriad of genetic and epigenetic alterations that ultimately generate plants and species with increased genome plasticity. Polyploids are the result of the fusion of two or more genomes into the same nucleus and can be classified as allopolyploids (different genomes) or autopolyploids (same genome). Triticeae synthetic allopolyploid species are excellent models to study polyploids evolution, particularly the wheat-rye hybrid triticale, which includes various ploidy levels and genome combinations. In this review, we reanalyze data concerning genomic analysis of octoploid and hexaploid triticale and different synthetic wheat hybrids, in comparison with other polyploid species. This analysis reveals high levels of genomic restructuring events in triticale and wheat hybrids, namely major parental band disappearance and the appearance of novel bands. Furthermore, the data shows that restructuring depends on parental genomes, ploidy level, and sequence type (repetitive, low copy, and (or) coding); is markedly different after wide hybridization or genome doubling; and affects preferentially the larger parental genome. The shared role of genetic and epigenetic modifications in parental genome size homogenization, diploidization establishment, and stabilization of polyploid species is discussed.

Anatomical distribution and genetic relatedness of antimicrobial-resistant Escherichia coli from healthy companion animals.

AIMS: Escherichia coli have been targeted for studying antimicrobial resistance in companion animals because of opportunistic infections and as a surrogate for resistance patterns in zoonotic organisms. The aim of our study is to examine antimicrobial resistance in E. coli isolated from various anatomical sites on healthy dogs and cats and identify genetic relatedness. METHODS AND RESULTS: From May to August, 2007, healthy companion animals (155 dogs and 121 cats) from three veterinary clinics in the Athens, GA, USA, were sampled. Escherichia coli was isolated from swabs of nasal, oral, rectal, abdomen and hindquarter areas. Antimicrobial susceptibility testing against 16 antimicrobials was performed using broth microdilution with the Sensititre™ system. Clonal types were determined by a standardized pulsed-field gel electrophoresis protocol. Although rectal swabs yielded the most E. coli (165/317; 52%) from dogs and cats, the organism was distributed evenly among the other body sites sampled. Escherichia coli isolates from both dogs and cats exhibited resistance to all antimicrobials tested with the exception of amikacin, cephalothin and kanamycin. Resistance to ampicillin was the most prevalent resistance phenotype detected (dogs, 33/199; 17%; and cats, 27/118; 23%). Among the resistant isolates, 21 resistance patterns were observed, where 18 patterns represented multidrug resistance (MDR; resistance ≥ 2 antimicrobial classes). Also among the resistant isolates, 33 unique clonal types were detected, where each clonal type contained isolates from various sampling sites. Similar resistance phenotypes were exhibited among clonal types, and three clonal types were from both dogs and cats. CONCLUSIONS: Healthy companion animals can harbour antimicrobial-resistant E. coli on body sites that routinely come in contact with human handlers. SIGNIFICANCE AND IMPACT OF THE STUDY: This study is the first report that demonstrates a diverse antimicrobial-resistant E. coli population distributed over various sites of a companion animal's body, thereby suggesting potential transfer of resistant microflora to human hosts during contact.