bluuebunny/crossref_metadata_2025 huggingface dataset:
Effective shutdown in the expression of celiac disease-related wheat gliadin T-cell epitopes by RNA interference
Authors: Gil-Humanes Javier , Pistón Fernando , Tollefsen Stig , Sollid Ludvig M. , Barro Francisco
Published: September 2010

Celiac disease (CD) is an enteropathy triggered by the ingestion of gluten proteins from wheat and similar proteins from barley and rye. The inflammatory reaction is controlled by T cells that recognize gluten peptides in the context of human leukocyte antigen (HLA) DQ2 or HLA-DQ8 molecules. The only available treatment for the disease is a lifelong gluten-exclusion diet. We have used RNAi to down-regulate the expression of gliadins in bread wheat. A set of hairpin constructs were designed and expressed in the endosperm of bread wheat. The expression of gliadins was strongly down-regulated in the transgenic lines. Total gluten protein was extracted from transgenic lines and tested for ability to stimulate four different T-cell clones derived from the intestinal lesion of CD patients and specific for the DQ2-α-II, DQ2-γ-VII, DQ8-α-I, and DQ8-γ-I epitopes. For five of the transgenic lines, there was a 1.5–2 log reduction in the amount of the DQ2-α-II and DQ2-γ-VII epitopes and at least 1 log reduction in the amount of the DQ8-α-I and DQ8-γ-I epitopes. Furthermore, transgenic lines were also tested with two T-cell lines that are reactive with ω-gliadin epitopes. The total gluten extracts were unable to elicit T-cell responses for three of the transgenic wheat lines, and there were reduced responses for six of the transgenic lines. This work shows that the down-regulation of gliadins by RNAi can be used to obtain wheat lines with very low levels of toxicity for CD patients.
Allele-specific copy number analysis of tumors
Authors: Van Loo Peter , Nordgard Silje H. , Lingjærde Ole Christian , Russnes Hege G. , Rye Inga H. , Sun Wei , Weigman Victor J. , Marynen Peter , Zetterberg Anders , Naume Bjørn , Perou Charles M. , Børresen-Dale Anne-Lise , Kristensen Vessela N.
Published: September 2010

We present an allele-specific copy number analysis of the in vivo breast cancer genome. We describe a unique bioinformatics approach, ASCAT (allele-specific copy number analysis of tumors), to accurately dissect the allele-specific copy number of solid tumors, simultaneously estimating and adjusting for both tumor ploidy and nonaberrant cell admixture. This allows calculation of “ASCAT profiles” (genome-wide allele-specific copy-number profiles) from which gains, losses, copy number-neutral events, and loss of heterozygosity (LOH) can accurately be determined. In an early-stage breast carcinoma series, we observe aneuploidy (>2.7n) in 45% of the cases and an average nonaberrant cell admixture of 49%. By aggregation of ASCAT profiles across our series, we obtain genomic frequency distributions of gains and losses, as well as genome-wide views of LOH and copy number-neutral events in breast cancer. In addition, the ASCAT profiles reveal differences in aberrant tumor cell fraction, ploidy, gains, losses, LOH, and copy number-neutral events between the five previously identified molecular breast cancer subtypes. Basal-like breast carcinomas have a significantly higher frequency of LOH compared with other subtypes, and their ASCAT profiles show large-scale loss of genomic material during tumor development, followed by a whole-genome duplication, resulting in near-triploid genomes. Finally, from the ASCAT profiles, we construct a genome-wide map of allelic skewness in breast cancer, indicating loci where one allele is preferentially lost, whereas the other allele is preferentially gained. We hypothesize that these alternative alleles have a different influence on breast carcinoma development.
Endocannabinoid signaling directs differentiation of trophoblast cell lineages and placentation
Authors: Sun Xiaofei , Xie Huirong , Yang Jie , Wang Haibin , Bradshaw Heather B. , Dey Sudhansu K.
Published: September 2010

In most mammals, placentation is critical for fetal development and pregnancy success. Exposure to marijuana during pregnancy has adverse effects, but whether the placenta is a target of cannabinoid/endocannabinoid signaling is not known. Using mice as a model system, we found that the endocannabinoid system is present in the ectoplacental cone and spongiotrophoblast cells. We also observed that aberrant endocannabinoid signaling confers premature trophoblast stem cell differentiation, and defective trophoblast development and invasion. These defects are reflected in retarded fetal development and compromised pregnancy outcome. Because the endocannabinoid system is conserved in mice and humans, our study suggests that endocannabinoid signaling is critical to placentation and pregnancy success in humans and implicates its potential significance in stem cell biology.
Probing electron transfer mechanisms in
Shewanella oneidensis
MR-1 using a nanoelectrode platform and single-cell imaging
Authors: Jiang Xiaocheng , Hu Jinsong , Fitzgerald Lisa A. , Biffinger Justin C. , Xie Ping , Ringeisen Bradley R. , Lieber Charles M.
Published: September 2010

Microbial fuel cells (MFCs) represent a promising approach for sustainable energy production as they generate electricity directly from metabolism of organic substrates without the need for catalysts. However, the mechanisms of electron transfer between microbes and electrodes, which could ultimately limit power extraction, remain controversial. Here we demonstrate optically transparent nanoelectrodes as a platform to investigate extracellular electron transfer in
Shewanella oneidensis
MR-1, where an array of nanoholes precludes or single window allows for direct microbe-electrode contacts. Following addition of cells, short-circuit current measurements showed similar amplitude and temporal response for both electrode configurations, while in situ optical imaging demonstrates that the measured currents were uncorrelated with the cell number on the electrodes. High-resolution imaging showed the presence of thin, 4- to 5-nm diameter filaments emanating from cell bodies, although these filaments do not appear correlated with current generation. Both types of electrodes yielded similar currents at longer times in dense cell layers and exhibited a rapid drop in current upon removal of diffusible mediators. Reintroduction of the original cell-free media yielded a rapid increase in current to ∼80% of original level, whereas imaging showed that the positions of > 70% of cells remained unchanged during solution exchange. Together, these measurements show that electron transfer occurs predominantly by mediated mechanism in this model system. Last, simultaneous measurements of current and cell positions showed that cell motility and electron transfer were inversely correlated. The ability to control and image cell/electrode interactions down to the single-cell level provide a powerful approach for advancing our fundamental understanding of MFCs.
Spontaneous
Irs1
passenger mutation linked to a gene-targeted
SerpinB2
allele
Authors: Westrick Randal J. , Mohlke Karen L. , Korepta Lindsey M. , Yang Angela Y. , Zhu Goujing , Manning Sara L. , Winn Mary E. , Dougherty Kristiann M. , Ginsburg David
Published: September 2010

In characterizing mice with targeted disruption of the
SerpinB2
gene, we observed animals that were small at birth with delayed growth and decreased life expectancy. Although this phenotype cosegregated with homozygosity for the inactive
SerpinB2
allele, analysis of homozygous
SerpinB2
-deficient mice derived from two additional independent embryonic stem (ES) cell clones exhibited no growth abnormalities. Examination of additional progeny from the original
SerpinB2
-deficient line revealed recombination between the small phenotype (
smla
) and the SerpinB2 locus. The locus responsible for
smla
was mapped to a 2.78-Mb interval approximately 30 Mb proximal to
SerpinB2
, bounded by markers D1Mit382 and D1Mit216. Sequencing of
Irs1
identified a nonsense mutation at serine 57 (S57X), resulting in complete loss of IRS1 protein expression. Analysis of ES cell DNA suggests that the S57X
Irs1
mutation arose spontaneously in an ES cell subclone during cell culture. Although the
smla
phenotype is similar to previously reported
Irs1
alleles, mice exhibited decreased survival, in contrast to the enhanced longevity reported for IRS1 deficiency generated by gene targeting. This discrepancy could result from differences in strain background, unintended indirect effects of the gene targeting, or the minimal genetic interference of the S57X mutation compared with the conventionally targeted
Irs1
-KO allele. Spontaneous mutations arising during ES cell culture may be a frequent but underappreciated occurrence. When linked to a targeted allele, such mutations could lead to incorrect assignment of phenotype and may account for a subset of markedly discordant results from experiments independently targeting the same gene.
Food pleasantness affects visual selective attention
Authors: di Pellegrino Giuseppe , Magarelli Silvia , Mengarelli Flavia
Published: September 2010

Fundamental to adaptive behaviour is the ability to select environmental objects that best satisfy current needs and preferences. Here we investigated whether temporary changes in food preference influence visual selective attention. To this end, we exploited the fact that when a food is eaten to satiety its motivational value and perceived pleasantness decrease relative to other foods not eaten in the meal, an effect termed sensory-specific satiety. A total of 26 hungry participants were fed until sated with one of two palatable foods. Before and after selective satiation, participants rated the pleasantness of the two foods and then viewed the same as stimuli on a computer screen while attention was assessed by a visual probe task. Results showed that the attentional bias for the food eaten decreased markedly from pre- to postsatiety, along with the subjective pleasantness for that food. By contrast, subjective pleasantness and attentional bias for the food not eaten did not show any such decrease. These findings suggest that the allocation of visual selective attention is flexibly and rapidly adjusted to reflect temporary shift in relative preference for different foods.
Recording performances in perpendicular magnetic patterned media
Authors: Asbahi M , Moritz J , Dieny B , Gourgon C , Perret C , van de Veerdonk R J M
Published: September 2010

We report on the recording performances and signal-to-noise ratio (SNR) analyses of perpendicular magnetic bit-patterned media. Two different types of magnetic samples are investigated. They differ by the way that they were patterned (nano-imprint versus e-beam lithography) as well as their magnetic properties (Co/Pt multilayers and CoCrPt alloy are the recording layers).Using a contact read/write quasi-static tester, we were able to characterize the write windows, the bit error rates and measure the SNR. The influence of magnetic properties and media microstructure on the writing processes is studied. We show also that the lithographical method used to replicate the media induces more or less noise due to structural distributions.
Current–voltage characteristics of dendrimer light-emitting diodes
Authors: Stevenson S G , Samuel I D W , Staton S V , Knights K A , Burn P L , Williams J H T , Walker Alison B
Published: September 2010

We have investigated current–voltage (I–V) characteristics of unipolar and bipolar organic diodes that use phosphorescent dendrimers as the emissive organic layer. Through simulation of the measured I–V characteristics we were able to determine the device parameters for each device structure studied, leading to a better understanding of injection and transport behaviour in these devices. It was found that the common practice of assuming injection barriers are equal to the difference between bare electrode work functions and molecular orbital levels is unsuitable for the devices considered here, particularly for gold contacts. The studies confirm that different aromatic units in the dendrons can give significant differences in the charge transporting properties of the dendrimers.
Measurement of collisional quenching rate of nitrogen states N2(C 3Πu, v = 0) and
Authors: Valk F , Aints M , Paris P , Plank T , Maksimov J , Tamm A
Published: September 2010

This paper presents an experimental investigation of the effect of the electric field strength on the collisional quenching rate of nitrogen states N2(C 
3Πu, v = 0) and
by nitrogen and oxygen molecules. In experiments, the pulses of non-self-sustained electrical discharge excite gas molecules. The range of reduced electric field strength is from 240 to 4000 Td at pressure range from 70 to 4300 Pa. The experiments show that the field strength has no effect on the quenching rate. The paper discusses the probable reasons for discrepancy of results obtained by different authors and proposes the preferable values for rate coefficients. These coefficients can be used for electric field determination in low temperature gas discharge plasmas via nitrogen emission spectrum, and are of interest to atmospheric air fluorescence investigations.
Electron drift velocity in SF6 in strong electric fields determined from rf breakdown curves
Authors: Lisovskiy V , Yegorenkov V , Booth J-P , Landry K , Douai D , Cassagne V
Published: September 2010

This paper presents measurements of the electron drift velocity V
dr in SF6 gas for high reduced electric fields (E/N = 330–5655 Td (1 Td = 10−17 V cm2)). The drift velocities were obtained using the method of Lisovskiy and Yegorenkov (1998 J. Phys. D: Appl. Phys.
31 3349) based on the determination of the pressure and voltage of the turning points of rf capacitive discharge breakdown curves for a range of electrode spacings. The V
dr values thus obtained were in good agreement with those calculated from the cross-sections of Phelps and Van Brunt (1988 J. Appl. Phys.
64 4269) using the BOLSIG code. The validity of the Lisovskiy–Yegorenkov method is discussed and we show that it is applicable over the entire E/N range where rf discharge ignition at breakdown occurs for rf frequencies of 13.56 MHz or above.
TEM characterization of oxidized AlGaAs/AlAs nonlinear optical waveguides
Authors: Guillotel E , Langlois C , Ghiglieno F , Leo G , Ricolleau C
Published: September 2010

The internal interfaces of multilayer Al
x
Ga1−x
As/AlAs nonlinear optical waveguides are investigated by high-angle annular-dark-field and energy-filtered scanning transmission electron microscopy, before and after partial wet oxidation of AlAs layers. Via a simple phenomenological model, the corresponding roughness parameters allow prediction of the scattering-induced waveguide optical losses, which are in reasonable agreement with the experimental value of 0.5 cm−1. We also find that Al
x
Ga1−x
As layers adjacent to oxidized AlAs tend to be oxidized through the interfaces, even for low Al fraction, with typical oxidation depths of 9 nm for x = 0.7 and 2 nm for x = 0.
Fidelity and Mutual Entropy in Mixed States for Fermi-resonance Coupling Vibrations of CS2
Authors: Peng Dong-ping , Hou Xi-wen
Published: September 2010

The dynamics of four fidelities is studied for mixed coherent states and mixed squeezed states of Fermi-resonance coupling vibrations in molecule CS2. It is demonstrated that those fidelities are dominant-positively correlated with each other, one of which by Wang et al. (Phys. Lett. A 373, 58 (2008)) is the most striking in dominant anti-correlation with quantum mutual entropy. That is useful for molecular quantum computing and quantum information.
Plasma-assisted MBE of GaN pn-junction Grown on Si(111) Substrate
Authors: Zaki Mohd Yusoff Mohd , Hassan Zainuriah , Che Woei Chin , Abu Hassan Haslan
Published: September 2010

We investigated growth of GaN pn-junction layers grown on silicon(111) by plasma-assisted molecular beam epitaxy system and its application for photo-devices. Si and Mg were used as n- and p-dopants, respectively. The reflection high energy electron diffraction images indicated a good surface morphology of GaN pn-junction layer. The thickness of GaN pn-junctions layers was about 0.705 nm. The absence of cubic phase GaN showed that this layer possessed hexagonal structure. According to XRD symmetric rocking curve ω/2θ scans of (0002) plane at room temperature, the full width at half-maximun of GaN pn-junction sample was calculated as 0.34°, indicating a high quality layer of GaN pn-junction. Surprisingly, there was no quenching of the A(LO) peak, with the presence of Si- and Mg-dopants in sample. The pn-junctions sample has a good optical quality which was measured by the photoluminescence system. For photo-devices applications, Ni and Al were used as front and back contacts, respectively. The current-voltage characteristics of the devices showed the typical rectifying behavior of heterojunction. The photo-current measurement was performed using a visible-lamp under forward and reverse biases. From the temperature-dependent measurements, the current at low bias exhibited much stronger temperature dependence and weaker field dependence. The effect of thermal annealing on front contact Ni was also carried out. The front contact Ni was annealed at 400 and 600 °C for 10 min in the nitrogen ambient. The results showed that 600 °C treated sample had a higher gain at 1.00 V/e than 400 °C treated and untreated samples.
Preparation of CuInS2 Thin Film Using Sulfides Nanoparticle Precursor Ink
Authors: Wang Wen , Xiong Jie , Zhu Chang-fei , Jiang Guo-shun
Published: September 2010

A low cost spin coating route of fabricating CuInS2 polycrystalline thin films by reactive sintering method was put forward. The ink for spin coating was optimized by pre-reducing the precursor powders in hydrogen, which turned the nanoparticle precursor powders from mixed sulfides into a mixture of CuInS2 and Cu-In metal alloys. The results of scanning electron microscopy, energy dispersive spectroscopy, X-ray diffraction, and Raman spectra showed that this optimization could highly improve the performance of CuInS2 polycrystalline thin films, including higher packing density, less impurity phases, and better quality. The energy gap of optimized CuInS2 thin film was determined to be about 1.45 eV by absorption spectroscopy measurement.
Nano-porous Composites Based on Heteropolyacid Functionalized Ionic Liquid: Synthesis, Characterization, and Catalytic Performance in Esterification
Authors: Zhou Fu-dong , Chu Wei , Dai Xiao-yan , Luo Shi-zhong
Published: September 2010

Functionalized ionic liquid samples (bmim-PW12) were synthesized by 1-butyl-3-methyl-imidazolium bromide (bmimBr) and 12-phosphotungstic heteropolyacid (PW12). The samples were annealed at 100–450°C and were characterized by Fourier transform infrared spectroscopy, X-ray diffraction, scanning electron microscope, thermal gravity-DTG, brunauer emmett teller, and NH3-temperature programmed desorption. The results showed that the bmim-PW12 samples were crystal and maintained intact Keggin structure. The organic parts of those samples were partly decomposed at a temperature more than 350°C. The sample annealed at 400°C exhibited nano-porous structure, strong acidity, and excellent catalytic activity on the esterification of n-butanol with acetic acid. The higher ester yield was obtained when the mass ratio of catalyst over the reactants amount was 5% for bmim-PW12 catalyst annealed at 400°C.
Highly Ordered Lattice Orientation of ZnO Nanoparticles Formed in Confined Space
Authors: Dou Shu-mei , Liu Qiao-hong , Wang Wen-lou , Liu Xian-ming
Published: September 2010

Oriented aggregation of nanoparticles has been accomplished by means of solid state reaction. Non-crystallized and crystallized ZnO nanoparticles/clusters could be accommodated in the lamellar spacing of inorganic-organic composite, which were prepared by thermolysis of layered solid zinc-oleate complex at 260 and 300°C in air, respectively. High-resolution transmission electron microscopy and selected area electron diffraction patterns indicate that aggregates are single crystals with various defects. The photoluminescence excitation spectra of both samples show two bands at 272 and 366 nm. The former may originate from electron transfer from valence band to conduction band in ZnO clusters composed of less than 200 ZnO molecules (2R < 2 nm).
Food Stamps and the Market Demand for Food
Authors: Reed Albert J. , Levedahl J. William
Published: September 2010

This article compares estimates of disaggregated market food demand responses to the Supplemental Nutrition Assistance Program benefits based on exact nonlinear aggregation to responses based on linear aggregation. By accounting for income inequality, nonlinear aggregation implies that only the households that receive benefits contribute to market demand responses. In contrast, linear aggregation presumes all households receive benefits and thus contribute to the market demand response. The consequence is that nonlinear market estimates are smaller than the linear estimates by roughly the fraction of households that receive benefits.
Antiviral Role of Plant-Encoded RNA-Dependent RNA Polymerases Revisited with Deep Sequencing of Small Interfering RNAs of Virus Origin
Authors: Qu Feng
Published: September 2010

Several recent studies profiled virus-specific small interfering RNAs (vsRNAs) using next generation sequencing platforms and compellingly implicated plant-encoded RNA-dependent RNA polymerases (RDR) in vsRNA biogenesis and vsRNA-mediated antiviral defense. Specifically, both RDR1 and RDR6 were found to contribute to the accumulation of vsRNAs in virus-infected cells. While RDR1 was responsible for the majority of vsRNAs in plants infected with three different viruses, RDR6 acted as a surrogate when RDR1 function was disrupted. Mechanistically, vsRNAs associated with RDR1 mostly mapped to viral RNA regions close to the 5′ ends, whereas those associated with RDR6 mapped to more 3′ regions and appeared to be dependent on higher viral RNA concentrations. Knocking out both RDR1 and RDR6 led to drastically diminished vsRNA levels concomitant with enhanced viral RNA accumulation. In conclusion, these studies established that RDR1 and RDR6 function synergistically to contain RNA virus infections through the RNA silencing–based antiviral defense.
Wheat Crown Rot Pathogens Fusarium graminearum and F. pseudograminearum Lack Specialization
Authors: Chakraborty Sukumar , Obanor Friday , Westecott Rhyannyn , Abeywickrama Krishanthi
Published: September 2010

This article reports a lack of pathogenic specialization among Australian Fusarium graminearum and F. pseudograminearum causing crown rot (CR) of wheat using analysis of variance (ANOVA), principal component and biplot analysis, Kendall's coefficient of concordance (W), and κ statistics. Overall, F. pseudograminearum was more aggressive than F. graminearum, supporting earlier delineation of the crown-infecting group as a new species. Although significant wheat line–pathogen isolate interaction in ANOVA suggested putative specialization when seedlings of 60 wheat lines were inoculated with 4 pathogen isolates or 26 wheat lines were inoculated with 10 isolates, significant W and κ showed agreement in rank order of wheat lines, indicating a lack of specialization. The first principal component representing nondifferential aggressiveness explained a large part (up to 65%) of the variation in CR severity. The differential components were small and more pronounced in seedlings than in adult plants. By maximizing variance on the first two principal components, biplots were useful for highlighting the association between isolates and wheat lines. A key finding of this work is that a range of analytical tools are needed to explore pathogenic specialization, and a statistically significant interaction in an ANOVA cannot be taken as conclusive evidence of specialization. With no highly resistant wheat cultivars, Fusarium isolates mostly differ in aggressiveness; however, specialization may appear as more resistant cultivars become widespread.
Propiconazole Distribution and Effects onCeratocystis fagacearumSurvival in Roots of Treated Red Oaks
Authors: Blaedow Ryan A. , Juzwik Jennifer , Barber Brian
Published: September 2010

We investigated the interaction between the oak wilt pathogen (Ceratocystis fagacearum) and propiconazole in lower stems and roots of Quercus rubra to better understand published reports of fungicide failure after 2 years. Propiconazole was infused into mature oaks in July 2004 and roots were inoculated with pathogen endoconidia 1.0 m from injection sites at ±2 weeks of fungicide treatment. Pathogen presence in wood samples was determined by isolation and fungicide concentrations measured using gas chromatography-mass spectrometry. Propiconazole was detected in the roots (≤1.0 m from injection sites) of all treated trees at 2, 12, and 24 months. Propiconazole was detected in all samples (n = 68) at 2 and 12 months and in 93% of samples (n = 72) at 24 months with concentrations ranging from 815 ppm (12 months in lower stem) to 0.7 ppm (24 months in most distal root segment). Although pathogen isolation incidence was lower in treated than disease control trees at 2 and 12 months, at no time did an infused oak fail to yield the fungus upon isolation. The results document basipetal movement and degradation of propiconazole, as well as the survival of the pathogen, over time in roots and lower stems of infused red oaks.
Diagnosis of Pierce's Disease Using Biomarkers Specific toXylella fastidiosarRNA andVitis viniferaGene Expression
Authors: Choi H.-K. , Goes da Silva F. , Lim H.-J. , Iandolino A. , Seo Y.-S. , Lee S.-W. , Cook D. R.
Published: September 2010

Pierce's disease (PD), caused by Xylella fastidiosa, represents one of the most damaging diseases of cultivated grape. Management of PD in the vineyard often relies on the removal of infected individuals, which otherwise serve as a source of inoculum for nearby healthy vines. Effective implementation of such control measures requires early diagnosis, which is complicated by the fact that infected vines often harbor high titers of the pathogen in advance of visual symptom development. Here, we report a biomarker system that simultaneously monitors Xylella-induced plant transcripts as well as Xylella ribosomal (r)RNA. Plant biomarker genes were derived from a combination of in silico analysis of grape expressed sequence tags and validation by means of reverse-transcriptase polymerase chain reaction (RT-PCR). Four genes upregulated upon PD infection were individually multiplexed with an X. fastidiosa marker rRNA and scored using either real-time RT-PCR or gel-based conventional RT-PCR techniques. The system was sufficiently sensitive to detect both host gene transcript and pathogen rRNA in asymptomatic infected plants. Moreover, these plant biomarker genes were not induced by water deficit, which is a component of PD development. Such biomarker genes could have utility for disease control by aiding early detection and as a screening tool in breeding programs.
A Test of Taxonomic and Biogeographic Predictivity: Resistance to Soft Rot in Wild Relatives of Cultivated Potato
Authors: Chung Yong Suk , Holmquist Karsten , Spooner David M. , Jansky Shelley H.
Published: September 2010

The concept that traits should be associated with related organisms and that nearby populations of the same species are likely to be more similar to each other than to populations spread far apart has long been accepted. Consequently, taxonomic relationships and biogeographical data are commonly believed to have the power to predict the distribution of disease resistance genes among plant species. In this study, we test claims of such predictivity in a group of widely distributed wild potato species. There was no clear association between resistance to soft rot and taxonomic relationships. However, we have found some associations between resistance to soft rot and environmental data such as annual precipitation and annual mean temperature. In addition, we have noted that high levels of resistance are mostly found in species with high levels of phenotypic plasticity. The three most resistant species were Solanum paucijugum, S. brevicaule, and S. commersonii.
The 3ADON Population of Fusarium graminearum Found in North Dakota Is More Aggressive and Produces a Higher Level of DON than the Prevalent 15ADON Population in Spring Wheat
Authors: Puri Krishna D. , Zhong Shaobin
Published: September 2010

Fusarium head blight (FHB) is primarily caused by Fusarium graminearum in North America. Isolates of F. graminearum can be identified as one of three chemotypes: 3-acetyl-deoxynivalenol (3ADON), 15-acetyl-deoxynivalenol (15ADON), and nivalenol (NIV). In this study, we characterized F. graminearum isolates collected in 1980 to 2000 (old collection) and in 2008 (new collection) from North Dakota and found a 15-fold increase of 3ADON isolates in the new collection. Evaluation of randomly selected 3ADON isolates and 15ADON isolates on three spring wheat genotypes (Grandin, Steele-ND, and ND 2710) by single-floret inoculation indicated that the 3ADON population caused a higher disease severity and produced more DON at a significant level than the 15ADON population on Grandin (susceptible to FHB) and ND 2710 (with FHB resistance from Sumai 3). However, no significant differences in disease severity and DON production were observed between the two populations on Steele-ND (with moderate resistance from Triticum dicoccoides). The 3ADON isolates also exhibited a higher DON production in rice culture and produced more spores on agar media than the 15ADON isolates, suggesting a fitness advantage of the newly emerging 3ADON population over the prevalent 15ADON population. Population genetic analyses using DNA markers revealed a significant genetic differentiation between the two populations. The information obtained in this study could have an impact on development of FHB-resistant wheat cultivars and disease management.
Factors Contributing to Seasonal Fluctuations in Rust Severity onRibes missourienseCaused byCronartium ribicola
Authors: Newcomb Maria , Upper Christen D. , Rouse Douglas I.
Published: September 2010

Cronartium ribicola, causal agent of white pine blister rust, is a macrocyclic heteroecious rust that cycles between white pines and members of the genus Ribes, which are typically wild plants in North America. To improve predictability of inoculum available for infection of ecologically and commercially important white pines, this research was conducted to identify the factors that influence the development and persistence of uredinia and telia on Ribes in their natural habitats. Numbers of infectious C. ribicola rust lesions (with potentially sporulating rust sori) on tagged Ribes missouriense plants in the woods fluctuated during the season. Changes in numbers of infectious rust lesions were related to rain that occurred 13 days earlier. In field experiments, supplemental leaf wetness provided for 2 days on Ribes shoots resulted in the development of rust lesions more frequently than on control shoots. Viable inoculum and susceptible hosts were present, and the environment was the limiting factor for disease development. Lesion necrosis and leaf abscission contributed to decreases in numbers of infectious rust lesions. Higher lesion density was significantly related to earlier leaf abscission. Telial fruiting bodies occurred in low numbers from early June throughout the remainder of the season.
Freeform surface filtering using the diffusion equation
Authors: Jiang X. , Cooper P. , Scott P. J.
Published: September 2010

The measurement of texture for geometric surfaces is well established for surfaces that are of a planar (Euclidean) nature. Gaussian filtering is the fundamental base for scale-limited surfaces used in surface texture, but cannot be applied to non-Euclidean surfaces without distortion of the results. A link exists between Gaussian filtering and solutions of the PDE that models linear isotropic diffusion. In particular, an analytical solution of this diffusion equation over a planar region at a time
t
is given by the continuous convolution of the initial distribution of the diffused quantity with a Gaussian function of standard deviation

. A practical implementation of the standard Gaussian filter on sampled data can be viewed as a discretization of this process. On a non-Euclidean surface, the diffusion equation is formulated by using the Laplace–Beltrami operator. Using this generalization, a method of Gaussian filtering for freeform surface data is proposed by solving the diffusion equation for approximation residuals defined on a freeform least-squares approximation of the measurement surface data. Results of the application of these methods to simulated and experimental data are presented.
Quantum matchgate computations and linear threshold gates
Authors: Van den Nest Maarten
Published: September 2010

The theory of matchgates is of interest in various areas in physics and computer science. Matchgates occur, for example, in the study of fermions and spin chains, in the theory of holographic algorithms and in several recent works in quantum computation. In this paper, we completely characterize the class of Boolean functions computable by unitary two-qubit matchgate circuits with some probability of success. We show that this class precisely coincides with that of the
linear threshold gates
. The latter is a fundamental family that appears in several fields, such as the study of neural networks. Using the above characterization, we further show that the power of matchgate circuits is surprisingly trivial in those cases where the computation is to succeed with high probability. In particular, the only functions that are matchgate-computable with success probability greater than 3/4 are functions depending on only a
single
bit of the input.
Helicobacter pylori dupA and gastric acid secretion are negatively associated with gastric cancer development
Authors: Imagawa Shinobu , Ito Masanori , Yoshihara Masaharu , Eguchi Hidetaka , Tanaka Shinji , Chayama Kazuaki
Published: September 2010

Few reports have described the cancer prevalence of peptic ulcer patients with long-term follow-up studies. We have conducted a long-term retrospective cohort study of Japanese peptic ulcer patients and evaluated the risk factors for the occurrence of gastric cancer (GCa). A total of 136 patients diagnosed with peptic ulcers from 1975 to 1983 were enrolled. These 136 cases [102 males and 34 females; 69 gastric ulcer (GU) and 67 duodenal ulcer (DU) patients at the time of enrolment; mean follow-up period of 14.4 years (range 1–30 years)] after being matched with a tumour registry database in Hiroshima prefecture were surveyed for GCa. We investigated Helicobacter pylori duodenal ulcer promoter gene A (dupA) using paraffin-embedded gastric biopsy specimens in 56 cases. Gastric acid secretion and basal acid output (BAO) in 40 cases, and maximal acid output in 68 cases, had been measured at first diagnosis of peptic ulcers. GCa was detected in 24 patients (17 with GU, 7 with DU) during the follow-up. The prevalence of GCa was significantly higher in GU patients than in DU patients (log-rank test P<0.05). dupA-positive H. pylori was detected not only in DU patients (9/20) but also in GU patients (9/36). Gastric acid output was significantly larger in quantity in patients with dupA-positive H. pylori than in those with dupA-negative H. pylori (P<0.05). The occurrence of GCa was significantly lower in patients with dupA-positive H. pylori and a high BAO level (log-rank test P<0.05). DUs, higher acid output and dupA-positive H. pylori were negatively associated with GCa.
Superantigen gene profiles and presence of exfoliative toxin genes in community-acquired meticillin-resistant Staphylococcus aureus isolated from Chinese children
Authors: Wu Dejing , Li Xiangmei , Yang Yonghong , Zheng Yaojie , Wang Chuanqing , Deng Li , Liu Lan , Li Changcong , Shang Yunxiao , Zhao Changan , Yu Sangjie , Shen Xuzhuang
Published: September 2010

This study aimed to evaluate the distribution of superantigen gene profiles and the presence of exfoliative toxin genes in community-acquired meticillin-resistant Staphylococcus aureus (CA-MRSA) isolated from Chinese children, and simultaneously to assess virulence gene profiles and genetic background. Of the CA-MRSA isolates, 88.9 % (88/99) harboured toxin genes, with sek as the most frequent toxin gene (62.6 %), followed by seq (61.6 %), seb (60.6 %) and sea (35.4 %). The eta gene was detected only in one ST398-IVa-spa t034 strain. The sed and etd genes were not found in any of the isolates tested. A total of 38 virulence genotypes were observed, of which the genotype seb-sek-seq (27.3 %, 24/88) comprised the majority, followed by sea-seb-sek-seq (18.2 %, 16/88). The enterotoxin gene cluster including seg-sei-sem-sen-seo-seu predominated at a rate of 15.1 %. The relationship among toxin genotypes, toxin genes encoding profiles of mobile genetic elements and genetic background was analysed. Among 66 clonal complex (CC) 59 isolates, 87.9 % (58/66) were positive for toxin genes, and 75.8 % (50/66) harboured the toxin gene combination seb-sek-seq. Among seb-sek-seq-positive CC59 strains, 42.0 % (21/50) also carried the sea gene. CC59 corresponded exclusively to accessory gene regulator 1 (agr-1). The data presented here enhance our current knowledge on the virulence determinants of CA-MRSA.
A report of Streptococcus pneumoniae serotype 6D in Europe
Authors: Nahm M. H. , Oliver M. B. , Siira L. , Kaijalainen T. , Lambertsen L. M. , Virolainen A.
Published: September 2010

Serotype 6D of Streptococcus pneumoniae has been reported in Asia and the Fijian islands among nasopharyngeal carriage isolates. We now report a 6D isolate from a Finnish adult with invasive pneumococcal disease. Interestingly, the Finnish isolate and Asian isolate capsule gene loci are almost identical.
Hetero-oligomeric glutamate dehydrogenase from Thermus thermophilus
Authors: Tomita Takeo , Miyazaki Takashi , Miyazaki Junichi , Kuzuyama Tomohisa , Nishiyama Makoto
Published: September 2010

An extremely thermophilic bacterium,Thermus thermophilus, possesses two glutamate dehydrogenase (GDH) genes,gdhAandgdhB, putatively forming an operon on the genome. To elucidate the functions of these genes, the gene products were purified and characterized. GdhA showed no GDH activity, while GdhB showed GDH activity for reductive amination 1.3-fold higher than that for oxidative deamination. When GdhA was co-expressed with His-tag-fused GdhB, GdhA was co-purified with His-tagged GdhB. Compared with GdhB alone, co-purified GdhA–GdhB had decreased reductive amination activity and increased oxidative deamination activity, resulting in a 3.1-fold preference for oxidative deamination over reductive amination. Addition of hydrophobic amino acids affected the GDH activity of the co-purified GdhA–GdhB hetero-complex. Among the amino acids, leucine had the largest effect on activity: addition of 1 mM leucine elevated the GDH activity of the co-purified GdhA–GdhB by 974 and 245 % for reductive amination and oxidative deamination, respectively, while GdhB alone did not show such marked activation by leucine. Kinetic analysis revealed that the elevation of GDH activity by leucine is attributable to the enhanced turnover number of GDH. In this hetero-oligomeric GDH system, GdhA and GdhB act as regulatory and catalytic subunits, respectively, and GdhA can modulate the activity of GdhB through hetero-complex formation, depending on the availability of hydrophobic amino acids. This study provides the first finding, to our knowledge, of a hetero-oligomeric GDH that can be regulated allosterically.
Functional and phenotypic characterization of a protein from Lactobacillus acidophilus involved in cell morphology, stress tolerance and adherence to intestinal cells
Authors: O'Flaherty Sarah J. , Klaenhammer Todd R.
Published: September 2010

Structural components of the cell surface have an impact on some of the beneficial attributes of probiotic bacteria. In silico analysis of the L. acidophilus NCFM genome sequence revealed the presence of a putative cell surface protein that was predicted to be a myosin cross-reactive antigen (MCRA). As MCRAs are conserved among many probiotic bacteria, we used the upp-based counterselective gene replacement system, designed recently for use in L. acidophilus, to determine the functional role of this gene (LBA649) in L. acidophilus NCFM. Phenotypic assays were undertaken with the parent strain (NCK1909) and deletion mutant (NCK2015) to assign a function for this gene. The growth of NCK2015 (ΔLBA649) was reduced in the presence of lactate, acetate, porcine bile and salt. Adhesion of NCK2015 to Caco-2 cells was substantially reduced for both stationary-phase (∼45 % reduction) and exponential-phase cells (∼50 % reduction). Analysis of NCK2015 by scanning electron microscopy revealed a longer cell morphology after growth in MRS broth compared to NCK1909. These results indicate a role for LBA649 in stress tolerance, cell wall division and adherence to Caco-2 cells.
Crystal structure and mutagenesis analysis of chitinase CrChi1 from the nematophagous fungus Clonostachys rosea in complex with the inhibitor caffeine
Authors: Yang Jinkui , Gan Zhongwei , Lou Zhiyong , Tao Nan , Mi Qili , Liang Lianming , Sun Yuna , Guo Yu , Huang Xiaowei , Zou Chenggan , Rao Zihe , Meng Zhaohui , Zhang Ke-Qin
Published: September 2010

Chitinases are a group of enzymes capable of hydrolysing theβ-(1,4)-glycosidic bonds of chitin, an essential component of the fungal cell wall, the shells of nematode eggs, and arthropod exoskeletons. Chitinases from pathogenic fungi have been shown to be putative virulence factors, and can play important roles in infecting hosts. However, very limited information is available on the structure of chitinases from nematophagous fungi. Here, we present the 1.8 Å resolution of the first structure of a Family 18 chitinase from this group of fungi, that ofClonostachys roseaCrChi1, and the 1.6 Å resolution of CrChi1 in complex with a potent inhibitor, caffeine. Like other Family 18 chitinases, CrChi1 has the DXDXE motif at the end of strandβ5, with Glu174 as the catalytic residue in the middle of the open end of the (β/α)8barrel. Two caffeine molecules were shown to bind to CrChi1 in subsites −1 to +1 in the substrate-binding domain. Moreover, site-directed mutagenesis of the amino acid residues forming hydrogen bonds with caffeine molecules suggests that these residues are important for substrate binding and the hydrolytic process. Our results provide a foundation for elucidating the catalytic mechanism of chitinases from nematophagous fungi and for improving the pathogenicity of nematophagous fungi against agricultural pest hosts.
Abelson family kinases regulate Frizzled planar cell polarity signaling via Dsh phosphorylation
Authors: Singh Jaskirat , Yanfeng Wang A. , Grumolato Luca , Aaronson Stuart A. , Mlodzik Marek
Published: September 2010

Abelson (Abl) family tyrosine kinases have been implicated in cell morphogenesis, adhesion, motility, and oncogenesis. Using a candidate approach for genes involved in planar cell polarity (PCP) signaling, we identified Drosophila Abl (dAbl) as a modulator of Frizzled(Fz)/PCP signaling. We demonstrate that dAbl positively regulates the Fz/Dishevelled (Dsh) PCP pathway without affecting canonical Wnt/Wg–Fz signaling. Genetic dissection suggests that Abl functions via Fz/Dsh signaling in photoreceptor R3 specification, a well-established Fz–PCP signaling readout. Molecular analysis shows that dAbl binds and phosphorylates Dsh on Tyr473 within the DEP domain. This phosphorylation event on Dsh is functionally critical, as the equivalent DshY473F mutant is nonfunctional in PCP signaling and stable membrane association, although it rescues canonical Wnt signaling. Strikingly, mouse embryonic fibroblasts (MEFs) deficient for Abl1 and Abl2/Arg genes also show reduced Dvl2 phosphorylation as compared with control MEFs, and this correlates with a change in subcellular localization of endogenous Dvl2. As in Drosophila, such Abl-deficient MEFs show no change in canonical Wnt signaling. Taken together, our results argue for a conserved role of Abl family members in the positive regulation of Dsh activity toward Fz–Dsh/PCP signaling by Dsh phosphorylation.
PARTISAN POLITICS, ELECTORAL COMPETITION AND IMPRISONMENT: AN ANALYSIS OF STATES OVER TIME*
Authors: STUCKY THOMAS D. , HEIMER KAREN , LANG JOSEPH B.
Published: September 2010

The now well‐documented explosion in prison populations over the last 30 years has spurred significant attention in the literature. Early research focused primarily on economic explanations. More recently it has focused on political explanations of prison growth. Here we extend research on political explanations of imprisonment by drawing on the literature on state politics and public policy. We argue that the effect of partisan politics on punishment is conditional on how much electoral competition legislators face. We test this hypothesis using annual state level data on imprisonment from 1978 to 1996. Our findings show that the effect of Republican state legislative strength on prison admissions depends on time and the level of competition in state legislative elections. We argue that these findings suggest the need for a more nuanced understanding of the link between partisan U.S. politics and imprisonment.
Ascertaining the Perspectives of Young Children in Care: Case Studies in the Use of Reality Boxes
Authors: Winter Karen
Published: September 2010

This article describes the use of an innovative method, reality boxes, to elicit the perspectives of children, ages four to seven years, in state care. Using examples from a broader research project based on children in Northern Ireland, which was concerned with their participation rights, the article considers how the children used the boxes to express their views. Informed by a child rights‐based approach, the article highlights the processes and practices involved and concludes by stressing the potential importance of this method, used in the context of this framework, in social work practice with young children.
The effect of isoflurane or propofol anaesthesia on liver injury after partial hepatectomy in cirrhotic patients
Authors: Yang L. Q. , Tao K. M. , Cheung C. W. , Liu Y. T. , Tao Y. , Wu F. X. , Yu W. F.
Published: September 2010

This study compared the effect of isoflurane or propofol anaesthesia on postoperative hepatocellular injury, liver function and pro‐inflammatory cytokine concentrations in 60 cirrhotic patients, after partial hepatectomy using Pringle’s manoeuvre. In the isoflurane group postoperatively, both mean (SD) aspartate aminotransferase (day 1: 197 (123) U.l−1 vs 261 (143) U.l−1; p = 0.01; day 3: 465 (258) U.l−1 vs 578 (311) U.l−1; p = 0.02) and alanine aminotransferase (day 1: 575 (312) U.l−1 vs 714 (434) U.l−1; p = 0.04 and day 3: 776 (443) U.l−1 vs 898 (746) U.l−1; p = 0.03) were significantly lower compared with the propofol group. Mean (SD) postoperative white cell count was significantly lower with isoflurane than propofol (day 1: 12 (4) × 103.mm−1 vs 16 (4) × 103.mm−1; p = 0.01 and day 3: 10 (6) × 103.mm−1; vs 14 (4); p = 0.01). Tumour necrosis factor‐α (day 1) and interleukin‐1 (days 1 and 3) concentrations were significantly lower with isoflurane. Compared with propofol, isoflurane is associated with an attenuated postoperative inflammatory response and less postoperative hepatocellular injury in patients having this procedure.