bluuebunny/crossref_metadata_2025 huggingface dataset:
Higher-order surface free energy in azimuthal nematic anchoring on nanopatterned grooves
Authors: Gwag Jin Seog , Kwon Jin Hyuk , Oh-e Masahito , Niitsuma Jun-ichi , Yoneya Makoto , Yokoyama Hiroshi
Published: September 2009

The higher-order component in liquid crystal (LC) surface free energy beyond the Rapini–Papoular anchoring potential was examined for azimuthal anchoring by analyzing nematic LC alignment on nanogrooved surfaces treated by rubbing or photoalignment. We confirmed that the surface anchoring energy for large director deviations cannot be properly described with the Rapini–Papoular form and should include higher order contributions in a power series of sin2 ϕ, as ∑n=12Wn sin2n ϕ, with ϕ being the azimuthal angular deviation. Based on the corrected Berreman’s theory, we obtained the anchoring ratio between the first and second order terms, W2/W1≈−1/4, and the surface elastic constant, K24≈−0.846K22, for 4-n-pentyl-4′-cyanobiphenyl.
Dispersion of dust sizes in the plasma of aluminum dust flame
Authors: Doroshenko J. A. , Poletaev N. I. , Vishnyakov V. I.
Published: September 2009

The result of an experimental study of the dispersion of sizes of alumina particles, obtained as a result of condensation in the thermal plasma formed in the two-phase diffusion flame of a burning aluminum dust cloud, is presented. The decrease in the average size of condensed particles and the size dispersion when the temperature of the flame increases is demonstrated.
Nuclear magnetic resonance measurement of shear-induced particle migration in Brownian suspensions
Authors: Brown Jennifer R. , Fridjonsson Einar O. , Seymour Joseph D. , Codd Sarah L.
Published: September 2009

The shear-induced migration of colloidal particles in capillary flow has been investigated using nuclear magnetic resonance. Nuclear magnetic resonance methods have the ability to measure spatially resolved velocity and probability distributions of displacement within a multiphase colloidal system. For a suspension of ∼2.49 μm Brownian model hard spheres under shear flow in a 1 mm diameter glass capillary, particle migration inward to the capillary center was found using spectrally resolved pulsed gradient spin echo techniques for a range of volume fractions. Particle migration was detected even in the dilute regime, down to ϕ<0.04. While particle migration has been measured and is expected in concentrated and noncolloidal suspensions, it has only recently been unequivocally detected in dilute Brownian suspensions.
Site-specific variation in wheat grain protein concentration and wheat grain yield measured on an Australian farm using harvester-mounted on-the-go sensors
Authors: Whelan Brett M. , Taylor James A. , Hassall James A.
Published: September 2009

Accurately measuring and understanding the fine-scale relationship between wheat grain yield (GY) and the concomitant grain protein concentration (GPC) should provide valuable information to improve the management of nitrogen inputs. Here, GPC and GY were monitored on-harvester for three seasons across 27 paddocks on an Australian farming enterprise using two independent, on-the-go sensing systems. A Zeltex Accuharvest measured GPC (%) and a John Deere GreenStar system measured GY (t/ha). Local calibration in each season for Australian spring wheat significantly improved the prediction accuracy, precision, and bias of the Zeltex Accuharvest when compared with the initial factory calibration. Substantial variation in GPC and GY was recorded at the field scale, with the least variation recorded in both parameters in the wetter season. GY (CV = 38%) was twice as variable on average as GPC (CV = 19%) across the enterprise. At this enterprise scale, a negative correlation between GPC and GY was observed for a composite of the field data from all seasons (r = –0.48); however, at the within-field scale the relationship was shown to vary from positive (max. = +0.41) to negative (min. = –0.65). Spatial variation in GPC and GY at the within-field scale was described best in the majority of cases by an exponential semivariogram model. Within-field spatial variability in GPC is more strongly autocorrelated than GY but on average they share a similar autocorrelated range (a′ = ~190 m). This spatial variability in GPC and GY gave rise to local spatial variation in the correlation between GPC and GY, with 85% of the fields registering regions of significant negative correlations (P < 0.01) and significant positive correlations observed in 70% of fields. The spatial pattern in these regions of significantly different correlations is shown to display spatial coherence from which inferences regarding the relative availability of soil nitrogen and moisture are suggested. The results point to the suitability of these on-the-go sensors for use in more sophisticated agronomic and environmentally targeted nitrogen-use analysis.
Grain yield and protein responses in wheat using the N-Sensor for variable rate N application
Authors: Mayfield A. H. , Trengove S. P.
Published: September 2009

Soil types, cereal crop growth and grain yields are typically variable across many paddocks in the cropping regions of South Australia. In this study the value of a variable rate nitrogen fertiliser application, using the Yara N-Sensor, was compared with the standard practice of a uniform application, at crop growth stage 31, on the grain yield and protein content of wheat. These comparisons were made using the same total amount of fertiliser in paired variable and uniform rate treatments in commercial crops at a total of 10 sites over two years in the medium to higher rainfall areas of the Mid North and Yorke Peninsula of South Australia.
The mean increase in wheat grain yield for the variable rate treatment was only 40 kg/ha, or 0.8%, when compared with the uniform rate treatment averaged over these 10 sites and two years. Grain yield differences ranged from 160 kg/ha more to 60 kg/ha less for the variable rate treatment when compared with the uniform rate treatment. Wheat grain yields with the uniform treatments ranged from 2.53 t/ha to 5.68t/ha and with a mean grain yield of 4.24 t/ha. The mean wheat grain protein content with the variable rate treatment was 11.0%, compared with 10.5% with the uniform rate treatment, a relative increase of 5.1%.
Where grain yield responses to the variable rate treatments were compared between different biomass areas within a paddock, the greatest grain yield increases to a variable rate of N compared with a uniform rate were in the areas with the lowest 20% of crop biomass whereas grain yield differences were negligible in areas with the highest 60% of crop biomass. These low biomass areas also had the greatest grain yield response to the applied post emergent nitrogen fertiliser when compared with areas with no post emergent nitrogen fertiliser.
N-Sensor outputs (biomass and N-rate) were compared with measurements of plant biomass, N uptake (kg N/ha) and %N content at points of contrasting biomass and N-rate within paddocks. There was a high correlation between the N-Sensor biomass and N-rate values and actual plant biomass and N uptake but not with the %N content.
Crop biomass maps made using sensors such as the N-Sensor could provide useful data layers, which in combination with other datasets such as grain yield maps or elevation maps, be used to produce zone maps for further analysis or for variable rate input treatments. The N-Sensor could also be used in some situations to map variations in weed biomass for possible site specific weed management.
Capturing the in-field spatial - temporal dynamic of yield variation
Authors: Lawes R. A. , Oliver Y. M. , Robertson M. J.
Published: September 2009

Many researchers have predicted that within-field spatial variation in crop yield could be exploited for economic benefit. However, the spatial variation of yield is influenced by season and is often temporally unstable. Parts of a field may yield well relative to the remainder of the field in one season and poorly in another, suggesting that regions in the field vary in their response to season type. We evaluate the capacity of two analytical techniques, the regression on the field mean and the regression on growing-season rainfall, to capture the variation in responsiveness of yield variation across a field. We applied these indices to a commercial 134-ha field that had been sown to wheat, Triticum aestivum cv. Calingiri, in 1996, 1999, 2001, 2003, and 2005. The slope from the regression on field mean was variable with a mean of 1 and standard deviation of 0.67. The technique successfully identified regions that were responsive and unresponsive to variations in the cropping environment. In contrast, the average slope derived from the regression on growing-season rainfall was just –0.003 ± 0.003 t/ha.mm of growing-season rainfall. This approach failed to capture the spatial–temporal dynamic of yield variation, and implies that the overall cropping environment was poorly characterised by growing-season rainfall.
Crop yields, derived from 10 soils in this field, were simulated from 1900 to 2006. The analytical techniques were applied to these simulated yields and revealed that the spatial–temporal dynamic observed in the field is partially explained by the interactions between soil type and climate. In addition, the spatial–temporal dynamic is best captured when mean field yields vary temporally by more than 1.2 t/ha if the assessments are made with 5 years of data. We further discuss the application and interpretation of these indices and the role they play in identifying soils that are responsive to season type.
Advances in precision agriculture in south-eastern Australia. III. Interactions between soil properties and water use help explain spatial variability of crop production in the Victorian Mallee
Authors: Armstrong R. D. , Fitzpatrick J. , Rab M. A. , Abuzar M. , Fisher P. D. , O'Leary G. J.
Published: September 2009

A major barrier to the adoption of precision agriculture in dryland cropping systems is our current inability to reliably predict spatial patterns of grain yield for future crops for a specific paddock. An experiment was undertaken to develop a better understanding of how edaphic and climatic factors interact to influence the spatial variation in the growth, water use, and grain yield of different crops in a single paddock so as to improve predictions of the likely spatial pattern of grain yields in future crops.
Changes in a range of crop and soil properties were monitored over 3 consecutive seasons (barley in 2005 and 2007 and lentils in 2006) in the southern section of a 167-ha paddock in the Mallee region of Victoria, which had been classified into 3 different yield (low, moderate, and high) and seasonal variability (stable and variable) zones using normalised difference vegetation index (NDVI) and historic yield maps. The different management zones reflected marked differences in a range of soil properties including both texture in the topsoil and potential chemical-physical constraints in the subsoil (SSCs) to root growth and water use. Dry matter production, grain yield, and quality differed significantly between the yield zones but the relative difference between zones was reduced when supplementary irrigation was applied to barley in 2005, suggesting that some other factor, e.g. nitrogen (N), may have become limiting in that year. There was a strong relationship between crop growth and the use of soil water and nitrate across the management zones, with most water use by the crop occurring in the pre-anthesis/flowering period, but the nature of this relationship appeared to vary with year and/or crop type. In 2006, lentil yield was strongly related to crop establishment, which varied with soil texture and differences in plant-available water. In 2007 the presence of soil water following a good break to the season permitted root growth into the subsoil where there was evidence that SSCs may have adversely affected crop growth. Because of potential residual effects of one crop on another, e.g. through differential N supply and use, we conclude that the utility of the NDVI methodology for developing zone management maps could be improved by using historical records and data for a range of crop types rather than pooling data from a range of seasons.
Advances in precision agriculture in south-eastern Australia. V. Effect of seasonal conditions on wheat and barley yield response to applied nitrogen across management zones
Authors: Anwar M. R. , O'Leary G. J. , Rab M. A. , Fisher P. D. , Armstrong R. D.
Published: September 2009

Spatial variability in grain yield across a paddock often indicates spatial variation in soil properties, especially in regions like the Victorian Mallee. We combined 2 years of field data and 119 years of simulation experiments (APSIM-Wheat and APSIM-Barley crop models) to simulate crop yield at various levels of N application in 4 different management zones to explore the robustness of the zones previously determined for an experimental site at Birchip. The crop models explained 96% and 67% of the observed variability in wheat and barley grain yields, with a root mean square error (RMSE) of 310 kg/ha and 230 kg/ha, respectively. The model produced consistent responses to the observed data from the field experiment in 2004 and 2005 where a high and stable yielding zone produced the highest dry matter as well as grain yield, while a low and variable zone recorded the lowest grain yield. However, from the long-term (119 years) simulation, the highest median wheat yield value was obtained on the low variable zone (2911 kg/ha) with high N fertiliser application, while the lowest was obtained on the high variable zone (851 kg/ha). Similarly, the highest barley yields (1880–3350 kg/ha) occurred on the low variable zone using the long-term simulation. In 10–20% of years the highest yield occurred in the high-yielding zones, with the variable and stable zones changing rank with interactive behaviour only under early-sown conditions. Our analyses highlight the problem of using a limited range of seasons of different weather conditions in agronomy to make strategic conclusions as the long-term simulation did not confirm the original yield zone determination. The challenge ahead is to predict in advance the seasons where application of N fertiliser will be beneficial.
Potential scope and impact of a transboundary model of nurse practitioners in aged care
Authors: Bail Kasia , Arbon Paul , Eggert Marlene , Gardner Anne , Hogan Sonia , Phillips Christine , van Dieman Nicole , Waddington Gordon
Published: September 2009

Aged care is a growing issue in Australia and other countries. There are significant barriers to meeting the health needs of this population. Current services have gaps between care and lack communication and integration between care providers. Research was conducted in the Australian Capital Territory to investigate the potential role of the aged care nurse practitioner in health service delivery in aged care settings. A multimethod case study design was utilised, with three student nurse practitioners (SNP) providing care to aged care clients across three sectors of health service delivery (residential aged care facilities, general medical practices and acute care). Data collection consisted of in-depth interviews and journal entries of the SNP, as well as focus groups and surveys of multidisciplinary staff and patients over the age of 65 years in the settings frequented by the SNP. The aged care SNP were found to cross professional and organisational boundaries, cross intra- as well as interorganisational boundaries and to contribute to more seamless patient care as members of a multidisciplinary aged care team. The aged care nurse practitioner role consequently has the potential to function in a networked rather than a hierarchical manner, and this could be a key element in addressing gaps in care across care locales and between disciplines.
Gold Coast Primary Care Partnership Council: partnership and innovation that makes a difference
Authors: Carrodus Matt , Dwonczyk Marcia
Published: September 2009

The Gold Coast Primary Care Partnership Council is bringing together diverse stakeholders to improve the health and wellbeing of their community. The inaugural chairperson and coordinator reflect on the high level of enthusiasm to work together as a promising start to building sustainable partnerships.
The origin of Neandertals
Authors: Hublin J. J.
Published: September 2009

Western Eurasia yielded a rich Middle (MP) and Late Pleistocene (LP) fossil record documenting the evolution of the Neandertals that can be analyzed in light of recently acquired paleogenetical data, an abundance of archeological evidence, and a well-known environmental context. Their origin likely relates to an episode of recolonization of Western Eurasia by hominins of African origin carrying the Acheulean technology into Europe around 600 ka. An enhancement of both glacial and interglacial phases may have played a crucial role in this event, as well as in the subsequent evolutionary history of the Western Eurasian populations. In addition to climatic adaptations and an increase in encephalization, genetic drift seems to have played a major role in their evolution. To date, a clear speciation event is not documented, and the most likely scenario for the fixation of Neandertal characteristics seems to be an accretion of features along the second half of the MP. Although a separation time for the African and Eurasian populations is difficult to determine, it certainly predates OIS 11 as phenotypic Neandertal features are documented as far back as and possibly before this time. It is proposed to use the term “
Homo rhodesiensis
” to designate the large-brained hominins ancestral to
H. sapiens
in Africa and at the root of the Neandertals in Europe, and to use the term “
Homo neanderthalensis
” to designate all of the specimens carrying derived metrical or non-metrical features used in the definition of the LP Neandertals.
The same systemic autoimmune disease provokes arthritis and endocarditis via distinct mechanisms
Authors: Binstadt Bryce A. , Hebert Jennifer L. , Ortiz-Lopez Adriana , Bronson Roderick , Benoist Christophe , Mathis Diane
Published: September 2009

The immune mechanisms that provoke concomitant inflammation of synovial joints and cardiac valves in disorders such as rheumatic fever and systemic lupus erythematosus remain poorly defined. Here, we report the discovery of spontaneous endocarditis—in addition to their well-studied autoimmune arthritis—in K/BxN T cell receptor (TCR) transgenic mice. The same adaptive immune system elements were required for initiation of arthritis and endocarditis, and both diseases were dependent on autoantibodies. In contrast, the participation of key innate immune system molecules and perhaps T cells as effectors of inflammation differed between the 2 target tissues. Arthritis in K/BxN TCR transgenic mice depended primarily on complement C5 and not FcRγ-using receptors; conversely, endocarditis depended essentially on FcRγ receptors and not C5. Elucidating how a single systemic autoimmune disease engages distinct immune effector pathways to damage different target tissues is essential for optimizing the treatment of such disorders.
Reform Transplanted: Parsi Agents of Change amongst Zoroastrians in Nineteenth-Century Iran
Authors: Ringer Monica
Published: September 2009

In the mid-nineteenth century, Parsis reestablished ties with Zoroastrians in Iran that had languished due to decades-long internal unrest in Iran. In 1854 reformists in India established the Society for the Amelioration of Conditions in Iran and sent a representative to Iran—Maneckji Hataria. Hataria was charged with eliminating the onerous non-Muslim tax owed by the Zoroastrians (the jaziyeh). Hataria also organized the Iranian Zoroastrian community, and funded a variety of community projects. He also brought Parsi reformist ideas to Iran, and attempted to reshape Iranian religious practice and belief along Parsi lines. This article explores the effects of Parsi reformist ideas on Iran, and Hataria's own writings concerning Zoroastrianism and its relationship to Iranian national identity.
Iranian Zoroastrians in Canada: Balancing Religious and Cultural Identities
Authors: Foltz Richard
Published: September 2009

Canada, now the number-one destination for Iranian migrants, is home to one of the world's most dynamic Zoroastrian communities, in which Iranians are increasingly represented and are playing ever more visible roles in maintaining and transforming the tradition. While exile has in some ways reunited Iranian and Parsi (South Asian) Zoroastrians after more than 1,000 years of separation, cultural and in some cases religious differences mean that they continue largely to live in separate spheres even while sharing their places of worship. Iranian Zoroastrians in Canada participate in some social settings as Iranians, in others as Zoroastrians, and in still others as Canadians, but to a large extent they remain a community unto themselves separate from these other three. Even so, their generally progressive interpretations of Zoroastrianism are having an influence on Parsi communities worldwide as well as on Zoroastrians in Iran, and being often recognized as “original Iranians” they are playing important roles in promoting awareness of Iranian culture within the broader community.
The Eighth Majles Elections in the Islamic Republic of Iran: A Division in Conservative Ranks and the Politics of Moderation
Authors: Sanandaji Kaveh-Cyrus
Published: September 2009

Since his inauguration in August 2005, President Mahmoud Ahmadinejad faced mounting criticism over his administration's political, economic, and social agenda. Observers noted a significant degree of rising discontent among various segments of the population as evidenced, for example, by the public unrest witnessed in June 2007 in response to the introduction of gasoline rationing.1 The situation in the months leading to the Eighth Majles Election was distinctive because this dissatisfaction also began resonating among segments of the political elite, prompting the emergence of not only reformist, but also conservative opposition to Ahmadinejad.
How to Select and Interpret Molecular Strain Typing Methods for Epidemiological Studies of Bacterial Infections A Review for Healthcare Epidemiologists
Authors: Tenover Fred C. , Arbeit Robert D. , Goering Richard V. ,   Molecular Typing Working Group of the Society for Healthcare Epidemiology of America
Published: September 2009

Strain typing is an integral part of epidemiological investigations of nosocomial infections. Methods for distinguishing among bacterial strains have improved dramatically over the last 5 years, due mainly to the introduction of molecular technology. Although not all molecular techniques are equally effective for typing all organisms, pulsed-field gel electrophoresis is the technique currently favored for most nosocomial pathogens. Criteria to aid epidemiologists in interpreting results have been published. Nucleic acid amplification-based typing methods also are applicable to many organisms and can be completed within a single day, but interpretive criteria still are under debate. Strain typing cannot be used to replace a sound epidemiological investigation, but serves as a useful adjunct to such investigations.
Predicting homologous signaling pathways using machine learning
Authors: Bostan Babak , Greiner Russell , Szafron Duane , Lu Paul
Published: September 2009

Motivation: In general, each cell signaling pathway involves many proteins, each with one or more specific roles. As they are essential components of cell activity, it is important to understand how these proteins work—and in particular, to determine which of the species' proteins participate in each role. Experimentally determining this mapping of proteins to roles is difficult and time consuming. Fortunately, many pathways are similar across species, so we may be able to use known pathway information of one species to understand the corresponding pathway of another.

Results: We present an automatic approach, Predict Signaling Pathway (PSP), which uses the signaling pathways in well-studied species to predict the roles of proteins in less-studied species. We use a machine learning approach to create a predictor that achieves a generalization F-measure of 78.2% when applied to 11 different pathways across 14 different species. We also show our approach is very effective in predicting the pathways that have not yet been experimentally studied completely.

Availability: The list of predicted proteins for all pathways over all considered species is available at http://www.cs.ualberta.ca/~bioinfo/signaling.

Contact:  bioinfo@cs.ualberta.ca; duane@cs.ualberta.ca
Updates to the RMAP short-read mapping software
Authors: Smith Andrew D. , Chung Wen-Yu , Hodges Emily , Kendall Jude , Hannon Greg , Hicks James , Xuan Zhenyu , Zhang Michael Q.
Published: September 2009

Summary: We report on a major new version of the RMAP software for mapping reads from short-read sequencing technology. General improvements to accuracy and space requirements are included, along with novel functionality. Included in the RMAP software package are tools for mapping paired-end reads, mapping using more sophisticated use of quality scores, collecting ambiguous mapping locations and mapping bisulfite-treated reads.

Availability: The applications described in this note are available for download at http://www.cmb.usc.edu/people/andrewds/rmap and are distributed as Open Source software under the GPLv3.0. The software has been tested on Linux and OS X platforms.

Contact:  andrewds@usc.edu; mzhang@cshl.edu

The RMAP algorithm was introduced by (Smith et al., 2008) as one of the earliest available programs for mapping reads from the Illumina second-generation sequencing technology. One important contribution of RMAP was to incorporate the use of quality scores directly into the mapping process: read positions with too low a quality score were not considered while mapping, and that quality score cutoff could be adjusted by the user. Subsequently, numerous mapping algorithm have appeared (Langmead et al., 2009; Li,H. et al., 2008; Li,R. et al., 2008; Lin et al., 2008; Schatz, 2009; Yanovsky et al., 2008), with improvements in both efficiency and breadth of functionality (e.g. ability to map paired-end reads; integrated SNP calling). Investigators requiring solutions to mapping problems now have many options. As new applications of short-read sequencing emerge, many variations on the analysis task of read mapping emerge. Diversity in performance characteristics of existing mapping tools becomes potentially valuable.

We report the first major update to RMAP. The basic algorithmic framework in RMAP is still to preprocess reads and scan the genome, but several modifications have been made and much additional functionality has been included. Importantly, RMAP has a memory footprint that depends on the number of reads being mapped. This feature allows RMAP to be used effectively in cluster environments with commodity nodes, because partitioning the reads allows natural parallelizations with linear reduction in memory requirements per processor core used.

Included in this release of the RMAP software package is functionality for mapping paired-end reads, making more sophisticated use of quality scores, collecting mapping locations for ambiguously mapping reads and mapping bisulfite-treated reads.
Phytochemical Composition and Antioxidant Capacity of Three Malian Medicinal Plant Parts
Authors: Muanda François , Koné Donatien , Dicko Amadou , Soulimani Rachid , Younos Chafique
Published: September 2009

This study evaluates the levels of total polyphenolic compounds in three Malian medicinal plants and determines their antioxidant potential. Quantitative and qualitative analysis of polyphenolics contained in plants extracts were carried out by RP‐C18 RP–HPLC using UV detector. The antioxidant activity was determined by three tests. They are phosphomolybdenum, DPPH (2,2‐diphenyl‐1 picrylhydrazyl) and ABTS [2,2′‐azino‐bis(3‐ethylbenzothiazoline‐6‐sulfonic)] tests. The total phenolic and the total flavonoid contents varied from 200 to 7600 mg 100 g−1 dry weight (dw), expressed as gallic acid equivalents and from 680 to 12 300 mg 100 g−1 dw expressed as catechin equivalents, respectively. The total anthocyanin concentrations expressed as cyanin‐3‐glycoside equivalent varied from 1670 to 28 388 mg 100 g−1 dw. The antioxidant capacity was measured by determining concentration of a polyphenolic (in mg ml−1) required to quench the free radicals by 50% (IC50) and expressed as vitamin C equivalent antioxidant capacity. The IC50 values were ranked between 2.68 and 8.80 μg ml−1 of a solution of 50% (v/v) methanol in water. The uses of plants are rationalized on the basis of their antioxidant capacity.
HMC05, Herbal Formula, Inhibits TNF‐α‐Induced Inflammatory Response in Human Umbilical Vein Endothelial Cells
Authors: Lee Jong Suk , Park Su-Young , Thapa Dinesh , Kim Ah Ra , Shin Heung-Mook , Kim Jung-Ae
Published: September 2009

Vascular inflammation has been implicated in the progression of cardiovascular diseases such as atherosclerosis. In the present study, we found that HMC05, an extract from eight different herbal mixtures, dose‐dependently inhibited tumor necrosis factor‐α (TNF‐α)‐induced adhesion of monocytes to endothelial cells. Such inhibitory effect of HMC05 correlated with suppressed expression of monocyte chemoattractant protein‐1, CC chemokine receptor 2, vascular cell adhesion molecule‐1 and intercellular cell adhesion molecule‐1. In addition, HMC05 significantly inhibited production of reactive oxygen species (ROS) and nuclear factor (NF)‐κB activation by TNF‐α. Those inhibitory effects of HMC05 (1–10 μg mL−1) on the TNF‐α‐induced inflammatory event was similar to those of berberine (1–10 μM), which is a major component of HMC05 and one of herbal compounds known to have vasorelaxing and lipid‐lowering activities. However, berberine significantly reduced the viability of HUVECs in a time‐ and concentration‐dependent manner. In contrast, HMC05 (1–10 μg ml−1) did not affect the cell viability for up to 48 h treatment. In conclusion, we propose that HMC05 may be a safe and potent herbal formula against vascular inflammation, and its action may be attributable to the inhibition of ROS‐ and NF‐κB‐dependent expression of adhesion molecules and chemokines.
Recognitional Specificity and Evolution in the Tomato–Cladosporium fulvum Pathosystem
Authors: Wulff B. B. H. , Chakrabarti A. , Jones D. A.
Published: September 2009

The interactions between plants and many biotrophic or hemibiotrophic pathogens are controlled by receptor proteins in the host and effector proteins delivered by the pathogen. Pathogen effectors facilitate pathogen growth through the suppression of host defenses and the manipulation of host metabolism, but recognition of a pathogen-effector protein by a host receptor enables the host to activate a suite of defense mechanisms that limit pathogen growth. In the tomato (Lycopersicon esculentum syn. Solanum lycopersicum)–Cladosporium fulvum (leaf mold fungus syn. Passalora fulva) pathosystem, the host receptors are plasma membrane–anchored, leucine-rich repeat, receptor-like proteins encoded by an array of Cf genes conferring resistance to C. fulvum. The pathogen effectors are mostly small, secreted, cysteine-rich, but otherwise largely dissimilar, extracellular proteins encoded by an array of avirulence (Avr) genes, so called because of their ability to trigger resistance and limit pathogen growth when the corresponding Cf gene is present in tomato. A number of Cf and Avr genes have been isolated, and details of the complex molecular interplay between tomato Cf proteins and C. fulvum effector proteins are beginning to emerge. Each effector appears to have a different role; probably most bind or modify different host proteins, but at least one has a passive role masking the pathogen. It is, therefore, not surprising that each effector is probably detected in a distinct and specific manner, some by direct binding, others as complexes with host proteins, and others via their modification of host proteins. The two papers accompanying this review contribute further to our understanding of the molecular specificity underlying effector perception by Cf proteins. This review, therefore, focuses on our current understanding of recognitional specificity in the tomato–C. fulvum pathosystem and highlights some of the critical questions that remain to be addressed. It also addresses the evolutionary causes and consequences of this specificity.
The Major Specificity-Determining Amino Acids of the Tomato Cf-9 Disease Resistance Protein Are at Hypervariable Solvent-Exposed Positions in the Central Leucine-Rich Repeats
Authors: Wulff Brande B. H. , Heese Antje , Tomlinson-Buhot Laurence , Jones David A. , de la Peña Marcos , Jones Jonathan D. G.
Published: September 2009

The interaction between tomato and the leaf mold pathogen Cladosporium fulvum is controlled in a gene-for-gene manner by plant Cf genes that encode membrane-anchored extracytoplasmic leucine-rich repeat (LRR) glycoproteins, which confer recognition of their cognate fungal avirulence (Avr) proteins. Cf-9 and Cf-4 are two such proteins that are 91% identical yet recognize the sequence-unrelated fungal avirulence determinants Avr9 and Avr4, respectively. As shown previously, Cf-4 specificity is determined by three putative solvent-exposed residues in the central LRR and a deletion of two LRR relative to Cf-9. In this study, we focused on identifying the specificity determinants of Cf-9. We generated chimeras between Cf-9 and its close homologue Cf-9B and identified five amino acid residues that constitute major specificity determinants of Cf-9. Introduction of these residues into Cf-9B allowed recognition of Avr9. Consistent with a role in recognition specificity, the identified residues are putatively solvent exposed in the central LRR and occupy hypervariable positions in the global Cf alignment. One of the specificity residues is not found in any other known Cf protein, suggesting the importance of diversifying selection rather than sequence exchange between homologues. Interestingly, there is an overlap between the Cf-4 and Cf-9 specificity-determining residues, precluding a protein with dual specificity.
Regions of the Cf-9B Disease Resistance Protein Able to Cause Spontaneous Necrosis in Nicotiana benthamiana Lie Within the Region Controlling Pathogen Recognition in Tomato
Authors: Chakrabarti Apratim , Panter Stephen N. , Harrison Kate , Jones Jonathan D. G. , Jones David A.
Published: September 2009

The tomato Cf-9 and Cf-9B genes both confer resistance to the leaf mold fungus Cladosporium fulvum but only Cf-9 confers seedling resistance and recognizes the avirulence (Avr) protein Avr9 produced by C. fulvum. Using domain swaps, leucine-rich repeats (LRR) 5 to 15 of Cf-9 were shown to be required for Cf-9-specific resistance to C. fulvum in tomato, and the entire N-terminus up to LRR15 of Cf-9B was shown to be required for Cf-9B-specific resistance. Finer domain swaps showed that nine amino-acid differences in LRR 13 to 15 provided sufficient Cf-9-specific residues in a Cf-9B context for recognition of Avr9 in Nicotiana tabacum or sufficient Cf-9B residues in a Cf-9 context for a novel necrotic response caused by the expression of Cf-9B in N. benthamiana. The responses conferred by LRR 13 to 15 were enhanced by addition of LRR 10 to 12, and either region of Cf-9B was found to cause necrosis in N. benthamiana when the other was replaced by Cf-9 sequence in a Cf-9B context. As a consequence, the domain swap with LRR 13 to 15 of Cf-9 in a Cf-9B context gained the dual ability to recognize Avr9 and cause necrosis in N. benthamiana. Intriguingly, two Cf-9B-specific domain swaps gave differing results for necrosis assays in N. benthamiana compared with disease resistance assays in transgenic tomato. The different domain requirements in these two cases suggest that the two assays detect unrelated ligands or detect related ligands in slightly different ways. A heat-sensitive necrosis-inducing factor present in N. benthamiana intercellular washing fluids was found to cause a necrotic response in N. tabacum plants carrying Hcr9-9A, Cf-9B, and Cf-9 but not in plants carrying only Cf-9. We postulate that this necrosis-inducing factor is recognized by Cf-9B either directly as a ligand or indirectly as a regulator of Cf-9B autoactivity.
TheArabidopsisATAF1, a NAC Transcription Factor, Is a Negative Regulator of Defense Responses Against Necrotrophic Fungal and Bacterial Pathogens
Authors: Wang Xiao'e , Basnayake B. M. Vindhya S. , Zhang Huijuan , Li Guojun , Li Wei , Virk Nasar , Mengiste Tesfaye , Song Fengming
Published: September 2009

Transcription factors of the NAC family are known to be involved in various growth or developmental processes and in regulation of response to environmental stresses. In the present study, we report that Arabidopsis ATAF1 is a negative regulator of defense responses against both necrotrophic fungal and bacterial pathogens. Expression of ATAF1 was downregulated after infection with Botrytis cinerea or Pseudomonas syringae pv. tomato or after treatment with salicylic acid (SA), jasmonic acid, and 1-amino cyclopropane-1-carboxylic acid (the precursor of ethylene biosynthesis). Transgenic plants that overexpress the ATAF1 gene (ATAF1-OE) showed increased susceptibility while expression of an ATAF1 chimeric repressor construct (ATAF1-SRDX) exhibited enhanced resistance to P. syringae pv. tomato DC3000, B. cinerea, and Alternaria brassicicola. The ataf1 mutant plants showed no significant resistance against the pathogens tested. After inoculation with B. cinerea or P. syringae pv. tomato DC3000, expressions of defense-related genes PR-1, PR-5. and PDF1.2 were upregulated in the ATAF1-SRDX plants but attenuated or unchanged in the ATAF1-OE plants. In ATAF1-OE plants, SA-induced expression of pathogenesis-related genes and disease resistance against P. syringae pv. tomato DC3000 was partially suppressed. Increased levels of reactive oxygen species (i.e., H2O2and superoxide anion) accumulated only in the ATAF1-OE but not in the ATAF1-SRDX plants after Botrytis spp. infection. Our studies provide direct genetic evidence for the role of ATAF1 as a negative regulator of defense response against different type of pathogens.
Differential Effects of Mild and Severe Cucumber mosaic virus Strains in the Perturbation of MicroRNA-Regulated Gene Expression in Tomato Map to the 3′ Sequence of RNA 2
Authors: Cillo Fabrizio , Mascia Tiziana , Pasciuto Marco M. , Gallitelli Donato
Published: September 2009

Viral infections interfere with the microRNA (miRNA)-mediated regulation of gene expression, determining developmental defects. In tomato leaves, the accumulation levels of six miRNA species and their target transcripts corresponding to transcription factors with roles in plant development and leaf morphogenesis and two genes involved in the short RNA processing, DCL1 and AGO1, were significantly enhanced upon infection with the severe strain Cucumber mosaic virus (CMV)-Fny, while that of AGO4 was reduced. In plants harboring the infection of the mild strain CMV-LS, the effects on miRNA pathway were reduced, although AGO1, DCL1, and NAC1 also were shown to overaccumulate during infections exhibiting a mild phenotype. The use of the recombinant strain CMV-Fny(LS2b), in which the 3′-terminal region of CMV-Fny RNA 2, including the 2b coding sequence, was replaced with the corresponding region of CMV-LS RNA 2, provided evidence that the exchanged region was implicated in the perturbation of miRNA metabolism. In tomato plants infected with CMV-Fny supporting the ameliorative satellite (sat)RNA variant Tfn-satRNA, the symptomless phenotype correlated, with the exception of NAC1 upregulation, with the absence of effects on mitochondrial RNA and miRNA expression. Some of the aspects of miRNA pathway perturbation described were peculiar to CMV–tomato interactions and involved in the etiology of the disease phenotype elicited in this host.
RNAi-Mediated Transgenic Tospovirus Resistance Broken by IntraspeciesSilencing Suppressor Protein Complementation
Authors: Hassani-Mehraban Afshin , Brenkman A. B. , van den Broek N. J. F. , Goldbach Rob , Kormelink Richard
Published: September 2009

Extension of an inverted repeat transgene cassette, containing partial nucleoprotein (N) gene sequences from four different tomato-infecting Tospovirus spp. with a partial N gene sequence from the tomato strain of Tomato yellow ring virus (TYRV-t), renders transgenic Nicotiana benthamiana plants additionally resistant to this strain but not to the soybean strain of this Tospovirus sp. (TYRV-s), both strains exhibiting 14.4% nucleotide sequence divergence in their N genes. Surprisingly, coinoculation of the TYRV-t-resistant transgenic lines with both TYRV-t and TYRV-s resulted in rescue of the former. Mass-spectrometric analysis of the viral ribonucleocapsids accumulating in the transgenic plants showed the presence of the N proteins of both strains excluding hetero-encapsidation as rescue mechanism and indicating suppression of TYRV-t N gene transcript breakdown by RNA interference. Prior (Potato virus X [PVX]-vector-mediated) expression of the TYRV-s silencing suppressor (NSs) gene also allowed TYRV-t to break the resistance. This phenomenon was also observed when the homologous (TYRV-t) NSs gene was provided from a PVX replicon, demonstrating that TYRV can break RNA-mediated host resistance upon a priori expression of its NSs protein. Remarkably, mixed inoculation of TYRV-t with other Tospovirus spp. or nonrelated viruses did not result in resistance breaking, indicating that the rescuing activity of NSs—though based on suppressing RNA silencing—is species-dependent.
Biosynthesis and Role in Virulence of the Histone Deacetylase Inhibitor Depudecin from Alternaria brassicicola
Authors: Wight Wanessa D. , Kim Kwang-Hyung , Lawrence Christopher B. , Walton Jonathan D.
Published: September 2009

Depudecin, an eleven-carbon linear polyketide made by the pathogenic fungus Alternaria brassicicola, is an inhibitor of histone deacetylase (HDAC). A chemically unrelated HDAC inhibitor, HC toxin, was earlier shown to be a major virulence factor in the interaction between Cochliobolus carbonum and its host, maize. In order to test whether depudecin is also a virulence factor for A. brassicicola, we identified the genes for depudecin biosynthesis and created depudecin-minus mutants. The depudecin gene cluster contains six genes (DEP1 to DEP6), which are predicted to encode a polyketide synthase (AbPKS9 or DEP5), a transcription factor (DEP6), two monooxygenases (DEP2 and DEP4), a transporter of the major facilitator superfamily (DEP3), and one protein of unknown function (DEP1). The involvement in depudecin production of DEP2, DEP4, DEP5, and DEP6 was demonstrated by targeted gene disruption. DEP6 is required for expression of DEP1 through DEP5 but not the immediate flanking genes, thus defining a coregulated depudecin biosynthetic cluster. The genes flanking the depudecin gene cluster but not the cluster itself are conserved in the same order in the related fungi Stagonospora nodorum and Pyrenophora tritici-repentis. Depudecin-minus mutants have a small (10%) but statistically significant reduction in virulence on cabbage (Brassica oleracea) but not on Arabidopsis. The role of depudecin in virulence is, therefore, less dramatic than that of HC toxin.
Functional Analysis of the N Terminus of the Erwinia amylovora Secreted Effector DspA/E Reveals Features Required for Secretion, Translocation, and Binding to the Chaperone DspB/F
Authors: Triplett Lindsay R. , Melotto Maeli , Sundin George W.
Published: September 2009

DspA/E is a type III secreted effector protein required for pathogenicity in the apple and pear pathogen Erwinia amylovora, and DspB/F is a small chaperone protein involved in DspA/E secretion. While the secretion and translocation signals of many type III secretion effector proteins in human enteric pathogens have been characterized extensively, relatively little is known about the translocation requirements of many effectors in plant pathogens, including large DspE-like proteins. In this study, we report a functional analysis of the N terminus of DspE. The minimal requirements for secretion, translocation, and chaperone binding were characterized. Translocation assays using an adenylate cyclase (CyaA) reporter indicated that the first 51 amino acids of DspE were sufficient for translocation and that 150 amino acids were required for optimal translocation levels. The minimal translocation signal corresponded with the requirements for secretion into culture media. Mutations of conserved regions in amino acids 2 through 10 and 31 through 40 were found to influence translocation levels of an N-terminal DspE-CyaA fusion. Yeast two-hybrid and in-vitro pull-down assays revealed a chaperone-binding site within amino acids 51 through 100 of DspE and binding to DspF in this region was disrupted by specific mutations. However, neither disruption of the chaperone-binding domain nor deletion of the dspF gene had a significant impact on translocation levels of N-terminal DspE-CyaA fusions. Our results indicate that the minimal translocation signal of DspE is not coincident with the signal for DspF binding and that translocation of the N terminus of DspE is not dependent on the N-terminal DspF-binding domain.
Calcineurin Is an Antagonist to PKA Protein Phosphorylation Required for Postmating Filamentation and Virulence, While PP2A Is Required for Viability in Ustilago maydis
Authors: Egan John D. , García-Pedrajas María D. , Andrews David L. , Gold Scott E.
Published: September 2009

Ustilago maydis is a dimorphic basidiomycete and the causal agent of corn smut disease. It serves as a genetic model for understanding dimorphism, pathogenicity, and mating response in filamentous fungi. Previous studies indicated the importance of regulated cAMP-dependent protein kinase A (PKA) for filamentous growth and pathogenicity in U. maydis. The roles of two protein phosphatases that potentially act antagonistically to PKA were assessed. A reverse genetics approach to mutate the catalytic subunits of calcineurin (CN, protein phosphatase [PP]2B) and PP2A in U. maydis was employed. A mutation in the CN catalytic subunit ucn1 caused a dramatic multiple-budding phenotype and mating between two ucn1 mutants was severely reduced. The pathogenicity of ucn1 mutant strains was also severely reduced, even in a solopathogenic haploid strain. Importantly, mutations disrupting protein phosphorylation by PKA were epistatic to ucn1 mutation, indicating a major role of ucn1 as a PKA antagonistic phosphatase. Genetic and inhibitor studies indicated that the U. maydis PP2A catalytic subunit gene (upa2) was essential.