bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical position clamping with predictive control
Authors: Ojala Heikki , Korsbäck Anders , Wallin Anders E. , Hæggström Edward
Published: November 2009

We increase the effective stiffness of optical tweezers by position clamping a polystyrene bead with a predictive feedback control algorithm. This algorithm mitigates the effect of feedback loop delay. Hence, higher gain than with proportional control can be employed, which results in higher effective trap stiffness, without trap instability. In experiments (initial trap stiffness 0.056 pN/nm with a 1.78 μm diameter polystyrene bead), predictive control increased the effective trap stiffness by 55% relative to proportional control. We also derive theoretical expressions for the power spectra of the bead position controlled by our algorithm.
Optimal shapes for best draining
Authors: Sherwood J. D.
Published: November 2009

The container shape that minimizes the volume of draining fluid remaining on the walls of the container after it has been emptied from its base is determined. The film of draining fluid is assumed to wet the walls of the container, and is sufficiently thin so that its curvature may be neglected. Surface tension is ignored. The initial value problem for the thickness of a film of Newtonian fluid is studied, and is shown to lead asymptotically to a similarity solution. From this, and from equivalent solutions for power-law fluids, the volume of the residual film is determined. The optimal container shape is not far from hemispherical, to minimize the surface area, but has a conical base to promote draining. The optimal shape for an axisymmetric mixing vessel, with a hole at the center of its base for draining, is also optimal when inverted in the manner of a washed wine glass inverted and left to drain.
The Science Case for PILOT II: the Distant Universe
Authors: Lawrence J. S. , Ashley M. C. B. , Bunker A. , Bouwens R. , Burgarella D. , Burton M. G. , Gehrels N. , Glazebrook K. , Pimbblet K. , Quimby R. , Saunders W. , Storey J. W. V. , Wheeler J. C.
Published: November 2009

PILOT (the Pathfinder for an International Large Optical Telescope) is a proposed 2.5-m optical/infrared telescope to be located at Dome C on the Antarctic plateau. The atmospheric conditions at Dome C deliver a high sensitivity, high photometric precision, wide-field, high spatial resolution, and high-cadence imaging capability to the PILOT telescope. These capabilities enable a unique scientific potential for PILOT, which is addressed in this series of papers. The current paper presents a series of projects dealing with the distant (redshift >1) Universe, that have been identified as key science drivers for the PILOT facility. The potential for PILOT to detect the first populations of stars to form in the early Universe, via infrared projects searching for pair-instability supernovae and gamma-ray burst afterglows, is investigated. Two projects are proposed to examine the assembly and evolution of structure in the Universe: an infrared survey searching for the first evolved galaxies at high redshift, and an optical survey aimed at characterising moderate-redshift galaxy clusters. Finally, a large-area weak-lensing survey and a program to obtain supernova infrared light-curves are proposed to examine the nature and evolution of dark energy and dark matter.
Ks-band, 2.14-µm Imaging of Southern Massive Star Formation Regions Traced by Methanol Masers
Authors: Longmore S. N. , Burton M. G.
Published: November 2009

We present deep, wide-field, Ks-band (2.14-μm) images towards 87 southern massive star formation regions traced by methanol maser emission. Using point-spread function fitting, we generate 2.14-μm point source catalogues (PSCs) towards each of the regions. For the regions between 10° < l < 350° and |b| < 1, we match the 2.14-μm sources with the GLIMPSE point source catalogue to generate a combined 2.14- to 8.0-μm point source catalogue. We provide this data for the astronomical community to utilise in studies of the stellar content of embedded clusters.
Phase-Mixing and Dissipation of Standing Shear Alfvén Waves
Authors: Karami K. , Ebrahimi Z.
Published: November 2009

We study the phase mixing and dissipation of a packet of standing shear Alfvén waves localized in a region with non-uniform Alfvén background velocity. We investigate the validity of the exponential damping law in time, exp (–At3), presented by Heyvaerts & Priest (1983) for different ranges of Lundquist, S, and Reynolds, R, numbers. Our numerical results shows that it is valid for (R,S) ≥ 107.
Spatial heterogeneity of soil chemical properties in a lowland tropical moist forest, Panama
Authors: Yavitt J. B. , Harms K. E. , Garcia M. N. , Wright S. J. , He F. , Mirabello M. J.
Published: November 2009

We evaluated spatial heterogeneity for pH and a comprehensive set of nutrient and trace elements in surface (0–0.1 m depth) and subsurface (0.3–0.4 m depth) soils across 26.6 ha of old-growth, lowland, tropical moist forest, established on a highly weathered soil in Panama. Little is known about spatial heterogeneity patterns of soil properties in tropical forest soils. Soil was moderately acidic (pH 5.28) with low concentrations of exchangeable base cations (13.4 cmolc/kg), Bray-extractable PO4 (2.2 mg/kg), KCl-extractable NO3 (5.0 mg/kg), and KCl-extractable NH4 (15.5 mg/kg). The coefficient of variation for soil properties ranged from 24% to >200%, with a median value of 84%. Geostatistical analysis revealed spatial dependence at a scale of 10–100 m for most of the soil properties; however, pH, NH4, Al, and B had spatial dependence at a scale up to 350 m. Best-fit models to individual variograms included random, exponential, spherical, Gaussian, linear, and power functions, indicating many different spatial patterns among the set of soil properties. Correlation among individual elements was poor, indicating independent patterns. Our results show complex spatial patterns in soil chemical properties and provide a basis for future investigations on soil–plant relationships and soil nutrient niche differentiation.
Effect of partial removal of adsorbed humus on kinetics of potassium and silica release by tartaric acid from clay - humus complex from two dissimilar soil profiles
Authors: Datta S. C. , Takkar P. N. , Verma U. K.
Published: November 2009

The aim of this investigation is to study how adsorbed humus on clay minerals affects kinetics of dissolution of clay mineral by an organic acid in terms of K and Si release. Clay–humus complexes were isolated from soil samples collected from different depths of 2 soil profiles from an Inceptisol of North India under long-term rice–wheat and maize–wheat cropping systems. Clay–humus complexes were subjected to repeat extraction with 100 mg/L of tartaric acid solutions before and after removal of humus with 30% hydrogen peroxide and the resultant release of potassium and silica was measured.
Before removal of humus, K release followed Elovich kinetics for the maize–wheat cropping system.For the rice–wheat cropping system, except surface soil, which followed Elovich kinetics, other subsurface soils followed the power form of kinetic equations. But when humus was partially removed, K release increased exponentially, therelease rate increasing with time. This indicated that for humus-depleted clay, initial release triggered further release of K.
Silica was released at a constant rate. The dissolution reaction was incongruent, i.e. the amount of constituents released in solution was not proportional to their mole fraction present in the mineral. X-ray diffraction analysis showed that micaceous mineral was partially dissolved and vermiculite was completely dissolved when humus was partially removed from clay before extraction. This observation indicates that humus adsorbed on clay plays an important role in preventing clay dissolution by organic acids.
Deletion of Drosophila insulin-like peptides causes growth defects and metabolic abnormalities
Authors: Zhang Hua , Liu Jingnan , Li Caroline R. , Momen Bahram , Kohanski Ronald A. , Pick Leslie
Published: November 2009

Insulin/Insulin-like growth factor signaling regulates homeostasis and growth in mammals, and is implicated in diseases from diabetes to cancer. In
Drosophila melanogaster
, as in other invertebrates, multiple Insulin-Like Peptides (DILPs) are encoded by a family of related genes. To assess DILPs' physiological roles, we generated small deficiencies that uncover single or multiple
dilps
, generating genetic loss-of-function mutations. Deletion of
dilps1–5
generated homozygotes that are small, severely growth-delayed, and poorly viable and fertile. These animals display reduced metabolic activity, decreased triglyceride levels and prematurely activate autophagy, indicative of “starvation in the midst of plenty,” a hallmark of Type I diabetes. Furthermore, circulating sugar levels are elevated in
Df [dilp1–5]
homozygotes during eating and fasting. In contrast,
Df[dilp6]
or
Df[dilp7]
animals showed no major metabolic defects. We discuss physiological differences between mammals and insects that may explain the unexpected survival of lean, ‘diabetic’ flies.
Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin
Authors: Wlodarski Tomasz , Zagrovic Bojan
Published: November 2009

Noncovalent binding interactions between proteins are the central physicochemical phenomenon underlying biological signaling and functional control on the molecular level. Here, we perform an extensive structural analysis of a large set of bound and unbound ubiquitin conformers and study the level of residual induced fit after conformational selection in the binding process. We show that the region surrounding the binding site in ubiquitin undergoes conformational changes that are significantly more pronounced compared with the whole molecule on average. We demonstrate that these induced-fit structural adjustments are comparable in magnitude to conformational selection. Our final model of ubiquitin binding blends conformational selection with the subsequent induced fit and provides a quantitative measure of their respective contributions.
Plasticity in Ca
2+
selectivity of Orai1/Orai3 heteromeric channel
Authors: Schindl Rainer , Frischauf Irene , Bergsmann Judith , Muik Martin , Derler Isabella , Lackner Barbara , Groschner Klaus , Romanin Christoph
Published: November 2009

A general cellular response following depletion of intracellular calcium stores involves activation of store-operated channels (SOCs). While Orai1 forms the native Ca
2+
release-activated Ca
2+
(CRAC) channel in mast and T cells, the molecular architecture of less Ca
2+
selective SOCs is insufficiently defined. Here we present evidence that diminished Ca
2+
selectivity and robust Cs
+
permeation together with a reduced fast inactivation are characteristics of heteromeric Orai1 and Orai3 channels in contrast to their homomeric forms. The first extracellular loop of these Orai isoforms differs by two aspartates replacing glutamates that affect the selectivity. Co-expression of an Orai3 mutant that mimicked the first loop of Orai1 with either Orai1 or Orai3 recovered or decreased Ca
2+
selectivity, respectively. Heteromeric Orai1/3 protein assembly provides a concept for less Ca
2+
-selective SOCs.
Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini
Authors: Xu Guoqiang , Shin Sung Bin Y. , Jaffrey Samie R.
Published: November 2009

Proteolysis has major roles in diverse biologic processes and regulates the activity, localization, and intracellular levels of proteins. Linking signaling pathways and physiologic processes to specific proteolytic processing events is a major challenge in signal transduction research. Here, we describe N-CLAP (N-terminalomics by chemical labeling of the α-amine of proteins), a general approach for profiling protein N-termini and identifying protein cleavage sites during cellular signaling. In N-CLAP, simple and readily available reagents are used to selectively affinity label the α-amine that characterizes the protein N terminus over the more highly abundant ε-amine on lysine residues. Protein cleavage sites are deduced by identifying the corresponding N-CLAP peptides, which are derived from the N-termini of proteins, including the N-termini of the newly formed polypeptide products of proteolytic cleavage. Through selective affinity purification and tandem mass spectrometry analysis of 278 N-CLAP peptides, we characterized proteolytic cleavage events associated with methionine aminopeptidases and signal peptide peptidases, as well as proteins that are proteolytically cleaved after cisplatin-induced apoptosis. Many of the protein cleavage sites that are elicited during apoptotic signaling are consistent with caspase-dependent cleavage. These data demonstrate the utility of N-CLAP for proteomic profiling of protein cleavage sites that are generated during cellular signaling.
Telomere shortening relaxes X chromosome inactivation and forces global transcriptome alterations
Authors: Schoeftner Stefan , Blanco Raquel , de Silanes Isabel Lopez , Muñoz Purificación , Gómez-López Gonzalo , Flores Juana M. , Blasco Maria A.
Published: November 2009

Telomeres are heterochromatic structures at chromosome ends essential for chromosomal stability. Telomere shortening and the accumulation of dysfunctional telomeres are associated with organismal aging. Using telomerase-deficient TRF2-overexpressing mice (
K5TRF2
/
Terc
−/−
) as a model for accelerated aging, we show that telomere shortening is paralleled by a gradual deregulation of the mammalian transcriptome leading to cumulative changes in a defined set of genes, including up-regulation of the mTOR and Akt survival pathways and down-regulation of cell cycle and DNA repair pathways. Increased DNA damage from dysfunctional telomeres leads to reduced deposition of H3K27me3 onto the inactive X chromosome (Xi), impaired association of the Xi with telomeric transcript accumulations (Tacs), and reactivation of an X chromosome-linked
K5TRF2
transgene that is subjected to X-chromosome inactivation in female mice with sufficiently long telomeres. Exogenously induced DNA damage also disrupts Xi-Tacs, suggesting DNA damage at the origin of these alterations. Collectively, these findings suggest that critically short telomeres activate a persistent DNA damage response that alters gene expression programs in a nonstochastic manner toward cell cycle arrest and activation of survival pathways, as well as impacts the maintenance of epigenetic memory and nuclear organization, thereby contributing to organismal aging.
Cellular stress created by intermediary metabolite imbalances
Authors: Lee Sang Jun , Trostel Andrei , Le Phuoc , Harinarayanan Rajendran , FitzGerald Peter C. , Adhya Sankar
Published: November 2009

Small molecules generally activate or inhibit gene transcription as externally added substrates or as internally accumulated end-products, respectively. Rarely has a connection been made that links an intracellular intermediary metabolite as a signal of gene expression. We report that a perturbation in the critical step of a metabolic pathway—the D-galactose amphibolic pathway—changes the dynamics of the pathways leading to accumulation of the intermediary metabolite UDP-galactose. This accumulation causes cell stress and transduces signals that alter gene expression so as to cope with the stress by restoring balance in the metabolite pool. This underscores the importance of studying the global effects of alterations in the level of intermediary metabolites in causing stress and coping with it by transducing signals to genes to reach a stable state of equilibrium (homeostasis). Such studies are an essential component in the integration of metabolomics, proteomics, and transcriptomics.
Cross-Cultural Perspectives on Secular Vocal Performance in Early Wales
Authors: Macklin Christopher
Published: November 2009

There are many historical repertories of interest for which documentary evidence is scant. In such areas traditional models of musicological research, driven by notation, may be of limited use, and there is thus a need to develop alternative formulations for the relationship between the performance, the performer and the text. In this study, textual analysis and ethnographic comparisons of structurally similar performance cultures (namely, classical Greece and Rome and bardic traditions of south-eastern Europe and eastern Africa) are combined to examine one such tradition: the secular music of the bards of medieval and early-modern Wales. Contemporary accounts pertaining to this repertory are characterized by a systematic ambiguity in their description of speech and song, and a selective use of musical notation for instrumental but not vocal figuration. Comparisons with other musical cultures that share this ambiguity lead to the development of a model of performance that accounts for these textual features.
Revisiting Key Predistribution Using Transversal Designs for a Grid-Based Deployment Scheme
Authors: Ruj Sushmita , Roy Bimal
Published: November 2009

We consider a grid-based deployment scheme in which keys are predistributed in sensor nodes following a transversal design. This scheme was first proposed by Ruj, Maitra, and Roy in [ 19 ]. In their scheme the RF region was considered to be the a square of appropriate dimension. In this article, we consider the RF region to be the Lee sphere of appropriate radius. This is a better approximation than the square RF region and all calculations of connectivity and resiliency is done with respect to this parameter.
Dynamics of Wireless Sensor Networks
Authors: Jiang Nan , Zhou Rigui , Ding Qiulin
Published: November 2009

Power-Law topology has been proved to be an effective technique to improve fault tolerance. With the motivation of construct reliable topology for wireless sensor networks, a Power-Law Evolving Model (PLEW) of wireless sensor networks by stochastic placement is proposed in this article. In a dynamic evolving process of Wireless Sensor Networks, there are four types of events as follows: adding new nodes, nodes failure, adding new links, and links failure. The dynamics of nodes and links are integrated into the evolving model consequently. By using the continuum theory, the theoretical computing and simulated results show that the degree distribution of this model follows a power law. The scale-free properties revealed in this model can be applied into the scenarios required high dependability, such as national defense or survivability systems.
Suppressing Temporal Data in Sensor Networks Using a Scheme Robust to Aberrant Readings
Authors: Reis Ilka A. , Câmara Gilberto , Assunção Renato , Monteiro Antônio Miguel V.
Published: November 2009

The main goal of a data collection protocol for sensor networks is to keep the network's database updated while saving the nodes' energy as much as possible. To achieve this goal without continuous reporting, data suppression is a key strategy. The basic idea behind data suppression schemes is to send data to the base station only when the nodes' readings are different from what both the nodes and the base station expect. Data suppression schemes can be sensitive to aberrant readings, since these outlying observations mean a change in the expected behavior for the data. Transmitting these erroneous readings is a waste of energy. In this article, we present a temporal suppression scheme that is robust to aberrant readings. We use a technique to detect outliers from a time series. Our proposal classifies the detected outliers as aberrant readings or change-points using a post-monitoring window. This idea is the basis for TS-SOUND (Temporal Suppression by Statistical OUtlier Notice and Detection). TS-SOUND detects outliers in the sequence of sensor readings and sends data to the base station only when a change-point is detected. Therefore, TS-SOUND filters aberrant readings and, even when this filter fails, TS-SOUND does not send the deviated reading to the base station. Experiments with real and simulated data have shown that the TS-SOUND scheme is more robust to aberrant readings than other temporal suppression schemes (value-based, PAQ and exponential regression). Furthermore, TS-SOUND has got suppression rates comparable or greater than the rates of the cited schemes, in addition to keeping the prediction errors at acceptable levels.
Real-Time Communications for Wireless Sensor Networks: A Two-Tiered Architecture
Authors: Al-Rousan Mohammad , Kullab Dima
Published: November 2009

While many approaches have been proposed to deal with energy/latency trade-offs, they are likely to be insufficient for the applications where reduced delay guarantee is the main concern. In this article, we investigated the potential application of a decentralized two-tiered network architecture, in large-scale wireless sensor networks, where an upper layer Wireless Local Area Network (WLAN), offering more powerful capabilities, serves as a backbone to an adaptively-clustered Low-Energy Adaptive Clustering Hierarch (LEACH)-based wireless sensor network. The WLAN layer will be involved in the communication between the sensor network and the control station, mitigating the impact of the limited capacities of the sensor nodes. With this two-tiered architecture we target to provide more reliable data delivery with reduced delay bounds, and lower energy consumption in the underlying sensor network, thereby increasing its lifetime. Simulation results show that the two-tiered network architecture achieved a relatively long lifetime, while preserving remarkably low latencies, compared to a single-tiered LEACH and a super-clustered LEACH-based network architectures.
Symmetry and Its Formalisms: Mathematical Aspects
Authors: Guay Alexandre , Hepburn Brian
Published: November 2009

This article explores the relation between the concept of symmetry and its formalisms. The standard view among philosophers and physicists is that symmetry is completely formalized by mathematical groups. For some mathematicians however, the groupoid is a competing and more general formalism. An analysis of symmetry that justifies this extension has not been adequately spelled out. After a brief explication of how groups, equivalence, and symmetries classes are related, we show that, while it's true in some instances that groups are too restrictive, there are other instances for which the standard extension to groupoids is too unrestrictive. The connection between groups and equivalence classes, when generalized to groupoids, suggests a middle ground between the two.
Schaffner's Model of Theory Reduction: Critique and Reconstruction
Authors: Winther Rasmus Gr⊘nfeldt
Published: November 2009

Schaffner's model of theory reduction has played an important role in philosophy of science and philosophy of biology. Here, the model is found to be problematic because of an internal tension. Indeed, standard antireductionist external criticisms concerning reduction functions and laws in biology do not provide a full picture of the limits of Schaffner's model. However, despite the internal tension, his model usefully highlights the importance of regulative ideals associated with the search for derivational, and embedding, deductive relations among mathematical structures in theoretical biology. A reconstructed Schaffnerian model could therefore shed light on mathematical theory development in the biological sciences and on the epistemology of mathematical practices more generally.
Selection and Causation
Authors: Matthen Mohan , Ariew André
Published: November 2009

We have argued elsewhere that natural selection is not a cause of evolution, and that a resolution-of-forces (or vector addition) model does not provide us with a proper understanding of how natural selection combines with other evolutionary influences. These propositions have come in for criticism recently, and here we clarify and defend them. We do so within the broad framework of our own ‘hierarchical realization model’ of how evolutionary influences combine.
In Vivo Anti‐Diabetic Activity of the Ethanolic Crude Extract of Sorbus decora C.K.Schneid. (Rosacea): A Medicinal Plant Used by Canadian James Bay Cree Nations to Treat Symptoms Related to Diabetes
Authors: Vianna Rose , Brault Antoine , Martineau Louis C. , Couture Réjean , Arnason John T. , Haddad Pierre S.
Published: November 2009

A number of potential anti‐diabetic plants were identified through an ethnobotanical survey of the traditional pharmacopeia of the Cree of Eeyou Istchee (CEI—Northeastern Canada) used against symptoms of diabetes and their biological activity assessed by in vitro bioassays. Among these, Sorbus decora C.K.Schneid. (Rosacea) ranked highly and increased the transport of glucose in skeletal muscle cells in culture. The present study thus aimed at confirming the antidiabetic potential of S. decora in in vivo models of insulin resistance and diabetes, notably the streptozotocin Type 1 diabetic rat (STZ), the genetic KK‐Ay Type 2 diabetic mouse and the rat rendered insulin resistant with 10% glucose water consumption for 6 weeks. Sorbus decora ethanolic crude extract (SDEE) was administered orally (200 mg kg−1) and compared to metformin (150 or 500 mg kg−1). The intragastric (i.g.) gavage of SDEE transiently decreased glycemia in STZ rats in a bi‐phasic manner but the effect was cumulative over several days. In KK‐Ay mice, SDEE incorporated in food (0.12%) decreased glycemia by 15% within 1 week as compared to vehicle controls. In pre‐diabetic insulin‐resistant rats, SDEE fed daily by i.g. gavage for 2 weeks significantly decreased the slight hyperglycemia and hyperinsulinemia, without affecting sugar water intake. Using the HOMA insulin resistance parameter, the effect of SDEE was equivalent to that of metformin. In conclusion, the ethanolic crude extract of S. decora demonstrates both anti‐hyperglycemic and insulin‐sensitizing activity in vivo, thereby confirming anti‐diabetic potential and validating CEI traditional medicine.
The impact of concurrent heart failure on prognosis in patients with chronic obstructive pulmonary disease
Authors: Boudestein Laura C.M. , Rutten Frans H. , Cramer Maarten J. , Lammers Jan Willem J. , Hoes Arno W.
Published: November 2009

Aims

To compare prognosis in patients with chronic obstructive pulmonary disease (COPD) with or without concomitant heart failure.

Methods and results

Patients aged 65 years or over with a general practitioner (GP)'s diagnosis of COPD but without a prior diagnosis of heart failure underwent an extensive diagnostic work‐up including echocardiography and pulmonary function tests in the period 2001–03. An expert panel then confirmed the presence or absence of COPD according to the GOLD criteria and (previously undiagnosed) heart failure according to the criteria of the ESC heart failure guidelines. This cohort of 405 patients was followed up for a mean duration of 4.2 (SD 1.4) years. The GP's electronic medical files relating to the participants, including any specialist letters, were scrutinized until April 2007 for information about drug use, exacerbations of COPD, pneumonia, hospitalizations, death, and cause of death. The mean age of patients at the start of the study was 73.0 (SD 5.3) years, and 54% were male. The presence of newly detected heart failure significantly increased all‐cause mortality independent of gender, age, history of ischaemic heart disease, hypertension, diabetes mellitus, atrial fibrillation, smoking, and cardiovascular drug use at baseline (adjusted hazard ratio, 2.1; 95% confidence interval, 1.2–3.6; P = 0.01).

Conclusion

Heart failure is a strong independent predictor of all‐cause mortality in patients with a diagnosis of COPD.
Ammonium Secretion by Colletotrichum coccodes Activates Host NADPH Oxidase Activity Enhancing Host Cell Death and Fungal Virulence in Tomato Fruits
Authors: Alkan Noam , Davydov Olga , Sagi Moshe , Fluhr Robert , Prusky Dov
Published: November 2009

Colletotrichum pathogens of fruit and leaves are known ammonium secretors. Here, we show that Colletotrichum coccodes virulence, as measured by tomato (Solanum lycopersicum cv. Motelle) fruit tissue necrosis, correlates with the amount of ammonium secreted. Ammonium application to fruit tissue induced hydrogen peroxide (H2O2) accumulation. To examine whether the tomato NADPH oxidase, SlRBOH, is a source for the ammonium-induced H2O2, wild-type and antisense lines abrogated for SlRBOH (SlRBOH-AS) were examined. Wild-type lines produced 7.5-fold more reactive oxygen species when exposed to exogenous ammonium than did SlRBOH-AS lines. C. coccodes colonization of wild-type tomato lines resulted in higher H2O2 production and faster fungal growth rate compared with colonization in the SlRBOH-AS mutant, although the amount of ammonium secreted by the fungi was similar in both cases. Enhanced ion leakage and cell death of fruit tissue were correlated with H2O2 accumulation, and treatment with the reactive oxygen scavenger N-acetyl-l-cysteine decreased H2O2 production, ion leakage, and cell death. Importantly, the activation of reactive oxygen species production by ammonium was positively affected by an extracellular pH increase from 4 to 9, implying that ammonium exerts its control via membrane penetration. Our results show that C. coccodes activates host reactive oxygen species and H2O2 production through ammonium secretion. The resultant enhancement in host tissue decay is an important step in the activation of the necrotrophic process needed for colonization.
Phytophthora infestans Isolates Lacking Class I ipiO Variants Are Virulent on Rpi-blb1 Potato
Authors: Champouret Nicolas , Bouwmeester Klaas , Rietman Hendrik , van der Lee Theo , Maliepaard Chris , Heupink Anika , van de Vondervoort Peter J. I. , Jacobsen Evert , Visser Richard G. F. , van der Vossen Edwin A. G. , Govers Francine , Vleeshouwers Vivianne G. A. A.
Published: November 2009

A strategy to control the devastating late blight disease is providing potato cultivars with genes that are effective in resistance to a broad spectrum of Phytophthora infestans isolates. Thus far, most late blight resistance (R) genes that were introgressed in potato were quickly defeated. In contrast, the Rpi-blb1 gene originating from Solanum bulbocastanum has performed as an exclusive broad-spectrum R gene for many years. Recently, the RXLR effector family ipiO was identified to contain Avr-blb1. Monitoring the genetic diversity of the ipiO family in a large set of isolates of P. infestans and related species resulted in 16 ipiO variants in three distinct classes. Class I and class II but not class III ipiO variants induce cell death when coinfiltrated with Rpi-blb1 in Nicotiana benthamiana. Class I is highly diverse and is represented in all analyzed P. infestans isolates except two Mexican P. infestans isolates, and these were found virulent on Rpi-blb1 plants. In its C-terminal domain, IPI-O contains a W motif that is essential for triggering Rpi-blb1–mediated cell death and is under positive selection. This study shows that profiling the variation of Avr-blb1 within a P. infestans population is instrumental for predicting the effectiveness of Rpi-blb1–mediated resistance in potato.
Effect of Wheat Roots Infected with the Pathogenic FungusGaeumannomyces graminisvar.triticion Gene Expression of the Biocontrol BacteriumPseudomonas fluorescensPf29Arp
Authors: Barret Matthieu , Frey-Klett Pascale , Guillerm-Erckelboudt Anne-Yvonne , Boutin Morgane , Guernec Gregory , Sarniguet Alain
Published: November 2009

Traits contributing to the competence of biocontrol bacteria to colonize plant roots are often induced in the rhizosphere in response to plant components. These interactions have been studied using the two partners in gnotobiotic systems. However, in nature, beneficial or pathogenic fungi often colonize roots. Influence of these plant–fungus interactions on bacterial behavior remains to be investigated. Here, we have examined the influence of colonization of wheat roots by the take-all fungus Gaeumannomyces graminis var. tritici on gene expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp. Bacteria were inoculated onto healthy, early G. graminis var. tritici-colonized and necrotic roots and transcriptomes were compared by shotgun DNA microarray. Pf29Arp decreased disease severity when inoculated before the onset of necrosis. Necrotic roots exerted a broader effect on gene expression compared with early G. graminis var. tritici-colonized and healthy roots. A gene encoding a putative type VI secretion system effector was only induced in necrotic conditions. A common pool of Pf29Arp genes differentially expressed on G. graminis var. tritici-colonized roots was related to carbon metabolism and oxidative stress, with a highest fold-change with necrosis. Overall, the data showed that the association of the pathogenic fungus with the roots strongly altered Pf29Arp adaptation with differences between early and late G. graminis var. tritici infection steps.
Overexpression of Rice (Oryza sativa L.) OsCDR1 Leads to Constitutive Activation of Defense Responses in Rice and Arabidopsis
Authors: Prasad Bishun Deo , Creissen Gary , Lamb Chris , Chattoo Bharat B.
Published: November 2009

Plant aspartic proteases (AP) play key roles in the regulation of biological processes, such as the recognition of pathogens and pests and the induction of effective defense responses. A large number of AP (>400) have been identified in silico in the rice genome. None have previously been isolated and functionally characterized for their involvement in disease resistance. We describe here the isolation and characterization of a gene (OsCDR1) from rice which encodes a predicted aspartate protease. Expression of OsCDR1 was activated upon treatments with benzothiadiazole and salicylic acid, which are signal molecules in plant disease resistance responses. Ectopic expression of OsCDR1 in Arabidopsis and rice conferred enhanced resistance against bacterial and fungal pathogens. The enhanced disease resistance observed in transgenic plants was correlated with induction of pathogenesis-related gene expression and was shown by mutational analysis to be dependent on AP activity of the transgene-encoded product. OsCDR1 accumulates in intercellular fluids (IF) in transgenic plants. Infiltration of IF from transgenic Arabidopsis plants into leaves of wild-type (WT) Arabidopsis induced the systemic defense response. These results demonstrate the conservation of CDR1 function between rice and Arabidopsis during the disease resistance response.
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
Authors: Cheng Yong , Wu Weisheng , Ashok Kumar Swathi , Yu Duonan , Deng Wulan , Tripic Tamara , King David C. , Chen Kuan-Bei , Zhang Ying , Drautz Daniela , Giardine Belinda , Schuster Stephan C. , Miller Webb , Chiaromonte Francesca , Zhang Yu , Blobel Gerd A. , Weiss Mitchell J. , Hardison Ross C.
Published: November 2009

The transcription factor GATA1 regulates an extensive program of gene activation and repression during erythroid development. However, the associated mechanisms, including the contributions of distal versus proximal cis-regulatory modules, co-occupancy with other transcription factors, and the effects of histone modifications, are poorly understood. We studied these problems genome-wide in a Gata1 knockout erythroblast cell line that undergoes GATA1-dependent terminal maturation, identifying 2616 GATA1-responsive genes and 15,360 GATA1-occupied DNA segments after restoration of GATA1. Virtually all occupied DNA segments have high levels of H3K4 monomethylation and low levels of H3K27me3 around the canonical GATA binding motif, regardless of whether the nearby gene is induced or repressed. Induced genes tend to be bound by GATA1 close to the transcription start site (most frequently in the first intron), have multiple GATA1-occupied segments that are also bound by TAL1, and show evolutionary constraint on the GATA1-binding site motif. In contrast, repressed genes are further away from GATA1-occupied segments, and a subset shows reduced TAL1 occupancy and increased H3K27me3 at the transcription start site. Our data expand the repertoire of GATA1 action in erythropoiesis by defining a new cohort of target genes and determining the spatial distribution of cis-regulatory modules throughout the genome. In addition, we begin to establish functional criteria and mechanisms that distinguish GATA1 activation from repression at specific target genes. More broadly, these studies illustrate how a “master regulator” transcription factor coordinates tissue differentiation through a panoply of DNA and protein interactions.
A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains
Authors: Wang Yongming , Liška František , Gosele Claudia , Šedová Lucie , Křen Vladimír , Křenová Drahomíra , Ivics Zoltán , Hubner Norbert , Izsvák Zsuzsanna
Published: November 2009

Endogenous retroviruses (ERVs) contribute to a range of germline, as well as somatic mutations in mammals. However, autonomous retrotransposition of potentially active elements has not been demonstrated in the rat genome. We cloned an insertion that disrupted the normal splicing of the Cntrob gene that was subsequently identified as a nonautonomous, novel endogenous retrovirus of the RnERV-K8e family. The RnERV-K8e family is closely related to the recently reported MmERV-K10c elements, but differs from the autonomous mouse MusD or IAP families. In addition, we identified a novel, unexpectedly close relative of RnERV-K8e in the mouse, suggesting ERV-K cross-species transmission between mice and rats. We cloned a potentially autonomous RnERV-K8e element identified by in silico analysis and, using an in vitro retrotransposition assay, demonstrated that it is capable of retrotransposition. This particular element (named Rat-ρ, pronounced “retro”) encodes a retroviral envelope gene (env); however, env is not required for de novo retrotransposition events. Significant levels of RnERV-K8e-associated genetic polymorphisms were detected among inbred rat strains, suggesting ongoing retrotransposition in the rat genome. This study identifies an ERV-K-type family in rats that shows obvious signs of recent activity. Ongoing retrotranspositional activity may significantly add to genomic variability among inbred rat strains.
Efficient calculation of a normal matrix–vector product for anisotropic full-matrix least-squares refinement of macromolecular structures
Authors: Strokopytov Boris V.
Published: November 2009

A novel algorithm is described for multiplying a normal equation matrix by an arbitrary real vector using the fast Fourier transform technique during anisotropic crystallographic refinement. The matrix–vector algorithm allows one to solve normal matrix equations using the conjugate-gradients or conjugate-directions technique without explicit calculation of a normal matrix. The anisotropic version of the algorithm has been implemented in a new version of the computer programFMLSQ. The updated program has been tested on several protein structures at high resolution. In addition, rapid methods for preconditioner and normal matrix–vector product calculations are described.
Molecular biological research on olfactory chemoreception in fishes
Authors: Hino H. , Miles N. G. , Bandoh H. , Ueda H.
Published: November 2009

This review describes recent molecular biological research on olfactory chemoreception in fishes. The recent rapid development of molecular biological techniques has provided new valuable information on the main and vomeronasal olfactory receptor (OR) genes, the axonal projection from ciliated, microvillous and crypt‐olfactory receptor cells to the olfactory bulb, properties of odorant substances and olfactory imprinting and homing in salmon. Many important questions, however, remain unanswered on functional differences among OR genes, on ligand binding to each OR and on the molecular biological mechanisms underlying olfactory imprinting and homing in salmon. Olfactory chemoreception is believed to be the oldest sensory cue for both animal survival and adaptation to various different environments. Further intensive molecular biological research on olfactory memory formation and remembrance should be carried out to clarify the fundamental process of olfactory chemoreception in fishes.
Identification of weakfishCynoscion(Gill) in the Bay of Panama with RFLP markers
Authors: Vergara‐Chen C. , González‐Wangüemert M. , Bermingham E. , D’Croz L.
Published: November 2009

A molecular approach, polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP), was developed to identify the planktonic larvae ofCynoscionspecies. Species‐specific mitochondrial DNA markers were developed using three restriction endonucleases (DdeI,HaeIII andHinfI). These markers permitted the accurate discrimination of the fiveCynoscionspecies in the Bay of Panama.
Phylogeography of bleaks Alburnus spp. (Cyprinidae) in Italy, based on cytochrome b data
Authors: Ketmaier V. , Finamore F. , Largiadèr C. , Milone M. , Bianco P. G.
Published: November 2009

Sequence variation of a fragment of the mitochondrial DNA encoding for the cytochrome b gene was used to reconstruct the phylogeography of the two species of bleaks occurring in Italy: the alborella Alburnus arborella in northern Italy and the vulturino Alburnus albidus in southern Italy. The study includes four populations of the alborella and 14 populations of the vulturino. A total of 57 haplotypes were identified; these could not be sorted into two reciprocally monophyletic clusters. Multiple phylogenetic methods and nested clade phylogeographical analysis consistently retrieved three well‐supported clades, two of which contained both Northern and Southern Italian haplotypes. A third clade is limited to southern Italy. This clade is tentatively assigned to the vulturino. The placement in the same clade of northern and southern Italian haplotypes is explained in light of the introductions of fishes operated from northern to central and southern Italy. The origin of the vulturino dates back to the last two million years. This divergence time estimate identifies the Pleistocene confluences between adjacent river basins along the Adriatic slope of the Italian peninsula and their subsequent isolation as the cause that triggered the diversification of the genus in the area. The existence of a clade endemic to southern Italy supports the recognition of the area as a new peri‐Mediterranean ichthyogeographic district, the borders of which correspond to the northern and southern edges of the vulturino range.
The importance of genetic cluster recognition for the conservation of migratory fish species: the example of the endangered European huchen Hucho hucho (L.)
Authors: Geist J. , Kolahsa M. , Gum B. , Kuehn R.
Published: November 2009

European huchen Hucho hucho (L.) is an endangered flagship species, which is endemic to the Danube drainage in central Europe. To date, no genetic information has been available as a basis for ongoing conservation and breeding programmes for the species. It is suspected that most populations in the wild share one common gene pool and that they exclusively depend on stocking with hatchery fish. In this study, highly variable microsatellite markers were established and the genetic diversity and differentiation from four important hatchery‐reared stocks were compared with that of eight H. hucho populations sampled in the wild. Overall, eight genetic clusters with a moderate to very great degree of genetic differentiation and high assignment rates were identified. Each cluster contained individuals from two to 10 different populations and 9–100% of specimens from hatchery stocks. It is proposed that genetic cluster‐based management in the conservation of European huchen is advantageous compared with the consideration of single local populations. A combined approach of maintaining the evolutionary potential of wild populations and genetically variable hatchery stocks can maximize the conservation of the species' evolutionary potential.
Factors affecting mark quality of alizarin complexone‐stained otoliths in juvenile black bream Acanthopagrus butcheri and a prescription for dosage
Authors: Partridge G. J. , Jenkins G. I. , Doupé R. G. , De Lestang S. , Ginbey B. M. , French D.
Published: November 2009

The relationships between otolith score, a function of increasing stain visibility, and the ratio of alizarin complexone (mg) to fish biomass (g) for 0·1, 0·6 and 7 g black bream Acanthopagrus butcheri show that acceptable marks are produced in all size classes using a stain‐to‐biomass ratio of 3·3 mg g−1 following an immersion period of 24 h.
The effect of pre‐emptive use of minimal dose fentanyl on fentanyl‐induced coughing
Authors: Hung K.‐C. , Chen C.‐W. , Lin V. C.‐H. , Weng H.‐C. , Hsieh S.‐W.
Published: November 2009

We performed a randomised, double‐blind study to evaluate the effect of the pre‐emptive use of minimal dose intravenous fentanyl (25 μg) on the incidence of cough caused by a larger bolus of intravenous fentanyl. Six hundred patients were randomly assigned to one of three groups to receive either 0.5 ml saline 0.9% 1 min before administration of fentanyl 150 μg (3 ml), or pre‐emptive fentanyl 25 μg (0.5 ml) 1 min before administration of fentanyl 125 μg or 150 μg. The incidence of fentanyl‐induced cough was significantly lower in both pre‐emptive groups (7 (3.5%) for 125 μg fentanyl and 15 (7.5%) for 150 μg fentanyl) than in the saline group (37 (18.5%); p = 0.001). We conclude that pre‐emptive use of fentanyl 25 μg, administered 1 min before bolus injection of fentanyl (125 or 150 μg), can effectively suppress fentanyl‐induced cough.
HLA‐DR expression and differential trafficking of monocyte subsets following low to intermediate risk surgery*
Authors: Handy J. M. , Scott A. J. , Cross A. M. , Sinha P. , O’Dea K. P. , Takata M.
Published: November 2009

Reduced HLA‐DR expression on monocytes has been suggested as a predictive marker of immunosuppression following very high risk surgery, but there are few reports in lower risk surgery. In 32 patients undergoing low to intermediate risk surgery, blood samples were analysed by flow cytometry for HLA‐DR expression and numbers in both CD14high and CD14lowCD16+ monocyte subsets. The numbers of CD14high monocytes increased at 24 h (mean (SD), 5.0 (2.2) vs 7.6 (3.9) × 105 cells.ml−1; p < 0.01) while CD14lowCD16+ monocytes decreased (0.68 (0.36) vs 0.44 (0.36) × 105 cells.ml−1; p < 0.01). HLA‐DR expression was significantly reduced in both subsets by 24 h (mean (SD) fluorescent intensity 440 (310) vs 160 (130) for CD14high and 1000 (410) vs 560 (380) for CD14lowCD16+ subsets; p < 0.01). This reduction of monocyte HLA‐DR expression 24 h following lower risk surgery raises questions about the purported clinical utility of this biomarker as an early predictor of postoperative complications. Our results also suggest that surgery induces significant trafficking (i.e. mobilisation, margination and extravasation) of monocyte subsets, and that monocyte HLA‐DR depression is the result of a down‐regulatory phenomenon (decreased protein expression on each cell) rather than the differential trafficking of monocyte subsets.
Bispectral index during cardiopulmonary resuscitation: a poor indicator of recovery. Two very different cases
Authors: Dumans‐Nizard V. , Hamada S. , Fischler M.
Published: November 2009

We report two cases of massive intra‐operative bleeding during lung transplantation requiring emergency cardiopulmonary bypass. In both cases the bispectral index dropped to 0, remained low for around 30 and 90 min respectively, and then returned to values consistent with a usual anaesthetic state (around 40). At the time bispectral monitoring provided some reassurance to the medical team about the adequacy of the resuscitation. However, this proved misleading since postoperative neurological recovery was favourable in one case but not in the other.