bluuebunny/crossref_metadata_2025 huggingface dataset:
Unique charge distribution in surface loops confers high velocity on the fast motor protein
Chara
myosin
Authors: Ito Kohji , Yamaguchi Yukie , Yanase Kenji , Ichikawa Yousuke , Yamamoto Keiichi
Published: December 2009

Most myosins have a positively charged loop 2 with a cluster of lysine residues that bind to the negatively charged N-terminal segment of actin. However, the net charge of loop 2 of very fast
Chara
myosin is zero and there is no lysine cluster in it. In contrast,
Chara
myosin has a highly positively charged loop 3. To elucidate the role of these unique surface loops of
Chara
myosin in its high velocity and high actin-activated ATPase activity, we have undertaken mutational analysis using recombinant
Chara
myosin motor domain. It was found that net positive charge in loop 3 affected V
max
and K
app
of actin activated ATPase activity, while it affected the velocity only slightly. The net positive charge in loop 2 affected K
app
and the velocity, although it did not affect V
max
. Our results suggested that
Chara
myosin has evolved to have highly positively charged loop 3 for its high ATPase activity and have less positively charged loop 2 for its high velocity. Since high positive charge in loop 3 and low positive charge in loop 2 seem to be one of the reasons for
Chara
myosin's high velocity, we manipulated charge contents in loops 2 and 3 of
Dictyostelium
myosin (class II). Removing positive charge from loop 2 and adding positive charge to loop 3 of
Dictyostelium
myosin made its velocity higher than that of the wild type, suggesting that the charge strategy in loops 2 and 3 is widely applicable.
Elevated cyclic AMP and PDE4 inhibition induce chemokine expression in human monocyte-derived macrophages
Authors: Hertz Angie L. , Bender Andrew T. , Smith Kimberly C. , Gilchrist Mark , Amieux Paul S. , Aderem Alan , Beavo Joseph A.
Published: December 2009

Macrophages are central mediators of the innate immune system that can be differentiated from monocytes upon exposure to cytokines. While increased cyclic adenosine monophosphate (cAMP) levels are known to inhibit many lipopolysaccharide-elicited macrophage inflammatory responses, the effects of elevated cAMP on monocyte/macrophage differentiation are not as well understood. We show here that during differentiation, cAMP agonists can cause a large increase in the mRNA and protein levels of several of the pro-inflammatory CXCL and CCL chemokines. The cAMP mediator-exchange protein activated by cAMP (Epac) contributes substantially to the increase in these chemokines. These chemokines are known to play an important role in the regulation of immune responses, particularly regarding the pathogenesis of asthma and chronic obstructive pulmonary disorder. We also found that a selective cAMP-degrading phosphodiesterase (PDE) 4 inhibitor can potentiate the chemokine expression elicited by low-dose forskolin or Prostaglandin E2 (PGE
2
). These data suggest that chemokine receptor antagonists administered in conjunction with a PDE4 inhibitor may improve both the efficacy and safety of PDE4-inhibitor therapy for chronic inflammatory disorders.
Sexual Occidentation: The Politics of Conversion, Christian-love and Boy-love in ‘Attār
Authors: Lewis Franklin
Published: December 2009

This article explores tales and tropes of conversion, especially conversion engendered by romantic attraction for the religious other, in the poetry ofFarīd al-Dīn ‘Attār. The plot dynamics of class, gender and confessional adherence are complex, and hold important clues to the poet's theology. One particularly rich example of the encoding of religious and social boundaries can be found in a body of ghazals written about the beautiful Christian boy (tarsā-bachcha). The history of this homoerotic sub-genre is traced, and ‘Attār's treatment of the theme is explored in juxtaposition not only to earlier authors, but to other motifs of the religious other and of religious conversion, appearing in his own oeuvre, including the narrative of Shaykh San‘ān with its representation of the Christian girl beloved. The terminology of Christianity and the markers by which ‘Attār construes Christian-ness are discussed, and these symbolically amorous encounters with Christianity are analyzed as part of a larger discourse of emasculation which ‘Attār constructs around conversion, religious affiliation, and insufficient commitment to spiritual growth. Analysis of the dynamic interplay of markers of gender and class in the tales and topoi dealing with religious conversion or cross-confessional interaction will ultimately afford a perspective into ‘Attār's conception of the specific religious traditions juxtaposed to Islam, as well as his beliefs about inter-religious relations.
To be Feared and Desired: Turks in the Collected Works of ‘Ubayd-i Zākānī
Authors: Brookshaw Dominic Parviz
Published: December 2009

This article discusses the representation of Turks in the kulliyāt (collected works) of the fourteenth-century poet ‘Ubayd-i Zākānī (d. 1371). ‘Ubayd is well known for his satirical works (e.g. Mūsh u gurba, Akhlāq al-ashrāf), but his courtly poetry (in particular his ghazals and qasīdas) have yet to receive substantial scholarly attention. This study examines the various ways in which ‘Ubayd presents Turks in his kulliyāt, whether as an object of erotic desire, a figure to be feared on account of his violent nature, or else as a metaphor for the royal patron or other member of the ruling elite of fourteenth-century Shiraz. This article explores the tension that exists in ‘Ubayd's works between these various depictions of the Turk, shows how references to Turks in bawdy prose works and other poetic genres (such as rubā‘ī) can be used to interpret those found in more chaste ghazals, and discusses the possible implications the depiction of the Turk found in ‘Ubayd's kulliyāt may have for our understanding of references to Turks in the poetry of his contemporaries, in particular Hāfiz (d. 1389).
Social Mobility and the Rise of the Politariat
Authors: Williams Dominic
Published: December 2009

Social mobility may be declining because policy over-emphasises the importance of higher education, which actually benefits the well off. The tendency of ruling classes to hold on to their gains is also important and policy makes unrealistic assumptions about whether this can be overcome. The rise of a meritocratic politariat accounts for some extra mobility in the last 15 years but this is on the wane. An overly statistical policy approach has not helped social mobility and more personalisation is required. Policy is likely to move in the same direction, regardless of whether there is a change in administration.
Expanding Travel Horizons: Overcoming Barriers to Travel for Socially Excluded Groups
Authors: Siraut John , Gay Nathalie
Published: December 2009

Low travel horizons can be a major barrier for socially excluded groups to fully participate in the economic, social and cultural life of modern society. This in turn can lead to socially deprived ghettos even in our most prosperous and dynamic cities. This paper examined the factors behind low travel horizons, including how mental geographies are influenced by access to different transport modes. Drawing upon original primary research in inner London the paper presents a wide range of recommendations as to how travel horizons can be broadened.
Knocking on a Wide-open Door: Chinese Investments in Africa
Authors: Kragelund Peter
Published: December 2009

The current strong foothold of Chinese enterprises on the African continent concerns many Western observers. They fear that the West will lose leverage in Africa and simultaneously postpone development. Paradoxically, the advance of Chinese enterprises in Africa is not only the result of deliberate Chinese policies to gain access to resources and markets, but also the consequence of liberal African investment policies imposed by Western donors in the past. This article uses Zambia as a case study to challenge the often one-sided view of the local consequences of China's engagement with Africa, and it shows that we need to consider the type of policies that guide investment flows, in order to increase the local benefits of China's growing presence in the continent.
Transnational Resource Flow and the Paradoxes of Belonging: Redirecting the Debate on Transnationalism, Remittances, State and Citizenship in Africa
Authors: Obadare Ebenezer , Adebanwi Wale
Published: December 2009

The rise in the volume of known global foreign worker remittances to countries of origin has sparked considerable academic and policy interest. Much attention has been paid to the assumed ‘development’ potential of these financial remittances, an approach which encapsulates the tendency to envisage the consequences of remittance flows in overwhelmingly economic terms. This article takes issue with such an approach, arguing for a refocusing of the debate on remittances in recipient societies on the crucially important, yet largely neglected, political realm. It posits that in formations where a significant aspect of the population relies on external grants for everyday provisioning, questions on the possible implications of their reliance for civic engagement, social citizenship and political allegiance become imperative. The article proposes a conceptual framework for interrogating the effects of the emergence of a discursive ‘remittance class’ for notions of citizenship, state–society relations, and the changing patterns and forms of identity in African and other remittance-dependent societies.
Do We Understand the Linkages between Economic Growth, Poverty Targets and Poverty Reduction?
Authors: Casse Thorkil , Jensen Stig
Published: December 2009

This article contributes to the debate on poverty trends in Africa, looking at the argument for a correspondence between economic growth and poverty reduction. It questions whether a link between economic growth and poverty reduction can be established. First there is a look at the general picture in Africa and no convincing evidence of this link is found, before the article turns to two countries, Burkina Faso and Madagascar, which on the surface seem to exemplify the link. However, in Burkina Faso the link exists only in a limited way and for only a short period (1998–2003), while in Madagascar, where the link appears more obvious, social and political unrest in 2009 casts doubt on the reliability of the data. Indeed, it is probable that an increase in poverty contributed to the crisis in Madagascar. Furthermore, there are signs that in both countries poverty strategies are increasingly giving way to Poverty Reduction Growth Facility programmes, closely related to former structural adjustment loans. It is concluded, first, that analysing poverty strategies through Poverty Reduction Strategy Papers does not help in resolving the uncertainty, since these strategies assume a priori the existence of a link between economic growth and poverty reduction; second, that collection and interpretation of poverty data could be biased, with the World Bank, for example, having an interest in showing improvements in poverty reduction in Africa; and, finally, that the paucity of data needs, at the very least, to be recognised as a major problem.
Current Trends in Knowledge Production: An Historical–Institutional Analysis
Authors: McNeely Ian F.
Published: December 2009

Building on the author’s recent survey of Western knowledge institutions since antiquity, this article assesses the impact of current trends in information technology, higher education, science, and the environment on knowledge production. Its focus on institutions diverges from conventional histories of ideas, media, and technologies but also from the understandings of knowledge and information prevalent among economists. It instead identifies patterns by which entirely new institutions of knowledge supersede their predecessors, reconceptualizing today’s changes around the fitful process by which the laboratory, broadly understood, outgrows the tutelage of the academic disciplines.
Knowledge Directed Economic Selection and Growth
Authors: Eliasson Gunnar
Published: December 2009

The single most important postulate in economics is what you assume about the totality of all possible states that the economy can be in (the state space). The assumption you make determines the costs of information and learning when exploring that state space, the nature of the equilibrating forces of the markets of the economy, towards what kind of equilibrium the economic system is heading and what that means for the modes of behavior of individuals and firms, in short the dynamics of the economy. The mainstream model of economics assumes a very narrow and, for all practical purposes, fully transparent state space and thus excludes all interesting dynamics from the analysis by assumption. I argue for the alternative assumption of a very large and non‐transparent state space, or investment opportunities space that takes us into the unpredictable world of an Experimentally Organized Economy that is more compatible with economic reality. In that brave new world of economics new answers to old questions appear. Above all, using the tools of analysis developed from, and for the mainstream neoclassical model to study the realities of an EOE will place the analyst in a misinformation situation. I illustrate that through simulation on the Swedish micro to macro (MM) model and with one Swedish business case.
English Language Learners: Developing Literacy in Second-Language Learners—Report of the National Literacy Panel on Language-Minority Children and Youth
Authors: August Diane , Shanahan Timothy , Escamilla Kathy
Published: December 2009

Based on concerns about the increasing numbers of English Language Learners in U.S. schools and the documented academic underperformance of this group, particularly in the domain of literacy, the federal government provided funding for a panel of experts to synthesize the knowledge base in the field and provide recommendations for future research. In 2006, the long awaited and much heralded Report of the National Literacy Panel on Language-Minority Children and Youth was published in a book entitled Developing Literacy in Second Language Learners (August & Shanahan, 2006). The purpose of this essay review is to describe the contents of this volume, and to examine it through the dual lenses of theory and policy.
Explicit solutions of a generalized Wick-type stochastic Korteweg–de Vries equation
Authors: Pan Xiaojun , Zhou Neng , Dai Chaoqing
Published: December 2009

With the help of Hermite transformation, we apply the exp-function method to solve a generalized Wick-type stochastic Korteweg–de Vries equation in the white noise environment. Some Wick-type stochastic exact solutions are obtained.
On perturbation theory for the Fokker–Planck equation
Authors: Fernández Francisco M
Published: December 2009

We discuss a recent application of the modified homotopy perturbation method to the Fokker–Planck equation and show that the selected examples do not have any connection with actual physical problems.
Darboux transformations for the time-dependent nonhomogeneous Burgers equation in (1+1) dimensions
Authors: Schulze-Halberg Axel , Manuel Carballo Jiménez Juan
Published: December 2009

We extend the formalism of nth order Darboux transformations to the time-dependent nonhomogeneous Burgers equation (NBE) in (1+1) dimensions. Similar to the Schrödinger case, our Darboux transformation retains the form of the NBE, while changing the nonhomogeneous term. The transformed solution of the NBE and the corresponding transformed nonhomogeneity are given in closed form. Furthermore, properties of the transformation are discussed and an application is given.
Inelastic interactions and double Wronskian solutions for the Whitham–Broer–Kaup model in shallow water
Authors: Wang Lei , Gao Yi-Tian , Gai Xiao-Ling , Sun Zhi-Yuan
Published: December 2009

Under investigation in this paper is the Whitham–Broer–Kaup (WBK) model for the dispersive long wave in shallow water. Connection between the WBK model and a second-order Ablowitz–Kaup–Newell–Segur (AKNS) system is revealed. By means of the Darboux transformation for the second-order AKNS system, the multisoliton solutions in terms of the double Wronskian determinant for the WBK model are derived. Inelastic interactions are graphically discussed. Our results could be helpful for interpreting certain nonlinear wave phenomena in shallow water.
Pseudospin symmetry for a new ring-shaped non-spherical harmonic oscillator potential
Authors: Zhang Min-Cang , Huang-Fu Guo-Qing , An Bo
Published: December 2009

A new ring-shaped non-spherical harmonic oscillator potential is proposed, which consists of a generalized non-harmonic oscillator potential plus an angle-dependent potential,
The pseudospin symmetry for a spin- particle moving in this potential is investigated by solving the Dirac equation with an equal mixture of scalar and vector potentials with opposite signs. The normalized spinor wave function and energy equation are obtained, and the algebraic property of the energy equation and some particular cases are also discussed.
Extension of the resonance line series of Mg III
Authors: Brown C M , Kramida A E , Feldman U , Reader J
Published: December 2009

Spectra of Mg emitted by a Penning discharge were recorded in the extreme ultraviolet (EUV) on a 10.7-m grazing-incidence spectrograph with phosphor image plates. The spectra provided nine new lines of Mg III between 156 and 166 Å and allowed us to improve previous wavelength measurements for another seven lines in this spectral region.
Quantum size effects on the thermal and potential conductivities of ideal gases
Authors: Ozturk Z F , Sisman A
Published: December 2009

Thermal and potential conductivities of ideal Maxwellian, Fermi and Bose gases are derived by considering the small corrections due to the wave character of gas particles. Potential conductivity is regarded as conductivity due to any potential gradient like electrical, gravitational or chemical ones. A long rectangular channel is considered as a transport domain. The size of the domain in the transport direction is much longer than the mean free path of particles l while the sizes in transverse directions are shorter than l. On the other hand, all sizes of the domain are assumed to be larger than the thermal de Broglie wavelength of particles. Therefore, quantum size effects (QSE) are weak enough to be considered as small corrections on conventional terms. Corrections on thermal and potential conductivities are examined. It is seen that the size and shape of the transport domain become additional control parameters on both conductivities. Since the size dependencies of thermal and electrical conductivities are different, the Lorenz number becomes size and shape dependent and deviations from the Wiedemann–Franz law may be expected in nanoscale due to QSE. Variations of the corrections with chemical potential are analysed.
Calorimetric studies of glass transition phenomenon in glassy Se80−
xTe20Snx alloys
Authors: Kumar H , Mehta N , Singh K
Published: December 2009

Glass transition kinetics has been studied in a glassy Se80−

x
Te20Sn
x
(0 ⩽x ⩽10) system. Differential scanning calorimetry (DSC) runs were taken at four different heating rates (5, 10, 15 and 20 K min−1) for this purpose. The heating rate dependence of the glass transition temperature (T
g) has been studied using different non-isothermal methods. The activation energy of glass transition (E
g) has been evaluated using Kissinger's relation and the theory of Moynihan. The composition dependence of T
g and E
g has also been discussed.
A Cdc42 Activation Cycle Coordinated by PI 3-Kinase during Fc Receptor-mediated Phagocytosis
Authors: Beemiller Peter , Zhang Youxin , Mohan Suresh , Levinsohn Erik , Gaeta Isabella , Hoppe Adam D. , Swanson Joel A.
Published: December 2009

Fcγ Receptor (FcR)-mediated phagocytosis by macrophages requires phosphatidylinositol 3-kinase (PI3K) and activation of the Rho-family GTPases Cdc42 and Rac1. Cdc42 is activated at the advancing edge of the phagocytic cup, where actin is concentrated, and is deactivated at the base of the cup. The timing of 3′ phosphoinositide (3′PI) concentration changes in cup membranes suggests a role for 3′PIs in deactivation of Cdc42. This study examined the relationships between PI3K and the patterns of Rho-family GTPase signaling during phagosome formation. Inhibition of PI3K resulted in persistently active Cdc42 and Rac1, but not Rac2, in stalled phagocytic cups. Patterns of 3′PIs and Rho-family GTPase activities during phagocytosis of 5- and 2-μm-diameter microspheres indicated similar underlying mechanisms despite particle size–dependent sensitivities to PI3K inhibition. Expression of constitutively active Cdc42(G12V) increased 3′PI concentrations in plasma membranes and small phagosomes, indicating a role for Cdc42 in PI3K activation. Cdc42(G12V) inhibited phagocytosis at a later stage than inhibition by dominant negative Cdc42(N17). Together, these studies identified a Cdc42 activation cycle organized by PI3K, in which FcR-activated Cdc42 stimulates PI3K and actin polymerization, and the subsequent increase of 3′PIs in cup membranes inactivates Cdc42 to allow actin recycling necessary for phagosome formation.
Receptor-interacting Protein Shuttles between Cell Death and Survival Signaling Pathways
Authors: Kamarajan Pachiyappan , Bunek Julius , Lin Yong , Nunez Gabriel , Kapila Yvonne L.
Published: December 2009

Cross-talk between apoptosis and survival signaling pathways is crucial for regulating tissue processes and mitigating disease. We report that anoikis—apoptosis triggered by loss of extracellular matrix contacts—activates a CD95/Fas-mediated signaling pathway regulated by receptor-interacting protein (RIP), a kinase that shuttles between CD95/Fas-mediated cell death and integrin/focal adhesion kinase (FAK)-mediated survival pathways. RIP's death domain was critical for RIP and Fas association to mediate anoikis. Fas or RIP attenuation reduced this association and suppressed anoikis, whereas their overexpression had the reverse effect. Overexpressing FAK restored RIP and FAK association and inhibited anoikis. Thus, RIP shuttles between CD95/Fas death and FAK survival signaling to mediate anoikis.
Genomic Study of Replication Initiation in Human Chromosomes Reveals the Influence of Transcription Regulation and Chromatin Structure on Origin Selection
Authors: Karnani Neerja , Taylor Christopher M. , Malhotra Ankit , Dutta Anindya
Published: December 2009

DNA replication in metazoans initiates from multiple chromosomal loci called origins. Currently, there are two methods to purify origin-centered nascent strands: lambda exonuclease digestion and anti-bromodeoxyuridine immunoprecipitation. Because both methods have unique strengths and limitations, we purified nascent strands by both methods, hybridized them independently to tiling arrays (1% genome) and compared the data to have an accurate view of genome-wide origin distribution. By this criterion, we identified 150 new origins that were reproducible across the methods. Examination of a subset of these origins by chromatin immunoprecipitation against origin recognition complex (ORC) subunits 2 and 3 showed 93% of initiation peaks to localize at/within 1 kb of ORC binding sites. Correlation of origins with functional elements of the genome revealed origin activity to be significantly enriched around transcription start sites (TSSs). Consistent with proximity to TSSs, we found a third of initiation events to occur at or near the RNA polymerase II binding sites. Interestingly, ∼50% of the early origin activity was localized within 5 kb of transcription regulatory factor binding region clusters. The chromatin signatures around the origins were enriched in H3K4-(di- and tri)-methylation and H3 acetylation modifications on histones. Affinity of origins for open chromatin was also reiterated by their proximity to DNAse I-hypersensitive sites. Replication initiation peaks were AT rich, and >50% of the origins mapped to evolutionarily conserved regions of the genome. In summary, these findings indicate that replication initiation is influenced by transcription initiation and regulation as well as chromatin structure.
Environmental Transition of Signal-Anchor Sequences during Membrane Insertion via the Endoplasmic Reticulum Translocon
Authors: Kida Yuichiro , Kume Chisato , Hirano Maki , Sakaguchi Masao
Published: December 2009

In biogenesis of membrane proteins on the endoplasmic reticulum, a protein-conducting channel called the translocon functions in both the membrane translocation of lumenal domains and the integration of transmembrane segments. Here we analyzed the environments of polypeptide chains during the processes by water-dependent alkylation of N-ethylmaleimide at site-directed Cys residues. Using the technique, the region embedded in the hydrophobic portion of the membrane within a signal-anchor sequence and its shortening by insertion of a Pro residue could be detected. When translocation of the N-terminal domain of the signal-anchor was arrested by trapping an N-terminally fused affinity tag sequence, the signal-anchor was susceptible to alkylation, indicating that its migration into the hydrophobic environment was also arrested. Furthermore, when the tag sequence was separated from the signal-anchor by insertion of a hydrophilic sequence, the signal-anchor became inaccessible to alkylation even in the N-terminally trapped state. This suggests that membrane integration of the signal-anchor synchronizes with partial translocation of its N-terminal domain. Additionally, in an integration intermediate of a membrane protein, both of the two translocation-arrested hydrophilic chains were in an aqueous environment flanking the translocon, suggesting that the translocon provides the hydrophilic pathway capable of at least two translocating chains.
A Bayesian Hierarchical Topic Model for Political Texts: Measuring Expressed Agendas in Senate Press Releases
Authors: Grimmer Justin
Published: December 2009

Political scientists lack methods to efficiently measure the priorities political actors emphasize in statements. To address this limitation, I introduce a statistical model that attends to the structure of political rhetoric when measuring expressed priorities: statements are naturally organized by author. The expressed agenda model exploits this structure to simultaneously estimate the topics in the texts, as well as the attention political actors allocate to the estimated topics. I apply the method to a collection of over 24,000 press releases from senators from 2007, which I demonstrate is an ideal medium to measure how senators explain their work in Washington to constituents. A set of examples validates the estimated priorities and demonstrates their usefulness for testing theories of how members of Congress communicate with constituents. The statistical model and its extensions will be made available in a forthcoming free software package for the R computing language.
Single Nucleotide Polymorphisms in a Gene for Translation Initiation Factor (eIF4G) of Rice (Oryza sativa) Associated with Resistance to Rice tungro spherical virus
Authors: Lee Jong-Hee , Muhsin Muhammad , Atienza Genelou A. , Kwak Do-Yeon , Kim Suk-Man , De Leon Teresa B. , Angeles Enrique R. , Coloquio Edgardo , Kondoh Hiroaki , Satoh Kouji , Cabunagan Rogelio C. , Cabauatan Pepito Q. , Kikuchi Shoshi , Leung Hei , Choi Il-Ryong
Published: December 2009

Rice tungro disease (RTD) is a serious constraint to rice production in South and Southeast Asia. RTD is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Rice cv. Utri Merah is resistant to RTSV. To identify the gene or genes involved in RTSV resistance, the association of genotypic and phenotypic variations for RTSV resistance was examined in backcross populations derived from Utri Merah and rice germplasm with known RTSV resistance. Genetic analysis revealed that resistance to RTSV in Utri Merah was controlled by a single recessive gene (tsv1) mapped within an approximately 200-kb region between 22.05 and 22.25 Mb of chromosome 7. A gene for putative translation initiation factor 4G (eIF4Gtsv1) was found in the tsv1 region. Comparison of eIF4Gtsv1 gene sequences among susceptible and resistant plants suggested the association of RTSV resistance with one of the single nucleotide polymorphism (SNP) sites found in exon 9 of the gene. Examination of the SNP site in the eIF4Gtsv1 gene among various rice plants resistant and susceptible to RTSV corroborated the association of SNP or deletions in codons for Val1060-1061 of the predicted eIF4Gtsv1 with RTSV resistance in rice.
Systemic Induction and Role of Mitochondrial Alternative Oxidase and Nitric Oxide in a Compatible Tomato–Tobacco mosaic virus Interaction
Authors: Fu Li-Jun , Shi Kai , Gu Min , Zhou Yan-Hong , Dong De-Kun , Liang Wu-Sheng , Song Feng-Ming , Yu Jing-Quan
Published: December 2009

The role of mitochondrial alternative oxidase (AOX) and the relationship between AOX and nitric oxide (NO) in virus-induced systemic defense to Tobacco mosaic virus (TMV) were investigated in susceptible tomato (Solanum lycopersicum) plants. TMV inoculation to the lower leaves induced a rapid NO synthesis and AOX activation in upper uninoculated leaves as early as 0.5 day postinoculation. Application of exogenous potassium cyanide (KCN, a cytochrome pathway inhibitor) at nonlethal concentrations and NO donor diethylamine NONOate (DEA/NO) to the upper uninoculated leaves greatly induced accumulation of AOX transcript, reduced TMV viral RNA accumulation, and increased the leaf photochemical quantum yield at photosystem II. Pretreatment with NO scavenger almost completely blocked TMV-induced AOX induction and substantially increased TMV susceptibility. Salicylhydroxamic acid (SHAM, an AOX inhibitor) pretreatment reduced the DEA/NO-induced cyanide-resistant respiration and partially compromised induced resistance to TMV. Conversely, KCN and SHAM pretreatment had very little effect on generation of NO, and pretreatment with NO scavenger did not affect KCN-induced AOX induction and TMV resistance. These results suggest that TMV-induced NO generation acts upstream and mediates AOX induction which, in turn, induces mitochondrial alternative electron transport and triggers systemic basal defense against the viral pathogen.
The AvrM Effector from Flax Rust Has a Structured C-Terminal Domain and Interacts Directly with the M Resistance Protein
Authors: Catanzariti Ann-Maree , Dodds Peter N. , Ve Thomas , Kobe Bostjan , Ellis Jeffrey G. , Staskawicz Brian J.
Published: December 2009

In plant immunity, recognition of pathogen effectors by plant resistance proteins leads to the activation of plant defenses and a localized cell death response. The AvrM effector from flax rust is a small secreted protein that is recognized by the M resistance protein in flax. Here, we investigate the mechanism of M–AvrM recognition and show that these two proteins directly interact in a yeast two-hybrid assay, and that this interaction correlates with the recognition specificity observed for each of the different AvrM variants. We further characterize this interaction by demonstrating that the C-terminal domain of AvrM is required for M-dependent cell death, and show that this domain also interacts with the M protein in yeast. We investigate the role of C-terminal differences among the different AvrM proteins for their involvement in this interaction and establish that M recognition is hindered by an additional 34 amino acids present at the C terminus of several AvrM variants. Structural characterization of recombinant AvrM-A protein revealed a globular C-terminal domain that dimerizes.
Improved Characterization of Nod Factors and Genetically Based Variation in LysM Receptor Domains Identify Amino Acids Expendable for Nod Factor Recognition in Lotus spp.
Authors: Bek Anita S. , Sauer Jørgen , Thygesen Mikkel B. , Duus Jens Ø. , Petersen Bent O. , Thirup Søren , James Euan , Jensen Knud J. , Stougaard Jens , Radutoiu Simona
Published: December 2009

Formation of functional nodules is a complex process depending on host–microsymbiont compatibility in all developmental stages. This report uses the contrasting symbiotic phenotypes of Lotus japonicus and L. pedunculatus, inoculated with Mesorhizobium loti or the Bradyrhizobium sp. (Lotus), to investigate the role of Nod factor structure and Nod factor receptors (NFR) for rhizobial recognition, infection thread progression, and bacterial persistence within nodule cells. A key contribution was the use of 800 MHz nuclear magnetic resonance spectroscopy and ultrahigh-performance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry for Nod factor analysis. The Nod factor decorations at the nonreducing end differ between Bradyrhizobium sp. (Lotus) and M. loti, and the NFR1/NFR5 extracellular regions of L. pedunculatus and L. japonicus were found to vary in amino acid composition. Genetic transformation experiments using chimeric and wild-type receptors showed that both receptor variants recognize the structurally different Nod factors but the later symbiotic phenotype remained unchanged. These results highlight the importance of additional checkpoints during nitrogen-fixing symbiosis and define several amino acids in the LysM domains as expendable for perception of the two differentially carbamoylated Nod factors.
Erl1, a Novel Era-Like GTPase from Magnaporthe oryzae, Is Required for Full Root Virulence and Is Conserved in the Mutualistic Symbiont Glomus intraradices
Authors: Heupel Stephanie , Roser Birgit , Kuhn Hannah , Lebrun Marc-Henri , Villalba Francois , Requena Natalia
Published: December 2009

Comparative analyses of genome sequences from several plant-infecting fungi have shown conservation and expansion of protein families with plant disease-related functions. Here, we show that this hypothesis can be extended to mutualistic symbiotic fungi. We have identified a gene encoding an Era (Escherichia coli Ras)-like GTPase in the rice blast fungus Magnaporthe oryzae and found that it is orthologous to the mature amino terminal part of the Gin1 protein from the arbuscular mycorrhizal (AM) fungus Glomus intraradices. M. oryzae Erl1 is required for full root virulence. Appressoria formation was not severely affected in Δerl1 strains, but invasive hyphae grew slower than in the wild type. Root browning defect of Δerl1 strains could be complemented by the AM gene under the control of the ERL1 promoter. Erl1 and Gin-N localized to the nucleus when carboxy-terminally labeled with green fluorescent protein (GFP). However, amino-terminal GFP-tagged versions of the proteins expressed in Aspergillus nidulans were shown to localize in the cytoplasm and to cause polarity defects. These data suggest that Erl1 and Gin-N are orthologs and might be involved in the control of hyphal growth in planta. This is the first characterization of an Era-like GTPase in filamentous fungi.
Altering Expression of Benzoic Acid/Salicylic Acid Carboxyl Methyltransferase 1 Compromises Systemic Acquired Resistance and PAMP-Triggered Immunity in Arabidopsis
Authors: Liu Po-Pu , Yang Yue , Pichersky Eran , Klessig Daniel F.
Published: December 2009

Methyl salicylate (MeSA), which is synthesized in plants from salicylic acid (SA) by methyltransferases, has roles in defense against microbial and insect pests. Most of the MeSA that accumulates after pathogen attack is synthesized by benzoic acid/SA carboxyl methyltransferase 1 (AtBSMT1). To investigate the role of AtBSMT1 in plant defense, transgenic Arabidopsis with altered AtBSMT1 function or expression were assessed for their ability to resist pathogen infection. A knockout mutant (Atbsmt1) failed to accumulate MeSA following pathogen infection; these plants also failed to accumulate SA or its glucoside in the uninoculated leaves and did not develop systemic acquired resistance (SAR). However, the Atbsmt1 mutant exhibited normal levels of effector-triggered immunity and pathogen-associated molecular pattern (PAMP)-triggered immunity to Pseudomonas syringae and Hyaloperonospora arabidopsidis. Analyses of transgenic Arabidopsis plants overexpressing AtBSMT1 revealed that they accumulate elevated levels of MeSA in pathogen-infected leaves but fail to develop SAR. Since the levels of SA and its glucoside were reduced in uninoculated systemic leaves of these plants whereas MeSA levels were elevated, AtBSMT1-mediated conversion of SA to MeSA probably compromised SAR development by suppressing SA accumulation in uninoculated leaves. PAMP-triggered immunity also was compromised in the AtBSMT1 overexpressing plants, although effector-triggered immunity was not.
Transmission of Phytophthora infestans from Infected Potato Seed Tubers to Emerged Shoots
Authors: Johnson Dennis A.
Published: December 2009

Transmission of Phytophthora infestans from infected seed tubers to emerged potato sprouts, infectivity of sporangia deposited on whole tubers before burial in soil, and infectivity of sporangia in a loamy fine sand to leaflets were investigated in the greenhouse under simulated spring planting conditions of the Columbia Basin. Incidence of late-blight-infected shoots from infected seed tubers was significantly greater when foliage was exposed to wet periods in mist chambers (mist for 45 s every 15 min) for either 24 or 48 h than when not exposed to a wet period. Proportion of infected shoots from infected tubers was 0.210 to 0.261 in a moist environment versus 0.013 to 0.052 in a nonmist environment. Development of chlorosis, necrosis, and sporangia occurred on shoots that emerged from infected, symptomatic tubers buried in soil. However, approximately 20% of the infected shoots produced sporangia before stems had visible discoloration of late-blight symptoms. Sporulation was sparse and formed near the soil line on some of the shoots after 24 h in the moist environment. The latent period or time from inoculation to sporulation on young stems of Russet Burbank was 5 to 6 days, which is too long to account for an infection from either sporangia or zoospores at the soil level of shoots during the wet period in this study. Sporangia were infective when placed directly on eyes of whole tubers before planting. Leaflets touching a loamy fine sand infested with sporangia developed typical late-blight lesions beginning at the leaflet tip within 7 days after a 24-h wet period and the infested loamy fine sand was infective when splashed on leaflets.
Effects of Temperature, Concentration, Age, and Algaecides on Phytophthora capsici Zoospore Infectivity
Authors: Granke L. L. , Hausbeck M. K.
Published: December 2009

Controlled laboratory studies were undertaken to determine the effects of water temperature (2, 9, 12, 19, 22, and 32°C), inoculum concentration (1 × 102, 1 × 103, 5 × 103, 1 × 104, 2 × 104, and 4 × 104 zoospores/ml), and zoospore suspension age (0, 1, 3, and 5 days old) on infection of pickling cucumbers (Cucumis sativus) by Phytophthora capsici. Zoospore motility and mortality in response to commercial algaecides were also investigated. Cucumbers became infected at all temperatures tested, except 2°C, and the highest infection incidence was observed for cucumbers incubated in suspensions held at ≥19°C. Fewer fruit (<40% at ≥19°C, 0% at ≤12°C) became infected when water contained 1 × 102 zoospores/ml. Almost 100% of fruit were infected when water contained ≥5 × 103 zoospores/ml at temperatures ≥12°C. While the incidence of fruit infection declined with the zoospore suspension age, infection still occurred when 5-day-old suspensions were used. Commercial algaecides inhibited zoospore motility and caused significant zoospore mortality in laboratory assays, and show promise for treatment of infested irrigation water. Avoidance of infested irrigation water throughout the growing season is warranted until effective and economically acceptable water treatments are developed for field use.
Dynamics of the Jacobian matrices arising in three-dimensional Euler equations: application of Riccati theory
Authors: Ohkitani Koji
Published: December 2009

An attempt is made to remove, at least partially, the non-local nature associated with the pressure term of the incompressible Euler equations. We consider the dynamics of the Jacobian matrix

J

(
t
) relating spatial and material coordinates in incompressible three-dimensional Euler equations. By applying the theory of matrix-valued Riccati equations to the velocity gradient tensor

V

(
t
) assuming time-symmetric pressure Hessian, we derive an identity which is local in material coordinates for a fluid particle with det

V

(0)≠0, as a result of invariance under time-reversal. This imposes constraints on the time evolution of the velocity gradients and generates a chain of exact infinite relationships on the Taylor coefficients of

V

(
t
) in time. Some of the first few are explicitly given. As a corollary, we prove that if the evolution of the velocity gradient is symmetric with regard to time

V

(
t
)=

V

(−
t
), it must be a constant and

. The key results herein may be summarized in equations (
3.10
) and (
3.11
).
Foraging in an oxidative environment: relationship between
δ
13
C values and oxidative status in Adélie penguins
Authors: Beaulieu Michaël , Ropert-Coudert Yan , Le Maho Yvon , Ancel André , Criscuolo François
Published: December 2009

The alternation of short/coastal and long/pelagic foraging trips has been proposed as a strategy for seabirds to reconcile self-feeding and parental care. Both types of foraging trips may result in different foraging efforts and diet qualities, and consequently are likely to modify the oxidative status of seabirds.

We examined the relationship between the oxidative status of Adélie penguins and (i) the duration of their foraging trips and (ii) their plasma
δ
13
C values reflecting their spatial distribution.

The oxidative status did not correlate with the foraging trip duration but with the
δ
13
C values: high values being associated with high levels of oxidative damage.

This relationship is likely to be related to the prey properties of penguins as both parameters are largely determined by the diet. Two non-exclusive hypotheses can be proposed to explain this relationship: (i) penguins foraging in coastal areas feed on a diet enriched in
13
C and depleted in antioxidant compounds; (ii) birds with low antioxidant capacity are constrained to forage in coastal areas.

Our study is the first to show that the adoption of different foraging strategies is associated with different levels of oxidative stress. However, further studies are needed to investigate the underlying mechanisms of this intriguing relationship.
Personality and collective decision-making in foraging herbivores
Authors: Michelena Pablo , Jeanson Raphaël , Deneubourg Jean-Louis , Sibbald Angela M.
Published: December 2009

The mechanisms by which group-living animals collectively exploit resources, and the role of individuals in group decisions, are central issues for understanding animal distribution patterns. We investigated the extent to which boldness and shyness affect the distribution of social herbivores across vegetation patches, using sheep as a model species. Using an experimental and a theoretical approach, we show that collective choices emerge through the nonlinear dynamics of interactions between individuals, at both short and long distances. Within a range of parameter values derived from the observation of homogeneous groups of each behavioural type, we propose a simple mechanism whereby the same interaction rules can result in different patterns of distribution across patches for bold and shy individuals. We present a mathematical model based on behavioural rules derived from experiments, in which crowding and conspecific attraction affect the probability of entering or leaving patches. Variation in the strength of social attraction is sufficient to account for differences in spatial distribution across patches. The model predicts that resource fragmentation more strongly affects the distribution patterns of shy groups, and suggests that the presence of both bold and shy individuals within groups would result in more flexible behaviour at the population level.
Helicobacter pylori CagA upregulation of CIP2A is dependent on the Src and MEK/ERK pathways
Authors: Zhao Dapeng , Liu Zhifang , Ding Jian , Li Wenjuan , Sun Yundong , Yu Han , Zhou Yabin , Zeng Jiping , Chen Chunyan , Jia Jihui
Published: December 2009

Helicobacter pylori is classified as a class I carcinogenic factor and its persistent colonization in the stomach induces gastric cancer. Cancerous Inhibitor of PP2A (CIP2A) is a newly identified oncoprotein overexpressed in gastric cancer. Serving as a key oncoprotein, CIP2A also participates in regulation of senescence and proliferation of gastric cells. The combination of aberrant CIP2A expression inducing unlimited cell proliferation, and H. pylori infection eliciting aberrant expression of some key proteins, results in the onset of gastric tumorigenesis. However, the relationship between H. pylori infection and CIP2A expression still remains undefined. The aim of our study was to verify the effect of H. pylori infection on CIP2A expression levels and identify H. pylori signalling molecules and corresponding pathways influencing CIP2A expression. Following plasmid-mediated expression of CagA in human gastric cell lines, the cells were infected with H. pylori and CIP2A expression levels were examined by immunoblotting. Signal inhibitors were used to verify which signal pathways were involved. We also performed CIP2A depletion and H. pylori infection after depletion in AGS cells. H. pylori infection-induced CIP2A expression was dependent on cagA gene expression and CagA phosphorylation. Bacterial oncoprotein CagA upregulated CIP2A expression and this upregulation effect was dependent on Src and Ras/mitogen-activated protein kinase kinase/extracellular signal-regulated kinase pathways. H. pylori infection-induced Myc stabilization was partially attenuated by CIP2A depletion. The results of our study provide further information for understanding the mechanism of H. pylori carcinogenesis.
Biochemical and Molecular Characterization of PvPAP3, a Novel Purple Acid Phosphatase Isolated from Common Bean Enhancing Extracellular ATP Utilization
Authors: Liang Cuiyue , Tian Jiang , Lam Hon-Ming , Lim Boon Leong , Yan Xiaolong , Liao Hong
Published: December 2009

Purple acid phosphatases (PAPs) play diverse physiological roles in plants. In this study, we purified a novel PAP, PvPAP3, from the roots of common bean (Phaseolus vulgaris) grown under phosphate (Pi) starvation. PvPAP3 was identified as a 34-kD monomer acting on the specific substrate, ATP, with a broad pH range and a high heat stability. The activity of PvPAP3 was insensitive to tartrate, indicating that PvPAP3 is a PAP-like protein. Amino acid sequence alignment and phylogenetic analysis suggest that PvPAP3 belongs to the group of plant PAPs with low molecular mass. Transient expression of 35S:PvPAP3-green fluorescent protein in onion (Allium cepa) epidermal cells verified that it might anchor on plasma membrane and be secreted into apoplast. Pi starvation led to induction of PvPAP3 expression in both leaves and roots of common bean, and expression of PvPAP3 was strictly dependent on phosphorus (P) availability and duration of Pi starvation. Furthermore, induction of PvPAP3 expression was more rapid and higher in a P-efficient genotype, G19833, than in a P-inefficient genotype, DOR364, suggesting possible roles of PvPAP3 in P efficiency in bean. In vivo analysis using a transgenic hairy root system of common bean showed that both growth and P uptake of bean hairy roots from the PvPAP3 overexpression transgenic lines were significantly enhanced when ATP was supplied as the sole external P source. Taken together, our results suggest that PvPAP3 is a novel PAP that might function in the adaptation of common bean to P deficiency, possibly through enhancing utilization of extracellular ATP as a P source.