bluuebunny/crossref_metadata_2025 huggingface dataset:
All-optical phase modulations in a silicon wire waveguide at ultralow light levels
Authors: Matsuda Nobuyuki , Shimizu Ryosuke , Mitsumori Yasuyoshi , Kosaka Hideo , Sato Aya , Yokoyama Hiroyuki , Yamada Koji , Watanabe Toshifumi , Tsuchizawa Tai , Fukuda Hiroshi , Itabashi Seiichi , Edamatsu Keiichi
Published: October 2009

Cross-phase modulation (XPM) in a silicon wire waveguide at 1.55 μm telecom band was studied down to ultralow light levels. In the low-power regime, we found that free-carrier dispersion as well as the optical Kerr effect contributes to the XPM. Possible mechanisms of the low-power XPM are discussed.
Photocurrent enhancement in polymer:fullerene bulk heterojunction solar cells doped with a phosphorescent molecule
Authors: Rand Barry P. , Girotto Claudio , Mityashin Alexander , Hadipour Afshin , Genoe Jan , Heremans Paul
Published: October 2009

We demonstrate photocurrent enhancement of up to 20% in polymer:fullerene bulk heterojunction photovoltaic cells via the incorporation of a phosphorescent dopant, without degradation in the open-circuit voltage or fill factor of the device. The enhancement is shown to originate from multiple sources. First, the phosphor is able to populate the long-lived triplet state of the polymer, leading to longer diffusion length and a larger polymer contribution. Also, there is direct absorption on the dopant leading to enhanced spectral coverage. Finally, the dopant acts as a donor site and therefore increases the fullerene signal.
Site-specific behavior in de-excitation spectra of F3SiCH2CH2Si(CH3)3 in the Si 1s excitation region
Authors: Suzuki I. H. , Nitta A. , Fukuzawa H. , Ueda K. , Takahashi O. , Tamenori Y. , Nagaoka S.
Published: October 2009

Excitation (total ion yield) and de-excitation (resonant photoemission) spectra have been measured in the Si 1s photoexcitation region of the F3SiCH2CH2Si(CH3)3 molecule using monochromatized undulator radiation. Theoretical calculations within the framework of density functional theory have reproduced the observed total ion yield spectrum very well. The first peak at the lowest photon energy, coming from Si 1s excitation at the trimethyl side into a vacant orbital, induces spectator Auger decays in which the excited electron remains in its valence orbital. The second peak produced through excitation of Si 1s electron at the trifluoride side generates resonant Auger decays in which the excited valence electron remains predominantly also in the valence orbital or is partly shaken up into higher Rydberg orbitals. The third peak generated through Si 1s excitation at the trifluoride side produces resonant Auger decays in which the excited Rydberg electron remains or is partly shaken down to a lower lying valence molecular orbital. These findings exhibit a clear distinction between resonant Auger decays following photoexcitation of Si 1s electrons under different chemical environments.
Interlayer magnetostatic coupling induced Co layer coercivity enhancement and exchange bias in [Pd/Co]/Cu/Co spin valves
Authors: Yang P. Y. , Zhu X. Y. , Zeng F. , Pan F.
Published: October 2009

Interlayer stray field coupling in hybrid perpendicular/Cu/in-plane magnetic anisotropy [Pd/Co]/Cu/Co single spin valves and [Pd/Co]/Cu/Co/Cu/[Co/Pd] dual spin valves was investigated. Enhancements of Co layer coercivity were observed after ac or dc demagnetization of the samples. This effect originates from the pinning of Co domain walls by the in-plane stray field from Co/Pd stripe domains, and the enhancements are more efficient as the Co/Pd domain size decreases. Moreover, the magnetostatic interaction between the net in-plane Co/Pd remanent moments and the Co moments leads to exchange bias in the Co layer of the dual spin valve after the dc demagnetization.
Mg-based metallic glass/titanium interpenetrating phase composite with high mechanical performance
Authors: Sun Y. , Zhang H. F. , Wang A. M. , Fu H. M. , Hu Z. Q. , Wen C. E. , Hodgson P. D.
Published: October 2009

We report an Mg-based metallic glass/titanium interpenetrating phase composite in which constituent phases form a homogeneously interconnected network. The porous titanium constrains shear bands propagation thoroughly and promotes shear bands branching and intersection subsequently. The homogeneous phase distribution promotes regularly distributed local shear deformation and leads to a uniform deformation for the composites. Moreover, the interpenetrating phase structure introduces a mutual-reinforcement between metallic glass and titanium. Therefore, the composite exhibits excellent mechanical performance with compressive fracture strength of 1783 MPa and fracture strain of 31%.
Plasmonic waveguide as an efficient transducer for high-density data storage
Authors: O’Connor D. , McCurry M. , Lafferty B. , Zayats A. V.
Published: October 2009

A design of high optical throughput nanoscale light sources has been proposed based on plasmonic wedge waveguides. It provides localization of the 1500 nm wavelength light at the output of less than 30×30 nm2 area at about 80% coupling efficiency from a dielectric loaded surface plasmon polariton waveguide and nearly 90% efficient power deposition in the absorbing media placed at the output for an experimentally viable 10 nm apex radius of the wedge. Such nanoscale light sources can be useful for high-density data storage, scanning near-field optical microscopy, and sensing.
The surface activation layer of GaAs negative electron affinity photocathode activated by Cs, Li, and NF3
Authors: Sun Y. , Kirby R. E. , Maruyama T. , Mulhollan G. A. , Bierman J. C. , Pianetta P.
Published: October 2009

The lifetime of GaAs photocathodes can be greatly improved by introducing Li in the Cs+NF3 activation process. The surface activation layer of such photocathodes is studied by synchrotron radiation photoemission and is compared with GaAs photocathodes activated without Li. The charge distributions of N, F, and Cs experience significant changes when Li is added in the activation. In addition, the presence of Li causes NFx molecules to take an orientation with F atoms on top. All these changes induced by Li hold the key for the lifetime improvement of GaAs photocathodes.
Reversible ferromagnetic spin ordering governed by hydrogen in Co-doped ZnO semiconductor
Authors: Cho Yong Chan , Kim Sung-Jin , Lee Seunghun , Kim Su Jae , Cho Chae Ryong , Nahm Ho-Hyun , Park Chul Hong , Jeong Il Kyoung , Park Sungkyun , Hong Tae Eun , Kuroda Shinji , Jeong Se-Young
Published: October 2009

We report a reversible manipulation of short-range spin ordering in Co-doped ZnO through hydrogenation and dehydrogenation processes. In both magnetic-circular dichroism and superconducting quantum interference device measurements, the ferromagnetism was clearly induced and removed by the injection and ejection of hydrogen, respectively. The x-ray photoelectron spectroscopy results and the first-principles electronic structure calculations consistently support the dependence of the ferromagnetism on the hydrogen position and the contribution of transition metal ions. The results suggest the ferromagnetic interaction between Co ions can be reversibly controlled by the hydrogen-mediated intrinsic spin ordering in Co doped ZnO.
Magnetization reversal process of ferromagnetic granular thin films probed by magnetization-induced second harmonic generation
Authors: Chiang Y. F. , Hsu Y. J. , Liu T. M. , Chu H. W. , Lin J. G. , Chen C. H. , Chang Y.-M.
Published: October 2009

We propose to use magnetization-induced second harmonic generation (MSHG) technique to explore the magnetization reversal process of cobalt granular thin films. The three-dimensional magnetization reversal process can be visualized by analyzing the polarization dependent MSHG hysteresis curves. It is found that the magnetization reversal process involves not only the in-plane but also the out-plane magnetization rotation because of the uniaxial anisotropy of cobalt granular thin films. This study demonstrates that MSHG can be a versatile optical technique to investigate the magnetic property of not only ferromagnetic epitaxial thin films but also ferromagnetic granular thin films.
Loss of parity between IL-2 and IL-21 in the NOD Idd3 locus
Authors: McGuire Helen M. , Vogelzang Alexis , Hill Natasha , Flodström-Tullberg Malin , Sprent Jonathan , King Cecile
Published: October 2009

IL-2 and IL-21 are two cytokines with great potential to affect autoimmune infiltration of nonlymphoid tissue, and are contained within the strongest non-MHC-linked locus for type 1 diabetes (T1D) susceptibility on the nonobese diabetic (NOD) mouse (Idd3). IL-21 is necessary for the development of diabetes in the NOD mouse, but a number of important studies argue that decreased expression of IL-2 explains Idd3. In this study, we demonstrate that the amount of IL-21, but not IL-2, correlated with T1D incidence. During our analyses of the IL-2/IL-21 interval, we found that mice segregate into one of two distinct expression profiles. In the first group, which includes the C57BL/6 strain, bothIl2andIl21were expressed at low levels. In the other group, which includes the NOD strain,Il2andIl21were both highly expressed. However, because NOD IL-2 mRNA was relatively unstable, IL-2 production was remarkably similar between strains. The increased production of IL-21 in NOD mice was found to result from two single nucleotide polymorphisms within the distal promoter region that conferred increased binding affinity for the transcription factor Sp1. Our findings indicate that a loss of locus parity after decreased IL-2 mRNA stability ensures that the high-expressing IL-21 allele persists in nature and provides a basis for autoimmunity.
Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in
Candida albicans
Authors: Uchida Maho , McDermott Gerry , Wetzler Modi , Le Gros Mark A. , Myllys Markko , Knoechel Christian , Barron Annelise E. , Larabell Carolyn A.
Published: October 2009

The opportunistic pathogen
Candida albicans
can undergo phenotypic switching between a benign, unicellular phenotype and an invasive, multicellular form that causes candidiasis. Increasingly, strains of
Candida
are becoming resistant to antifungal drugs, making the treatment of candidiasis difficult, especially in immunocompromised or critically ill patients. Consequently, there is a pressing need to develop new drugs that circumvent fungal drug-resistance mechanisms. In this work we used soft X-ray tomography to image the subcellular changes that occur as a consequence of both phenotypic switching and of treating
C. albicans
with antifungal peptoids, a class of candidate therapeutics unaffected by drug resistance mechanisms. Peptoid treatment suppressed formation of the pathogenic hyphal phenotype and resulted in striking changes in cell and organelle morphology, most dramatically in the nucleus and nucleolus, and in the number, size, and location of lipidic bodies. In particular, peptoid treatment was seen to cause the inclusion of lipidic bodies into the nucleus.
Nitrogen recycling and nutritional provisioning byBlattabacterium, the cockroach endosymbiont
Authors: Sabree Zakee L. , Kambhampati Srinivas , Moran Nancy A.
Published: October 2009

Nitrogen acquisition and assimilation is a primary concern of insects feeding on diets largely composed of plant material. Reclaiming nitrogen from waste products provides a rich reserve for this limited resource, provided that recycling mechanisms are in place. Cockroaches, unlike most terrestrial insects, excrete waste nitrogen within their fat bodies as uric acids, postulated to be a supplement when dietary nitrogen is limited. The fat bodies of most cockroaches are inhabited byBlattabacterium, which are vertically transmitted, Gram-negative bacteria that have been hypothesized to participate in uric acid degradation, nitrogen assimilation, and nutrient provisioning. We have sequenced completely theBlattabacteriumgenome fromPeriplaneta americana. Genomic analysis confirms thatBlattabacteriumis a member of the Flavobacteriales (Bacteroidetes), with its closest known relative being the endosymbiontSulcia muelleri, which is found in many sap-feeding insects. Metabolic reconstruction indicates that it lacks recognizable uricolytic enzymes, but it can recycle nitrogen from urea and ammonia, which are uric acid degradation products, into glutamate, using urease and glutamate dehydrogenase. Subsequently,Blattabacteriumcan produce all of the essential amino acids, various vitamins, and other required compounds from a limited palette of metabolic substrates. The ancient association withBlattabacteriumhas allowed cockroaches to subsist successfully on nitrogen-poor diets and to exploit nitrogenous wastes, capabilities that are critical to the ecological range and global distribution of cockroach species.
The conceptual semantics of numbers and counting
Authors: Goddard Cliff
Published: October 2009

This study explores the conceptual semantics of numbers and counting, using the natural semantic metalanguage (NSM) technique of semantic analysis (Wierzbicka 1996; Goddard & Wierzbicka (eds.) 2002). It first argues that the concept of a number in one of its senses (number1, roughly, “number word”) and the meanings of low number words, such as one, two, and three, can be explicated directly in terms of semantic primes, without reference to any counting procedures or practices. It then argues, however, that the larger numbers, and the productivity of the number sequence, depend on the concept and practice of counting, in the intransitive sense of the verb. Both the intransitive and transitive senses of counting are explicated, and the semantic relationship between them is clarified. Finally, the study moves to the semantics of abstract numbers (number2), roughly, numbers as represented by numerals, e.g. 5, 15, 27, 36, as opposed to number words. Though some reference is made to cross-linguistic data and cultural variation, the treatment is focused primarily on English.
Discourse coherence and gesture interpretation
Authors: Lascarides Alex , Stone Matthew
Published: October 2009

In face-to-face conversation, communicators orchestrate multimodal contributions that meaningfully combine the linguistic resources of spoken language and the visuo-spatial affordances of gesture. In this paper, we characterise this meaningful combination in terms of the COHERENCE of gesture and speech. Descriptive analyses illustrate the diverse ways gesture interpretation can supplement and extend the interpretation of prior gestures and accompanying speech. We draw certain parallels with the inventory of COHERENCE RELATIONS found in discourse between successive sentences. In both domains, we suggest, interlocutors make sense of multiple communicative actions in combination by using these coherence relations to link the actions’ interpretations into an intelligible whole. Descriptive analyses also emphasise the improvisation of gesture; the abstraction and generality of meaning in gesture allows communicators to interpret gestures in open-ended ways in new utterances and contexts. We draw certain parallels with interlocutors’ reasoning about underspecified linguistic meanings in discourse. In both domains, we suggest, coherence relations facilitate meaning-making by RESOLVING the meaning of each communicative act through constrained inference over information made salient in the prior discourse. Our approach to gesture interpretation lays the groundwork for formal and computational models that go beyond previous approaches based on compositional syntax and semantics, in better accounting for the flexibility and the constraints found in the interpretation of speech and gesture in conversation. At the same time, it shows that gesture provides an important source of evidence to sharpen the general theory of coherence in communication.
Across time, across the body
Authors: Cooperrider Kensy , Núñez Rafael
Published: October 2009

Talk about time is commonly accompanied by co-speech gesture. Though much recent work has looked at how time is construed as space in the languages of the world, few studies have examined temporal gestures in any detail. Our focus is on a particular pattern among American English speakers — transversal temporal gestures — in which time is conceptualized as moving from left to right across the body. Based on numerous examples elicited in a controlled observational paradigm, we suggest a classification of American English speakers’ transversal temporal gestures into five types — placing, pointing, duration-marking, bridging, and animating — and provide examples of each type. Discussion focuses on the following three topics: the usefulness of quasi-experimental approaches for the study of gesture; variation in temporal gestures across cultures; and how temporal gestures fit into a broader understanding of metaphorical gestures.
When do people start to recognize signs?
Authors: Arendsen Jeroen , Doorn Andrea J. van , Ridder Huib de
Published: October 2009

The aim of this paper is to examine when signers start to recognize the lexical meaning of a sign. This is studied with movies of 32 mono-morphemic signs of Sign Language of the Netherlands (SLN). Signs were presented in isolation or with preceding fidgets (e.g., rubbing your nose). Signers watched these movies at normal playing speed and had to respond as soon as they recognized a sign, which they were able to do, on average, about 850 ms after the coded beginning of the sign. By subtracting the time participants need to generate a motor response to a visible event, which was 310 ms on average, sign recognition was estimated to occur after around 540 ms. The results were further analyzed in relation to the sign’s movement phases (preparation, nucleus, and recovery) and for effects of participant characteristics, sign characteristics, and embedding conditions. The current findings are compared with earlier work on the time course of lexical sign recognition. Moreover, they are compared with findings from an earlier experiment on detecting the beginning of a sign (Arendsen et al., 2007) to study possible interference of lexical recognition with sign detection by signers.
Discourse style and theme–rheme progression in biomedical research article discussions
Authors: Williams Ian A.
Published: October 2009

This paper examines the Discussions of Spanish medical research articles and Spanish translations of comparable English-language texts in order to determine how far their discourse and theme–rheme patterns differ. Quantitative analysis revealed two discourse patterns. Spanish authors preferred a progressive style characterized by considerable initial background information, and a commentary opening with a statement of result and ending with the main claim. In contrast, most translations exhibited a retrogressive style with little or no background information, and the main claim located early or at the start. The Spanish texts showed a highly cohesive thematic pattern, most within-paragraph links being with the immediately preceding theme or rheme, whereas the translations, influenced by the source texts, contained comparatively more distant links, thus creating thematic ‘jumps’. Thematic progression was independent of discourse pattern. Qualitative analysis identified a number of strategies that can help translators align their texts with the target language norm for theme–rheme progression.
The effect of marked topic on memory in Hebrew and English
Authors: Netz Hadar , Kuzar Ron
Published: October 2009

This study examines and compares the effect of marked sentence structure on cognition and memory in English and Hebrew. It has been shown elsewhere that marked topic constructions in English have a significant effect on memory. Now, since Hebrew, like English, is an SV(O) (Subject-Verb-Object) language, the cognitive effect of marking the topic in Hebrew could be expected to be similar to the effect witnessed in English. However, the study presents data which attest unequivocally to the prevalence of marked topic constructions in Hebrew in comparison to English. In addition, through psycholinguistic experimentation, it is shown that in Hebrew deviations from the SV(O) structure are not as prominently marked as they are in English.
The cultural inertia of the habitus: Gendered narrations of agency amongst educated female Palestinians in Israel
Authors: Alayan Samira , Yair Gad
Published: October 2009

Key experiences are short and intense instructional episodes that students remember to have had a decisive effect on their lives and are usually equated with a sense of self‐direction and empowerment. This study analyzes gender differences in the narrations of key educational experiences of Palestinian Israeli students—an educated segment in Israeli‐Palestinian society. The results suggest that while female Palestinians in Israeli academic programs have attained more than equal gender representation, a significant number of respondents still express traditional gendered conceptions. Though academically successful, many female students hide motives of agency, while expressing their stories as traditional gendered narratives. These results imply that while gender equality has been formally attained amongst Palestinians in Israel, gender differences persist with regard to women's basic cultural habitus, even amongst educated students. It thus suggests that while efforts to achieve formal and institutional gender equality are necessary, they are hardly sufficient conditions for changing cultural conceptions of gender subjectivity.
Model aggregation: a building-block approach to creating large macromolecular regulatory networks
Authors: Randhawa Ranjit , Shaffer Clifford A. , Tyson John J.
Published: October 2009

Motivation: Models of regulatory networks become more difficult to construct and understand as they grow in size and complexity. Modelers naturally build large models from smaller components that each represent subsets of reactions within the larger network. To assist modelers in this process, we present model aggregation, which defines models in terms of components that are designed for the purpose of being combined.

Results: We have implemented a model editor that incorporates model aggregation, and we suggest supporting extensions to the Systems Biology Markup Language (SBML) Level 3. We illustrate aggregation with a model of the eukaryotic cell cycle ‘engine’ created from smaller pieces.

Availability: Java implementations are available in the JigCell Aggregation Connector. See http://jigcell.biol.vt.edu.

Contact:  shaffer@vt.edu
inGAP: an integrated next-generation genome analysis pipeline
Authors: Qi Ji , Zhao Fangqing , Buboltz Anne , Schuster Stephan C.
Published: October 2009

Summary: We develop a novel mining pipeline, Integrative Next-generation Genome Analysis Pipeline (inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. inGAP can be applied to the mapping of both Roche/454 and Illumina reads with no restriction of read length. Experiments on simulated and experimental data show that this pipeline can achieve overall 97% accuracy in SNP detection and 94% in the finding of indels. All the detected SNPs/indels can be further evaluated by a graphical editor in our pipeline. inGAP also provides functions of multiple genomes comparison and assistance of bacterial genome assembly.

Availability: inGAP is available at http://sites.google.com/site/nextgengenomics/ingap

Contact:  scs@bx.psu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Simulation-based model selection for dynamical systems in systems and population biology
Authors: Toni Tina , Stumpf Michael P. H.
Published: October 2009

Motivation: Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not straightforward. We therefore require suitable statistical tools that allow us to choose rationally between different mechanistic models of, e.g. signal transduction or gene regulation networks. This is particularly challenging in systems biology where only a small number of molecular species can be assayed at any given time and all measurements are subject to measurement uncertainty.

Results: Here, we develop such a model selection framework based on approximate Bayesian computation and employing sequential Monte Carlo sampling. We show that our approach can be applied across a wide range of biological scenarios, and we illustrate its use on real data describing influenza dynamics and the JAK-STAT signalling pathway. Bayesian model selection strikes a balance between the complexity of the simulation models and their ability to describe observed data. The present approach enables us to employ the whole formal apparatus to any system that can be (efficiently) simulated, even when exact likelihoods are computationally intractable.

Contact:  ttoni@imperial.ac.uk; m.stumpf@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bayesian model selection for characterizing genomic imprinting effects and patterns
Authors: Yang Runqing , Wang Xin , Wu Zeyuan , Prows Daniel R. , Lin Min
Published: October 2009

Motivation: Although imprinted genes have been ubiquitously observed in nature, statistical methodology still has not been systematically developed for jointly characterizing genomic imprinting effects and patterns. To detect imprinting genes influencing quantitative traits, the least square and maximum likelihood approaches for fitting a single quantitative trait loci (QTL) and Bayesian method for simultaneously modeling multiple QTLs have been adopted in various studies.

Results: In a widely used F2 reciprocal mating population for mapping imprinting genes, we herein propose a genomic imprinting model which describes additive, dominance and imprinting effects of multiple imprinted quantitative trait loci (iQTL) for traits of interest. Depending upon the estimates of the above genetic effects, we categorized imprinting patterns into seven types, which provides a complete classification scheme for describing imprinting patterns. Bayesian model selection was employed to identify iQTL along with many genetic parameters in a computationally efficient manner. To make statistical inference on the imprinting types of iQTL detected, a set of Bayes factors were formulated using the posterior probabilities for the genetic effects being compared. We demonstrated the performance of the proposed method by computer simulation experiments and then applied this method to two real datasets. Our approach can be generally used to identify inheritance modes and determine the contribution of major genes for quantitative variations.

Contact:  annie.lin@duke.edu; runqingyang@sjtu.edu.cn
MATICCE: mapping transitions in continuous character evolution
Authors: Hipp Andrew L. , Escudero Marcial
Published: October 2009

Summary: MATICCE is a new software package in the R language for mapping phylogenetic transitions in organismal traits that have continuous distributions. MATICCE integrates over phylogenetic and model uncertainty and provides simulation functions for visualizing evolutionary scenarios based on estimated parameter values.

Availability and Implementation: MATICCE is written in the open source R language and freely available through the Comprehensive R Archive Network (http://cran.r-project.org/web/packages/maticce).

Contact:  ahipp@mortonarb.org
Brevundimonas vancanneytii sp. nov., isolated from blood of a patient with endocarditis
Authors: Estrela Andréia B. , Abraham Wolf-Rainer
Published: October 2009

A Gram-negative, rod-shaped, non-spore-forming bacterial strain, designated LMG 2337T, was isolated from the blood of a patient with endocarditis and characterized. The strain was affiliated with the alphaproteobacterial genus Brevundimonas, with Brevundimonas diminuta LMG 2089T (98.3 % 16S rRNA gene sequence similarity) and Brevundimonas terrae KSL-145T (97.5 %) as its closest relatives. This affiliation was supported by chemotaxonomic data: the G+C content was 66.3 mol %, the major polar lipids were phosphatidyl diacylglycerol, sulfoquinovosyl diacylglycerol and phosphatidyl glucopyranosyl diacylglycerol and the major fatty acids were summed feature 7 (one or more of C18 : 1
ω7c, C18 : 1
ω9t and C18 : 1
ω12t) and C16 : 0. Strain LMG 2337T displayed an unusually broad substrate spectrum. The results from DNA–DNA hybridization and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain LMG 2337T from all of the type strains of hitherto-described Brevundimonas species. The strain therefore represents a novel species, for which the name Brevundimonas vancanneytii sp. nov. is proposed, with type strain LMG 2337T (=CCUG 1797T =ATCC 14736T).
Partial recN gene sequencing: a new tool for identification and phylogeny within the genus Streptococcus
Authors: Glazunova Olga O. , Raoult Didier , Roux Véronique
Published: October 2009

Partial sequences of therecNgene (1249 bp), which encodes a recombination and repair protein, were analysed to determine the phylogenetic relationship and identification of streptococci. The partial sequences presented interspecies nucleotide similarity of 56.4–98.2 % and intersubspecies similarity of 89.8–98 %. The mean DNA sequence similarity ofrecNgene sequences (66.6 %) was found to be lower than those of the 16S rRNA gene (94.1 %),rpoB(84.6 %),sodA(74.8 %),groEL(78.1 %) andgyrB(73.2 %). Phylogenetically derived trees revealed six statistically supported groups:Streptococcus salivarius,S. equinus,S. hyovaginalis/S. pluranimalium/S. thoraltensis,S. pyogenes,S. mutansandS. suis. The ‘mitis’ group was not supported by a significant bootstrap value, but three statistically supported subgroups were noted:Streptococcus sanguinis/S. cristatus/S. sinensis,S. anginosus/S. intermedius/S. constellatus(the ‘anginosus’ subgroup) andS. mitis/S. infantis/S. peroris/S. oralis/S. oligofermentans/S. pneumoniae/S. pseudopneumoniae. The partialrecNgene sequence comparison highlighted a high percentage of divergence betweenStreptococcus dysgalactiaesubsp.dysgalactiaeandS. dysgalactiaesubsp.equisimilis. This observation is confirmed by other gene sequence comparisons (groEL,gyrB,rpoBandsodA). A high percentage of similarity was found betweenS. intermediusandS. constellatusafter sequence comparison of therecNgene. To study the genetic diversity among the ‘anginosus’ subgroup,recN,groEL,sodA,gyrBandrpoBsequences were determined for 36 clinical isolates. The results that were obtained confirmed the high genetic diversity within this group of streptococci.
Cystobasidiomycetes yeasts from Patagonia (Argentina): description of Rhodotorula meli sp. nov. from glacial meltwater
Authors: Libkind Diego , Sampaio José Paulo , van Broock Maria
Published: October 2009

A basidiomycetous yeast, strain CRUB 1032T, which formed salmon-pink colonies, was isolated from glacial meltwater in Patagonia, Argentina. Morphological, physiological and biochemical characterization indicated that this strain belonged to the genus Rhodotorula. Molecular taxonomic analysis based on the 26S rDNA D1/D2 domain and internal transcribed spacer region sequences showed that strain CRUB 1032T represents an undescribed yeast species, for which the name Rhodotorula meli sp. nov. is proposed (type strain is CRUB 1032T=CBS 10797T=JCM 15319T). Phylogenetic analysis showed that Rhodotorula lamellibrachii was the closest known species, which, together with R. meli, formed a separate cluster related to the Sakaguchia clade within the Cystobasidiomycetes. Additional Patagonian yeast isolates of the class Cystobasidiomycetes are also investigated in the present work.
Modulation of hippocampal theta oscillations and spatial memory by relaxin-3 neurons of the nucleus incertus
Authors: Ma Sherie , Olucha-Bordonau Francisco E. , Hossain M. Akhter , Lin Feng , Kuei Chester , Liu Changlu , Wade John D. , Sutton Steven W. , Nuñez Angel , Gundlach Andrew L.
Published: October 2009

Hippocampal theta rhythm is thought to underlie learning and memory, and it is well established that “pacemaker” neurons in medial septum (MS) modulate theta activity. Recent studies in the rat demonstrated that brainstem-generated theta rhythm occurs through a multisynaptic pathway via the nucleus incertus (NI), which is the primary source of the neuropeptide relaxin-3 (RLN3). Therefore, this study examined the possible contribution of RLN3 to MS activity, and associated hippocampal theta activity and spatial memory. In anesthetized and conscious rats, we identified the ability of intraseptal RLN3 signaling to modulate neuronal activity in the MS and hippocampus and promote hippocampal theta rhythm. Behavioral studies in a spontaneous alternation task indicated that endogenous RLN3 signaling within MS promoted spatial memory and exploratory activity significantly increased c-Fos immunoreactivity in RLN3-producing NI neurons. Anatomical studies demonstrated axons/terminals from NI/RLN3 neurons make close contact with septal GABAergic (and cholinergic) neurons, including those that project to the hippocampus. In summary, RLN3 neurons of the NI can modulate spatial memory and underlying hippocampal theta activity through axonal projections to pacemaker neurons of the MS. NI/RLN3 neurons are highly responsive to stress and express corticotropin-releasing factor type-1 receptors, suggesting that the effects observed could be an important component of memory processing associated with stress responses.
MODIFIED VACUOLE PHENOTYPE1 Is an Arabidopsis Myrosinase-Associated Protein Involved in Endomembrane Protein Trafficking
Authors: Agee April E. , Surpin Marci , Sohn Eun Ju , Girke Thomas , Rosado Abel , Kram Brian W. , Carter Clay , Wentzell Adam M. , Kliebenstein Daniel J. , Jin Hak Chul , Park Ohkmae K. , Jin Hailing , Hicks Glenn R. , Raikhel Natasha V.
Published: October 2009

We identified an Arabidopsis (Arabidopsis thaliana) ethyl methanesulfonate mutant, modified vacuole phenotype1-1 (mvp1-1), in a fluorescent confocal microscopy screen for plants with mislocalization of a green fluorescent protein-δ tonoplast intrinsic protein fusion. The mvp1-1 mutant displayed static perinuclear aggregates of the reporter protein. mvp1 mutants also exhibited a number of vacuole-related phenotypes, as demonstrated by defects in growth, utilization of stored carbon, gravitropic response, salt sensitivity, and specific susceptibility to the fungal necrotroph Alternaria brassicicola. Similarly, crosses with other endomembrane marker fusions identified mislocalization to aggregate structures, indicating a general defect in protein trafficking. Map-based cloning showed that the mvp1-1 mutation altered a gene encoding a putative myrosinase-associated protein, and glutathione S-transferase pull-down assays demonstrated that MVP1 interacted specifically with the Arabidopsis myrosinase protein, THIOGLUCOSIDE GLUCOHYDROLASE2 (TGG2), but not TGG1. Moreover, the mvp1-1 mutant showed increased nitrile production during glucosinolate hydrolysis, suggesting that MVP1 may play a role in modulation of myrosinase activity. We propose that MVP1 is a myrosinase-associated protein that functions, in part, to correctly localize the myrosinase TGG2 and prevent inappropriate glucosinolate hydrolysis that could generate cytotoxic molecules.
Grain Unloading of Arsenic Species in Rice
Authors: Carey Anne-Marie , Scheckel Kirk G. , Lombi Enzo , Newville Matt , Choi Yongseong , Norton Gareth J. , Charnock John M. , Feldmann Joerg , Price Adam H. , Meharg Andrew A.
Published: October 2009

Rice (Oryza sativa) is the staple food for over half the world's population yet may represent a significant dietary source of inorganic arsenic (As), a nonthreshold, class 1 human carcinogen. Rice grain As is dominated by the inorganic species, and the organic species dimethylarsinic acid (DMA). To investigate how As species are unloaded into grain rice, panicles were excised during grain filling and hydroponically pulsed with arsenite, arsenate, glutathione-complexed As, or DMA. Total As concentrations in flag leaf, grain, and husk, were quantified by inductively coupled plasma mass spectroscopy and As speciation in the fresh grain was determined by x-ray absorption near-edge spectroscopy. The roles of phloem and xylem transport were investigated by applying a ± stem-girdling treatment to a second set of panicles, limiting phloem transport to the grain in panicles pulsed with arsenite or DMA. The results demonstrate that DMA is translocated to the rice grain with over an order magnitude greater efficiency than inorganic species and is more mobile than arsenite in both the phloem and the xylem. Phloem transport accounted for 90% of arsenite, and 55% of DMA, transport to the grain. Synchrotron x-ray fluorescence mapping and fluorescence microtomography revealed marked differences in the pattern of As unloading into the grain between DMA and arsenite-challenged grain. Arsenite was retained in the ovular vascular trace and DMA dispersed throughout the external grain parts and into the endosperm. This study also demonstrates that DMA speciation is altered in planta, potentially through complexation with thiols.
TheO-Mannosyltransferase PMT4 Is Essential for Normal Appressorium Formation and Penetration inUstilago maydis
Authors: Fernández-Álvarez Alfonso , Elías-Villalobos Alberto , Ibeas José I.
Published: October 2009

In Saccharomyces cerevisiae, the PMT, KRE2/MNT1, and MNN1 mannosyltransferase protein families catalyze the steps of the O-mannosylation pathway, sequentially adding mannoses to target proteins. We have identified members of all three families and analyzed their roles in pathogenesis of the maize smut fungus Ustilago maydis. Furthermore, we have shown that PMT4, one of the three PMT family members in U. maydis, is essential for tumor formation in Zea mays. Significantly, PMT4 seems to be required only for pathogenesis and is dispensable for other aspects of the U. maydis life cycle. We subsequently show that the deletion of pmt4 results in a strong reduction in the frequency of appressorium formation, with the few appressoria that do form lacking the capacity to penetrate the plant cuticle. Our findings suggest that the O-mannosylation pathway plays a key role in the posttranslational modification of proteins involved in the pathogenic development of U. maydis. The fact that PMT homologs are not found in plants may open new avenues for the development of fungal control strategies. Moreover, the discovery of a highly specific requirement for a single O-mannosyltransferase should aid in the identification of the proteins directly involved in fungal plant penetration, thus leading to a better understanding of plant–fungi interactions.
Fleshy Fruit Expansion and Ripening Are Regulated by the Tomato SHATTERPROOF Gene TAGL1
Authors: Vrebalov Julia , Pan Irvin L. , Arroyo Antonio Javier Matas , McQuinn Ryan , Chung MiYoung , Poole Mervin , Rose Jocelyn , Seymour Graham , Grandillo Silvana , Giovannoni James , Irish Vivian F.
Published: October 2009

The maturation and ripening of fleshy fruits is a developmental program that synchronizes seed maturation with metabolism, rendering fruit tissues desirable to seed dispersing organisms. Through RNA interference repression, we show that Tomato AGAMOUS-LIKE1 (TAGL1), the tomato (Solanum lycopersicum) ortholog of the duplicated SHATTERPROOF (SHP) MADS box genes of Arabidopsis thaliana, is necessary for fruit ripening. Tomato plants with reduced TAGL1 mRNA produced yellow-orange fruit with reduced carotenoids and thin pericarps. These fruit are also decreased in ethylene, indicating a comprehensive inhibition of maturation mediated through reduced ACC Synthase 2 expression. Furthermore, ectopic expression of TAGL1 in tomato resulted in expansion of sepals and accumulation of lycopene, supporting the role of TAGL1 in ripening. In Arabidopsis, the duplicate SHP1 and SHP2 MADS box genes regulate the development of separation layers essential for pod shatter. Expression of TAGL1 in Arabidopsis failed to completely rescue the shp1 shp2 mutant phenotypes, indicating that TAGL1 has evolved distinct molecular functions compared with its Arabidopsis counterparts. These analyses demonstrate that TAGL1 plays an important role in regulating both fleshy fruit expansion and the ripening process that together are necessary to promote seed dispersal of fleshy fruit. From this broad perspective, SHP1/2 and TAGL1, while distinct in molecular function, regulate similar activities via their necessity for seed dispersal in Arabidopsis and tomato, respectively.
Domain Swapping to Assess the Mechanistic Basis ofArabidopsisPhototropin 1 Receptor Kinase Activation and Endocytosis by Blue Light
Authors: Kaiserli Eirini , Sullivan Stuart , Jones Matthew A. , Feeney Kevin A. , Christie John M.
Published: October 2009

Phototropins (phot1 and phot2) are plasma membrane–associated receptor kinases that respond specifically to blue and UV wavelengths. In addition to a C-terminal Ser/Thr kinase domain, phototropins contain two N-terminal chromophore binding LOV domains that function as photoswitches to regulate a wide range of enzymatic activities in prokaryotes and eukaryotes. Through domain swapping, we show that the photochemical properties of Arabidopsis thaliana phot1 rely on interactions between LOV1 and LOV2, which are facilitated by their intervening linker sequence. Functional analysis of domain-swap proteins supports a mechanism whereby LOV2 acts as a dark-state repressor of phot1 activity both in vitro and in vivo. Moreover, we find a photoactive role for LOV1 in arresting chloroplast accumulation at high light intensities. Unlike LOV2, LOV1 cannot operate as a dark-state repressor, resulting in constitutive receptor autophosphorylation and accelerated internalization from the plasma membrane. Coexpression of active and inactive forms of phot1 demonstrates that autophosphorylation can occur intermolecularly, independent of LOV1, via light-dependent receptor dimerization in vivo. Indeed, transphosphorylation is sufficient to promote phot1 internalization through a clathrin-dependent endocytic pathway triggered primarily by phosphorylation of Ser-851 within the kinase activation loop. The mechanistic implications of these findings in regard to light-driven receptor activation and trafficking are discussed.
A Zinc Finger Transcription Factor ART1 Regulates Multiple Genes Implicated in Aluminum Tolerance in Rice
Authors: Yamaji Naoki , Huang Chao Feng , Nagao Sakiko , Yano Masahiro , Sato Yutaka , Nagamura Yoshiaki , Ma Jian Feng
Published: October 2009

Aluminum (Al) toxicity is the major limiting factor of crop production on acid soils, but some plant species have evolved ways of detoxifying Al. Here, we report a C2H2-type zinc finger transcription factor ART1 (for Al resistance transcription factor 1), which specifically regulates the expression of genes related to Al tolerance in rice (Oryza sativa). ART1 is constitutively expressed in the root, and the expression level is not affected by Al treatment. ART1 is localized in the nucleus of all root cells. A yeast one-hybrid assay showed that ART1 has a transcriptional activation potential and interacts with the promoter region of STAR1, an important factor in rice Al tolerance. Microarray analysis revealed 31 downstream transcripts regulated by ART1, including STAR1 and 2 and a couple of homologs of Al tolerance genes in other plants. Some of these genes were implicated in both internal and external detoxification of Al at different cellular levels. Our findings shed light on comprehensively understanding how plants detoxify aluminum to survive in an acidic environment.
Total phenols and vitamin C contents of Iranian fruits
Authors: Nikniaz Zeinab , Mahdavi Reza , Rafraf Maryam , Jouyban Abolghasem
Published: October 2009

Purpose

The antioxidant characteristics of fruits can be attributed to their contents of polyphenols and vitamins. Because of the interest in the role of antioxidants in human health, the purpose of this paper is to examine the major compounds associated with antioxidant activity, namely total phenolic and vitamin C contents, of some regularly cultivated and consumed fruits in Iran.

Design/methodology/approach

In total, 66 fruits from 22 families were chosen for this study. Terbium sensitized fluorescence assay and spectrophotometric method were used to determine total polyphenol and vitamin C contents respectively. The ANOVA with Tukey post‐hoc test was used for statistical analyses.

Findings

The total mean polyphenol content of fruits was 4.93 ± 2.86 mg QE/100 g that were ranging from 0.8 ± 0.05 to 11.94 ± 0.02 mg QE/100 g with the lowest amount obtained for pear and the highest amount detected in black grape. The polyphenol contents of black grape, sourcherry and pomegranate were significantly higher than those of other fruits (p < 0.001). The total mean vitamin C content of fresh fruits was 18.34 ± 9.77 mg/100 g that were ranging from 57.38 ± 0.02 (strawberry) to 11.44 ± 0.02 (melon) mg/100 g. The vitamin C contents of strawberry was significantly higher than all other fruits (p < 0.001). Despite the differences in the polyphenol and vitamin C contents of various fruits, as a good source of nutritious compounds and functional foods, they can be effective in enhancing health status.

Originality/value

This paper is believed to be the only one which provides information about the polyphenol and vitamin C contents of Iranian fruits. Also, the polyphenol content was measured by using a newly‐developed method.
An exploratory study of students' consumption of non‐alcoholic beverages in Nigeria
Authors: Gbadamosi Ayantunji , Olukayode Iwaloye Ojo , Bamber David
Published: October 2009

Purpose

Given the diversity which exists among various groups of consumers, the purpose of this paper is to explore students' consumption of non‐alcoholic beverages in Nigeria.

Design/methodology/approach

Three focus groups and 20 in‐depth interviews were conducted with students in three universities located in Lagos, Nigeria.

Findings

Initial findings indicate that these students' consumption of non‐alcoholic beverages is influenced in many ways. Nevertheless, the most striking of these influences are found to be convenience of purchase, along with availability, price, health concerns, and culture/social reasons.

Originality/value

The main contribution of the study lies in the relevance of segmentation, targeting, and positioning activities of business organisations in respect of marketing of non‐alcoholic beverages. Based on the findings, the empirical study will serve as a valuable input to marketers in their planning, analysis, and implementation of appropriate marketing strategies to students vis‐à‐vis the highlighted influences on their consumption of this category of food. It will thus serve as a tool for creating competitive advantage in this prevailing volatile business environment.