bluuebunny/crossref_metadata_2025 huggingface dataset:
Agos—a universal web tool for GW Argonaute-binding domain prediction
Authors: Zielezinski Andrzej , Karlowski Wojciech M.
Published: March 2011

Motivation: AGO(Argonaute)-binding domains, composed of repeated motifs, in which only binary combinations of tryptophan and glycine are conserved, bind AGO proteins and are essential during RNAi-mediated gene silencing. The amino acid sequence of this domain is extremely divergent and therefore very difficult to detect. Commonly used bioinformatic tools fail to identify tryptophan–glycine and/or glycine–tryptophan motifs (WG/GW) domains and currently there is no publicly available software which can detect these weakly conserved, but functional AGO-binding segments.

Results: Recently, we have developed an algorithm based on compositional analysis of the amino acid content of the domain. We have demonstrated that the algorithm can be successfully applied for the identification of the new WG/GW proteins in the Arabidopsis genome. Here we introduce Agos (Argonaute-binding domain screener), a novel universal web service for de novo identification of WG/GW domains in protein sequences. The web implementation of the algorithm contains several new features and enhancements: (i) one universal scoring matrix which allows identification of AGO-binding proteins in sequences representing all organisms; (ii) reduction of false positive predictions by improved selectivity of the algorithm; (iii) graphical interface to easily browse the prediction results; and (iv) the option to submit a DNA sequence which will be automatically translated in six frames before running the prediction algorithm.

Availability: Freely available at: http://bioinfo.amu.edu.pl/agos/.

Contact:  wmk@amu.edu.pl

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Evaluation of the design and efficiency of the Norwegian self-sampling purse-seine reference fleet
Authors: Pennington Michael , Helle Kristin
Published: March 2011

Pennington, M., and Helle, K. 2011. Evaluation of the design and efficiency of the Norwegian self-sampling purse-seine reference fleet. – ICES Journal of Marine Science, 68: 1764–1768. A self-sampling reference fleet is employed by the Institute of Marine Research to estimate the characteristics of the Norwegian commercial catch for a number of species. The reference fleet is composed of commercial fishing vessels that are paid to measure a subsample of fish from selected catches and, less frequently, to take and preserve otolith, stomach, and genetic samples. In this study, the sampling design for monitoring the catches of herring, mackerel, and blue whiting used by the recently established purse-seine segment of the reference fleet is evaluated. The precision of the estimated mean lengths, and hence that of the estimated length distributions of the entire commercial catch, was bounded by the number of boats in the purse-seine reference fleet. Therefore, the only way to improve survey precision significantly is to increase the number of boats in the reference fleet. In addition, the effective sample sizes were much smaller than the total number of fish measured, from which it followed that too many fish were measured in each selected catch. Based on this analysis, the prescribed number of fish sampled from each selected catch has been reduced by more than 50%.
The dawn of symbiosis between plants and fungi
Authors: Bidartondo Martin I. , Read David J. , Trappe James M. , Merckx Vincent , Ligrone Roberto , Duckett Jeffrey G.
Published: March 2011

The colonization of land by plants relied on fundamental biological innovations, among which was symbiosis with fungi to enhance nutrient uptake. Here we present evidence that several species representing the earliest groups of land plants are symbiotic with fungi of the Mucoromycotina. This finding brings up the possibility that terrestrialization was facilitated by these fungi rather than, as conventionally proposed, by members of the Glomeromycota. Since the 1970s it has been assumed, largely from the observation that vascular plant fossils of the early Devonian (400 Ma) show arbuscule-like structures, that fungi of the Glomeromycota were the earliest to form mycorrhizas, and evolutionary trees have, until now, placed Glomeromycota as the oldest known lineage of endomycorrhizal fungi. Our observation that
Endogone
-like fungi are widely associated with the earliest branching land plants, and give way to glomeromycotan fungi in later lineages, raises the new hypothesis that members of the Mucoromycotina rather than the Glomeromycota enabled the establishment and growth of early land colonists.
Critically endangered blonde capuchins fish for termites and use new techniques to accomplish the task
Authors: Souto Antonio , Bione Camila B. C. , Bastos Monique , Bezerra Bruna M. , Fragaszy Dorothy , Schiel Nicola
Published: March 2011

We report the spontaneous modification and use of sticks to fish for termites, above the ground, in wild blonde capuchins (
Cebus flavius
). These critically endangered Neotropical primates inhabit remnants of the Atlantic Forest. They used two previously undescribed techniques to enhance their termite capture success: nest tapping and stick rotation. The current ecologically based explanation for tool use in wild capuchins (i.e. terrestrial habits and bipedalism) must be viewed cautiously. Instead, remarkable manual skills linked to a varied diet seem important in promoting tool use in different contexts. The repertoire of tool-using techniques employed by wild capuchins has been expanded, highlighting the behavioural versatility in this genus.
Rapid behavioural diagnosis of domoic acid toxicosis in California sea lions
Authors: Cook Peter , Reichmuth Colleen , Gulland Frances
Published: March 2011

Domoic acid is a neurotoxic metabolite of widely occurring algal blooms that has caused multiple marine animal stranding events. Exposure to high doses of domoic acid, a glutamate agonist, may lead to persistent medial temporal seizures and damage to the hippocampus. California sea lions (
Zalophus californianus
) are among the most visible and frequent mammalian victims of domoic acid poisoning, but rapid, reliable diagnosis in a clinical setting has proved difficult owing to the fast clearance of the toxin from the blood stream. Here, we show that the behavioural orienting responses of stranded sea lions diagnosed with domoic acid toxicosis habituate more slowly to a series of non-aversive auditory stimuli than do those of sea lions with no apparent neurological deficits. A signal detection analysis based on these habituation measures was able to correctly identify 50 per cent of subjects with domoic acid toxicosis while correctly rejecting approximately 93 per cent of controls, suggesting potential diagnostic merit.
Nuclear magnetic resonance analysis of protein–DNA interactions
Authors: Campagne S. , Gervais V. , Milon A.
Published: March 2011

Recent methodological and instrumental advances in solution-state nuclear magnetic resonance have opened up the way to investigating challenging problems in structural biology such as large macromolecular complexes. This review focuses on the experimental strategies currently employed to solve structures of protein–DNA complexes and to analyse their dynamics. It highlights how these approaches can help in understanding detailed molecular mechanisms of target recognition.
The time machine: a simulation approach for stochastic trees
Authors: Jasra Ajay , De Iorio Maria , Chadeau-Hyam Marc
Published: March 2011

In this paper, we consider a simulation technique for stochastic trees. One of the most important areas in computational genetics is the calculation and subsequent maximization of the likelihood function associated with such models. This typically consists of using importance sampling and sequential Monte Carlo techniques. The approach proceeds by simulating the tree, backward in time from observed data, to a most recent common ancestor. However, in many cases, the computational time and variance of estimators are often too high to make standard approaches useful. In this paper, we propose to stop the simulation, subsequently yielding biased estimates of the likelihood surface. The bias is investigated from a theoretical point of view. Results from simulation studies are also given to investigate the balance between loss of accuracy, saving in computing time and variance reduction.
Study of 40-atom Pt–Au clusters using a combined empirical potential-density functional approach
Authors: Tran Dung T. , Johnston Roy L.
Published: March 2011

This work is a theoretical study of 40-atom Pt–Au clusters which are of interest owing to the electronic shell closure of 40-atom noble metal clusters and the current focus on bimetallic Pt–Au clusters as catalysts. The methodology is a complementary combination of a genetic algorithm search for an empirical potential and density functional theory (DFT) reoptimization. Structures based on truncated-octahedral, icosahedral, decahedral and fivefold pancake geometries are found to be energetically favoured for different composition regions at the empirical-potential level and this is partially confirmed at the DFT level. The large HOMO–LUMO gaps found for the icosahedral and fivefold pancake structures indicate electronic shell closure effects, while the truncated-octahedral and decahedral structures have small gaps. The DFT calculations confirm that, for Pt
20
Au
20
truncated-octahedral structures, the Pt
core
Au
shell
configuration which has two Au atoms capping the (100) facets is most energetically favoured, and the layered (phase segregated) configuration also has lower energy compared with the Au
core
Pt
shell
and mixed configurations.
Challenges to assessing connectivity between massive populations of the Australian plague locust
Authors: Chapuis Marie-Pierre , Popple Julie-Anne M. , Berthier Karine , Simpson Stephen J. , Deveson Edward , Spurgin Peter , Steinbauer Martin J. , Sword Gregory A.
Published: March 2011

Linking demographic and genetic dispersal measures is of fundamental importance for movement ecology and evolution. However, such integration can be difficult, particularly for highly fecund species that are often the target of management decisions guided by an understanding of population movement. Here, we present an example of how the influence of large population sizes can preclude genetic approaches from assessing demographic population structuring, even at a continental scale. The Australian plague locust,Chortoicetes terminifera, is a significant pest, with populations on the eastern and western sides of Australia having been monitored and managed independently to date. We used microsatellites to assess genetic variation in 12C. terminiferapopulation samples separated by up to 3000 km. Traditional summary statistics indicated high levels of genetic diversity and a surprising lack of population structure across the entire range. An approximate Bayesian computation treatment indicated that levels of genetic diversity inC. terminiferacorresponded to effective population sizes conservatively composed of tens of thousands to several million individuals. We used these estimates and computer simulations to estimate the minimum rate of dispersal,m, that could account for the observed range-wide genetic homogeneity. The rate of dispersal between both sides of the Australian continent could be several orders of magnitude lower than that typically considered as required for the demographic connectivity of populations.
The impact of projected increases in urbanization on ecosystem services
Authors: Eigenbrod F. , Bell V. A. , Davies H. N. , Heinemeyer A. , Armsworth P. R. , Gaston K. J.
Published: March 2011

Alteration in land use is likely to be a major driver of changes in the distribution of ecosystem services before 2050. In Europe, urbanization will probably be the main cause of land-use change. This increase in urbanization will result in spatial shifts in both supplies of ecosystem services and the beneficiaries of those services; the net outcome of such shifts remains to be determined. Here, we model changes in urban land cover in Britain based on large (16%) projected increases in the human population by 2031, and the consequences for three different services—flood mitigation, agricultural production and carbon storage. We show that under a scenario of densification of urban areas, the combined effect of increasing population and loss of permeable surfaces is likely to result in 1.7 million people living within 1 km of rivers with at least 10 per cent increases in projected peak flows, but that increasing suburban ‘sprawl’ will have little effect on flood mitigation services. Conversely, losses of stored carbon and agricultural production are over three times as high under the sprawl as under the ‘densification’ urban growth scenarios. Our results illustrate the challenges of meeting, but also of predicting, future demands and patterns of ecosystem services in the face of increasing urbanization.
Convergent patterns of long-distance nocturnal migration in noctuid moths and passerine birds
Authors: Alerstam Thomas , Chapman Jason W. , Bäckman Johan , Smith Alan D. , Karlsson Håkan , Nilsson Cecilia , Reynolds Don R. , Klaassen Raymond H. G. , Hill Jane K.
Published: March 2011

Vast numbers of insects and passerines achieve long-distance migrations between summer and winter locations by undertaking high-altitude nocturnal flights. Insects such as noctuid moths fly relatively slowly in relation to the surrounding air, with airspeeds approximately one-third of that of passerines. Thus, it has been widely assumed that windborne insect migrants will have comparatively little control over their migration speed and direction compared with migrant birds. We used radar to carry out the first comparative analyses of the flight behaviour and migratory strategies of insects and birds under nearly equivalent natural conditions. Contrary to expectations, noctuid moths attained almost identical ground speeds and travel directions compared with passerines, despite their very different flight powers and sensory capacities. Moths achieved fast travel speeds in seasonally appropriate migration directions by exploiting favourably directed winds and selecting flight altitudes that coincided with the fastest air streams. By contrast, passerines were less selective of wind conditions, relying on self-powered flight in their seasonally preferred direction, often with little or no tailwind assistance. Our results demonstrate that noctuid moths and passerines show contrasting risk-prone and risk-averse migratory strategies in relation to wind. Comparative studies of the flight behaviours of distantly related taxa are critically important for understanding the evolution of animal migration strategies.
Trabecular bone scales allometrically in mammals and birds
Authors: Doube Michael , Kłosowski Michał M. , Wiktorowicz-Conroy Alexis M. , Hutchinson John R. , Shefelbine Sandra J.
Published: March 2011

Many bones are supported internally by a latticework of trabeculae. Scaling of whole bone length and diameter has been extensively investigated, but scaling of the trabecular network is not well characterized. We analysed trabecular geometry in the femora of 90 terrestrial mammalian and avian species with body masses ranging from 3 g to 3400 kg. We found that bone volume fraction does not scale substantially with animal size, while trabeculae in larger animals' femora are thicker, further apart and fewer per unit volume than in smaller animals. Finite element modelling indicates that trabecular scaling does not alter the bulk stiffness of trabecular bone, but does alter strain within trabeculae under equal applied loads. Allometry of bone's trabecular tissue may contribute to the skeleton's ability to withstand load, without incurring the physiological or mechanical costs of increasing bone mass.
High sensitivity to short wavelengths in a lizard and implications for understanding the evolution of visual systems in lizards
Authors: Fleishman Leo J. , Loew Ellis R. , Whiting Martin J.
Published: March 2011

Progress in developing animal communication theory is frequently constrained by a poor understanding of sensory systems. For example, while lizards have been the focus of numerous studies in visual signalling, we only have data on the spectral sensitivities of a few species clustered in two major clades (Iguania and Gekkota). Using electroretinography and microspectrophotometry, we studied the visual system of the cordylid lizardPlatysaurus broadleyibecause it represents an unstudied clade (Scinciformata) with respect to visual systems and because UV signals feature prominently in its social behaviour. The retina possessed four classes of single and one class of double cones. Sensitivity in the ultraviolet region (UV) was approximately three times higher than previously reported for other lizards. We found more colourless oil droplets (associated with UV-sensitive (UVS) and short wavelength-sensitive (SWS) photoreceptors), suggesting that the increased sensitivity was owing to the presence of more UVS photoreceptors. Using the Vorobyev–Osorio colour discrimination model, we demonstrated that an increase in the number of UVS photoreceptors significantly enhances a lizard's ability to discriminate conspecific male throat colours. Visual systems in diurnal lizards appear to be broadly conserved, but data from additional clades are needed to confirm this.
Frontier mutualism: coevolutionary patterns at the northern range limit of the leaf-cutter ant–fungus symbiosis
Authors: Mueller Ulrich G. , Mikheyev Alexander S. , Solomon Scott E. , Cooper Michael
Published: March 2011

Tropical leaf-cutter ants cultivate the fungusAttamyces bromatificusin a many-to-one, diffuse coevolutionary relationship where ant and fungal partners re-associate frequently over time. To evaluate whether ant–Attamycescoevolution is more specific (tighter) in peripheral populations, we characterized the host-specificities ofAttamycesgenotypes at their northern, subtropical range limits (southern USA, Mexico and Cuba). Population-genetic patterns of northernAttamycesreveal features that have so far not been observed in the diffusely coevolving, tropical ant–Attamycesassociations. These unique features include (i) cases of one-to-one ant–Attamycesspecialization that tighten coevolution at the northern frontier; (ii) distributions of genetically identicalAttamycesclones over large areas (up to 81 000 km2, approx. the area of Ireland, Austria or Panama); (iii) admixture rates betweenAttamyceslineages that appear lower in northern than in tropical populations; and (iv) long-distance gene flow ofAttamycesacross a dispersal barrier for leaf-cutter ants (ocean between mainland North America and Cuba). The latter suggests thatAttamycesfungi may occasionally disperse independently of the ants, contrary to the traditional assumption thatAttamycesfungi depend entirely on leaf-cutter queens for dispersal. Peripheral populations in Argentina or at mid-elevation sites in the Andes may reveal additional regional variants in ant–Attamycescoevolution. Studies of such populations are most likely to inform models of coextinctions of obligate mutualistic partners that are doubly stressed by habitat marginality and by environmental change.
Linking individual phenotype to density-dependent population growth: the influence of body size on the population dynamics of malaria vectors
Authors: Russell Tanya L. , Lwetoijera Dickson W. , Knols Bart G. J. , Takken Willem , Killeen Gerry F. , Ferguson Heather M.
Published: March 2011

Understanding the endogenous factors that drive the population dynamics of malaria mosquitoes will facilitate more accurate predictions about vector control effectiveness and our ability to destabilize the growth of either low- or high-density insect populations. We assessed whether variation in phenotypic traits predict the dynamics of
Anopheles gambiae sensu lato
mosquitoes, the most important vectors of human malaria.
Anopheles gambiae
dynamics were monitored over a six-month period of seasonal growth and decline. The population exhibited density-dependent feedback, with the carrying capacity being modified by rainfall (97%
w
AIC
c
support). The individual phenotypic expression of the maternal (
p
= 0.0001) and current (
p
= 0.040) body size positively influenced population growth. Our field-based evidence uniquely demonstrates that individual fitness can have population-level impacts and, furthermore, can mitigate the impact of exogenous drivers (e.g. rainfall) in species whose reproduction depends upon it. Once frontline interventions have suppressed mosquito densities, attempts to eliminate malaria with supplementary vector control tools may be attenuated by increased population growth and individual fitness.
Sex-specific differential survival of extra-pair and within-pair offspring in song sparrows,Melospiza melodia
Authors: Sardell Rebecca J. , Arcese Peter , Keller Lukas F. , Reid Jane M.
Published: March 2011

It is widely hypothesized that the evolution of female extra-pair reproduction in socially monogamous species reflects indirect genetic benefits to females. However, a critical prediction of this hypothesis, that extra-pair young (EPY) are fitter than within-pair young (WPY), has rarely been rigorously tested. We used 18 years of data from free-living song sparrows,Melospiza melodia, to test whether survival through major life-history stages differed between EPY and WPY maternal half-siblings. On average, survival of hatched chicks to independence from parental care and recruitment, and their total lifespan, did not differ significantly between EPY and WPY. However, EPY consistently tended to be less likely to survive, and recruited EPY survived for significantly fewer years than recruited WPY. Furthermore, the survival difference between EPY and WPY was sex-specific; female EPY were less likely to survive to independence and recruitment and lived fewer years than female WPY, whereas male EPY were similarly or slightly more likely to survive and to live more years than male WPY. These data indicate that extra-pair paternity may impose an indirect cost on females via their female offspring and that sex-specific genetic, environmental or maternal effects may shape extra-pair reproduction.
Why mammalian lineages respond differently to sexual selection: metabolic rate constrains the evolution of sperm size
Authors: Gomendio Montserrat , Tourmente Maximiliano , Roldan Eduardo R. S.
Published: March 2011

The hypothesis that sperm competition should favour increases in sperm size, because it results in faster swimming speeds, has received support from studies on many taxa, but remains contentious for mammals. We suggest that this may be because mammalian lineages respond differently to sexual selection, owing to major differences in body size, which are associated with differences in mass-specific metabolic rate. Recent evidence suggests that cellular metabolic rate also scales with body size, so that small mammals have cells that process energy and resources from the environment at a faster rate. We develop the ‘metabolic rate constraint hypothesis’ which proposes that low mass-specific metabolic rate among large mammals may limit their ability to respond to sexual selection by increasing sperm size, while this constraint does not exist among small mammals. Here we show that among rodents, which have high mass-specific metabolic rates, sperm size increases under sperm competition, reaching the longest sperm sizes found in eutherian mammals. By contrast, mammalian lineages with large body sizes have small sperm, and while metabolic rate (corrected for body size) influences sperm size, sperm competition levels do not. When all eutherian mammals are analysed jointly, our results suggest that as mass-specific metabolic rate increases, so does maximum sperm size. In addition, species with low mass-specific metabolic rates produce uniformly small sperm, while species with high mass-specific metabolic rates produce a wide range of sperm sizes. These findings support the hypothesis that mass-specific metabolic rates determine the budget available for sperm production: at high levels, sperm size increases in response to sexual selection, while low levels constrain the ability to respond to sexual selection by increasing sperm size. Thus, adaptive and costly traits, such as sperm size, may only evolve under sexual selection when metabolic rate does not constrain cellular budgets.
Ethylene Receptor ETHYLENE RECEPTOR1 Domain Requirements for Ethylene Responses in Arabidopsis Seedlings
Authors: Kim Heejung , Helmbrecht Elizabeth E. , Stalans M. Blaine , Schmitt Christina , Patel Nesha , Wen Chi-Kuang , Wang Wuyi , Binder Brad M.
Published: March 2011

Ethylene influences many processes in Arabidopsis (Arabidopsis thaliana) through the action of five receptor isoforms. We used high-resolution, time-lapse imaging of dark-grown Arabidopsis seedlings to better understand the roles of each isoform in the regulation of growth in air, ethylene-stimulated nutations, and growth recovery after ethylene removal. We found that ETHYLENE RECEPTOR1 (ETR1) is both necessary and sufficient for nutations. Transgene constructs in which the ETR1 promoter was used to drive expression of cDNAs for each of the five receptor isoforms were transferred into etr1-6;etr2-3;ein4-4 triple loss-of-function mutants that have constitutive growth inhibition in air, fail to nutate in ethylene, and take longer to recover a normal growth rate when ethylene is removed. The patterns of rescue show that ETR1, ETR2, and ETHYLENE INSENSITIVE4 (EIN4) have the prominent roles in rapid growth recovery after removal of ethylene whereas ETR1 was the sole isoform that rescued nutations. ETR1 histidine kinase activity and phosphotransfer through the receiver domain are not required to rescue nutations. However, REVERSION TO SENSITIVITY1 modulates ethylene-stimulated nutations but does not modulate the rate of growth recovery after ethylene removal. Several chimeric receptor transgene constructs where domains of EIN4 were swapped into ETR1 were also introduced into the triple mutant. The pattern of phenotype rescue by the chimeric receptors used in this study supports a model where a receptor with a receiver domain is required for normal growth recovery and that nutations specifically require the full-length ETR1 receptor.
Overexpression of ArabidopsisECERIFERUM1Promotes Wax Very-Long-Chain Alkane Biosynthesis and Influences Plant Response to Biotic and Abiotic Stresses
Authors: Bourdenx Brice , Bernard Amélie , Domergue Frédéric , Pascal Stéphanie , Léger Amandine , Roby Dominique , Pervent Marjorie , Vile Denis , Haslam Richard P. , Napier Johnathan A. , Lessire René , Joubès Jérôme
Published: March 2011

Land plant aerial organs are covered by a hydrophobic layer called the cuticle that serves as a waterproof barrier protecting plants against desiccation, ultraviolet radiation, and pathogens. Cuticle consists of a cutin matrix as well as cuticular waxes in which very-long-chain (VLC) alkanes are the major components, representing up to 70% of the total wax content in Arabidopsis (Arabidopsis thaliana) leaves. However, despite its major involvement in cuticle formation, the alkane-forming pathway is still largely unknown. To address this deficiency, we report here the characterization of the Arabidopsis ECERIFERUM1 (CER1) gene predicted to encode an enzyme involved in alkane biosynthesis. Analysis of CER1 expression showed that CER1 is specifically expressed in the epidermis of aerial organs and coexpressed with other genes of the alkane-forming pathway. Modification of CER1 expression in transgenic plants specifically affects VLC alkane biosynthesis: waxes of TDNA insertional mutant alleles are devoid of VLC alkanes and derivatives, whereas CER1 overexpression dramatically increases the production of the odd-carbon-numbered alkanes together with a substantial accumulation of iso-branched alkanes. We also showed that CER1 expression is induced by osmotic stresses and regulated by abscisic acid. Furthermore, CER1-overexpressing plants showed reduced cuticle permeability together with reduced soil water deficit susceptibility. However, CER1 overexpression increased susceptibility to bacterial and fungal pathogens. Taken together, these results demonstrate that CER1 controls alkane biosynthesis and is highly linked to responses to biotic and abiotic stresses.
Phosphorylation of the Nicotiana benthamiana WRKY8 Transcription Factor by MAPK Functions in the Defense Response
Authors: Ishihama Nobuaki , Yamada Reiko , Yoshioka Miki , Katou Shinpei , Yoshioka Hirofumi
Published: March 2011

Mitogen-activated protein kinase (MAPK) cascades have pivotal roles in plant innate immunity. However, downstream signaling of plant defense-related MAPKs is not well understood. Here, we provide evidence that the Nicotiana benthamiana WRKY8 transcription factor is a physiological substrate of SIPK, NTF4, and WIPK. Clustered Pro-directed Ser residues (SP cluster), which are conserved in group I WRKY proteins, in the N-terminal region of WRKY8 were phosphorylated by these MAPKs in vitro. Antiphosphopeptide antibodies indicated that Ser residues in the SP cluster of WRKY8 are phosphorylated by SIPK, NTF4, and WIPK in vivo. The interaction of WRKY8 with MAPKs depended on its D domain, which is a MAPK-interacting motif, and this interaction was required for effective phosphorylation of WRKY8 in plants. Phosphorylation of WRKY8 increased its DNA binding activity to the cognate W-box sequence. The phospho-mimicking mutant of WRKY8 showed higher transactivation activity, and its ectopic expression induced defense-related genes, such as 3-hydroxy-3-methylglutaryl CoA reductase 2 and NADP-malic enzyme. By contrast, silencing of WRKY8 decreased the expression of defense-related genes and increased disease susceptibility to the pathogens Phytophthora infestans and Colletotrichum orbiculare. Thus, MAPK-mediated phosphorylation of WRKY8 has an important role in the defense response through activation of downstream genes.
Real-time synchrotron powder X-ray diffraction study of the antisite defect formation during sub- and supercritical synthesis of LiFePO4and LiFe1−xMnxPO4nanoparticles
Authors: Jensen Kirsten , Christensen Mogens , Tyrsted Christoffer , Brummerstedt Iversen Bo
Published: March 2011

In situsynchrotron powder X-ray diffraction (PXRD) is used to study the formation of LiFePO4nanoparticles during hydrothermal synthesis from LiOH, H3PO4, and two different iron precursors, FeSO4and (NH4)2Fe(SO4)2. Furthermore, the synthesis of Li(Fe1−xMnx)PO4(x= 0.25, 0.50 and 0.75) from LiOH, H3PO4and FeSO4/MnSO4is studied. The reactions involve an unknown intermediate phase, which is not the previously observed intermediate NH4FePO4·H2O. The intermediate phase quickly transforms into LiFePO4and Li(Fe1−xMnx)PO4even at rather low temperatures. The presence of ammonium enhances the formation of LiFePO4, and it also leads to a significant reduction in the concentration of Li–Fe antisite defects. Thein situPXRD technique allows one to follow the influence of time, temperature and manganese doping on the antisite defect concentration, and it is shown that even under supercritical conditions a reaction time of several minutes is required to suppress the defects. This makes flow synthesis of defect-free LiFePO4and Li(Fe1−xMnx)PO4nanoparticles challenging.
CYCLOPS – a reciprocal-space explorer based on CCD neutron detectors
Authors: Ouladdiaf Bachir , Archer John , Allibon John R. , Decarpentrie Philippe , Lemée-Cailleau Marie-Hélène , Rodríguez-Carvajal Juan , Hewat Alan W. , York Scott , Brau Daniel , McIntyre Garry J.
Published: March 2011

The key technical aspects of the multiple CCD diffractometer CYCLOPS (Cylindrical CCD Laue Octagonal Photo Scintillator) at the Institut Laue–Langevin are described. Laue patterns subtending 270° horizontally by 92° vertically are read out in less than 3 s to allow nearly real time exploration of reciprocal space and rapid data collection through phase transitions. The first experiments on the same thermal beam as OrientExpress have exceeded expectations and promise exciting new applications for neutron Laue diffraction.
Three-dimensional spatially resolved neutron diffraction from a disordered vortex lattice
Authors: Wang Xi , Hanson Helen A. , Ling Xinsheng Sean , Majkrzak Charles F. , Maranville Brian B.
Published: March 2011

The vortex matter in bulk type II superconductors serves as a prototype system for studying the random pinning problem in condensed matter physics. Since the vortex lattice is embedded in an atomic lattice, small-angle neutron scattering (SANS) is the only technique that allows for direct structural studies. In traditional SANS methods, the scattering intensity is a measure of the structure factor averaged over the entire sample. Recent studies in vortex physics have shown that it is highly desirable to develop a SANS technique that is capable of resolving the spatial inhomogeneities in the bulk vortex state. This article reports a novel slicing neutron diffraction technique using atypical collimation and an areal detector, which allows for observing the three-dimensional disorder of the vortex matter inside an as-grown Nb single crystal.
Charge-density analysis in polymorphs of urea–barbituric acid co-crystals
Authors: Gryl Marlena , Krawczuk-Pantula Anna , Stadnicka Katarzyna
Published: March 2011

High-resolution single-crystal X-ray diffraction measurements at 100 K were performed for the two polymorphs of urea–barbituric acid co-crystals: (I) P21/c and (II) Cc. Experimental and theoretical charge density and its properties were analysed for (I) and (II) in order to confirm the previous observation that in the polymorphs studied the barbituric acid molecules adopt different mesomeric forms, leading to different hydrogen-bond systems. Koch and Popelier criteria were applied to distinguish between hydrogen bonds and van der Waals interactions in the structures presented.
Detailed study of the phase transition in [Ni(H2O)6](NO3)2·(15-crown-5)·H2O and analysis in terms of mean-field theory
Authors: Siegler Maxime A. , Parkin Sean , Angel Ross J. , Brock Carolyn Pratt
Published: March 2011

The transition between 190 and 200 K in [Ni(H2O)6](NO3)2·(15-crown-5)·H2O has been followed by determining the structure at 22 temperatures in the range 90–273 K. The structural change is a zone-boundary transition with a critical point at (½, 0, ½) in the Brillouin zone of the high-temperature phase; both phases have space-group symmetry P21 but the volume of the unit cell is halved when a crystal is heated through the transition. The only obvious disorder in the high-temperature phase is of the lattice water molecule, which occupies two sites; some disorder persists below the transition. The greatest changes in the structure below the transition are the rotations of one of the two 15-crown-5 molecules and of one of the two nitrate ions; above the transition the two molecules are related by symmetry as are the two ions. Below the transition these two rotation angles evolve linearly with one another, and can thus be associated with a single order parameter that describes the structural evolution. The evolution of the spontaneous strain arising from the transition does not, however, follow the same evolution as the structural order parameter. This observation indicates that the transition cannot be described in terms of a Landau-type expansion that is characterized by a single order parameter, perhaps because the potential-energy surface for this essentially molecular crystal is more complicated than for the inorganic and framework structures in which such simple behaviour is observed.
Review of the relevance of aberrant antigen expression by flow cytometry in myeloid neoplasms
Authors: Ossenkoppele Gert J. , van de Loosdrecht Arjan A. , Schuurhuis Gerrit Jan
Published: March 2011

This article reviews the use of aberrant antigen expression detected by flow cytometry in the diagnosis and clinical handling of acute myeloid leukaemia (AML) and the myelodysplastic syndromes (MDS). Such aberrancies offer a valuable tool for the proper classification of these myeloid malignancies according the World Health Organization 2008 classification. Aberrant antigen expression by flow cytometry is also important for prognostification. This review supports the view, that minimal residual disease detection methods that make use of such aberrancies should be part of the routine management of AML patients to guide therapy, but also suggests the introduction of flow cytometry in MDS for diagnosis and treatment decisions in the near future.
Feasibility of DNA diagnosis of haemoglobinopathies on coelocentesis
Authors: Giambona Antonino , Makrydimas George , Leto Filippo , Damiani Gianfranca , Jakil Maria Cristina , Picciotto Francesco , Renda Disma , Fiorino Rosanna , Renda Maria Concetta , Schillaci Giovanna , Gueli‐Alletti Desiderio , Nicolaides Kypros H. , Maggio Aurelio
Published: March 2011

At 5–12 weeks of gestation the amniotic sac is surrounded by celomic fluid, which contains cells of fetal origin. This fluid can be sampled by celocentesis, which involves the ultrasound‐guided insertion of a needle through the vagina. The aim of this study was to examine the feasibility of prenatal diagnosis of haemoglobinopathies from the celomic fluid using a specific protocol. Celocentesis was performed at 7–9 weeks gestation in 26 singleton pregnancies at risk for haemoglobinopathies. In 25 cases more than 30 fetal cells were recovered from the celomic fluid and in all these cases molecular analysis for haemoglobinopathies was possible and the results were confirmed by subsequent chorionic villus sampling or amniocentesis. The results of this study suggest that reliable diagnosis of thalassemia syndromes can be performed from 7 weeks gestation by celocentesis. Further work is necessary to demonstrate the safety of celocentesis before widespread use.
90Yttrium‐hydroxyapatite: a new therapeutic option for radioactive synovectomy in haemophilic synovitis
Authors: THOMAS S. , GABRIEL M. C. , DE SOUZA S. A. L. , GOMES S. C. , ASSI P. E. , PINHEIRO PERRI M. L. , LIBERATO W. , MATUSHITA C. S. , GUTFILEN B. , DA FONSECA L. M. B.
Published: March 2011

Summary.  Recurrent haemarthroses often lead to chronic synovitis in patients with haemophilia and von Willebrand disease. Radioactive synovectomy with yttrium‐90 (90Y) citrate is frequently used to treat this complication, usually with good results. Since 2006, the Nuclear Energy Research Institute (IPEN, Sao Paulo, Brazil) has produced hydroxyapatite particles labelled with 90Y for radioactive synovectomy. The aim of this study was to compare the results achieved by both forms of 90Y in the treatment of haemophilic synovitis. We included 221 joints from 136 patients (age range: 6–20 years), treated by one of the two radiopharmaceuticals, at the Hemocenter of Mato Grosso, Brazil. The outcomes analysed were the annual frequency of haemarthrosis, articular pain and joint range of motion before and 1 year after RS. Similar results were achieved regardless of whether 90Y hydroxyapatite or 90Y citrate was used, and results were independent of the joint type, age, gender, radiologic stage and presence of inhibitors. 90Y hydroxyapatite appears to be equivalent to the reference product 90Y citrate in the treatment of chronic synovitis associated with bleeding disorders.
Physicochemical aspects of hydrocolloid extract from the seeds of Lepidium sativum
Authors: Karazhiyan Hojjat , Razavi Seyed M. A. , Phillips Glyn O. , Fang Yapeng , Al‐Assaf Saphwan , Nishinari Katsuyoshi
Published: March 2011

Acid equivalent weight, intrinsic viscosity and FT‐IR measurements have demonstrated a polyelectrolyte nature to Lepidium sativum seed extract. The polyelectrolyte nature relates to the carboxyl groups carried by galacturonic acid and glucuronic acid unit. The seed extract exhibited pronounced shear thinning in steady shear rheology and a weak gel type behaviour in dynamic rheology when the concentration is high i.e. > 1%. Such behaviour suggests the ability of L. sativum seed extract to structure a liquid, thus showing the possibility of applying it as a novel thickener and stabiliser in aqueous systems. The characteristic could be due to a strong tendency of molecular association of L. sativum seed extract as found for high M/G ratio galactomannans, and possibly also the enhanced macromolecular entanglement due to relatively rigid chain conformation. Temperature dependence study showed that the rheological properties of L. sativum structured solution is stable against temperature variation.
Volatile composition and key flavour compounds of spirits from unifloral honeys
Authors: Pino Jorge A. , Fajardo Mario
Published: March 2011

The volatile components of industrially produced spirits from three unifloral honeys of campanilla morada (Ipomoea crassicaulis [Benth.] B.L. Robinson), citrus (Citrus spp. L.) and romerillo de costa (Viguiera dentata [Cav.] Spreng.) were studied by combined sensory and instrumental techniques. GC and GC‐MS analyses of the isolated extracts led to the detection of 205 volatile compounds, 150 of them were positively identified. In general, the most abundant classes were saturated alcohols, ethyl esters of saturated fatty acids and terpenes in all samples. Relative aroma intensity of individual volatile components was evaluated by aroma extract dilution analysis of solvent extracts, by gas chromatography‐olfactometry and by odour activity values. Results indicated that 11 compounds: ethanol, ethyl esters of isopentanoic, hexanoic, octanoic and decanoic acids, 2‐phenylethyl acetate, (E)‐β‐damascenone, hotrienol, decanal, methyl anthranilate and ethyl (E)‐cinnamate were the most potent odorants in the honey spirits.
Anxiety and uncertainty in Korean mothers of children with febrile convulsion: cross‐sectional survey
Authors: Ju Hyeon Ok , McElmurry Beverly J , Park Chang Gi , McCreary Linda , Kim Minju , Kim Eun Joo
Published: March 2011

Aims and objectives.  The purpose of this study was to assess the level of anxiety and uncertainty in Korean mothers of children with febrile convulsion and to indentify factors associated with maternal anxiety.

Background.  In general, febrile convulsions are harmless to the child, but parents perceive the convulsion as frightening. Previous authors of a few studies suggested that providing information was helpful for parents’ knowledge, attitude and fear about a febrile convulsion.

Design.  This was a descriptive, cross‐sectional survey.

Methods.  The sample comprised 102 mothers whose children had been diagnosed with a febrile convulsion and admitted to paediatric wards in five general hospitals in South Korea. The researchers gave the questionnaires to nursing departments for distribution and collection by paediatric nurses. To test differences in anxiety and uncertainty by participants’ characteristics, t‐tests and anova were conducted. Linear regression was used to identify factors associated with maternal state anxiety. Statistical significance level was set at 0·05.

Results.  A multiple linear regression of maternal anxiety showed that four statistically significant predictors explained 56% of the total variations of maternal anxiety. The significant predictors were uncertainty, frequency of febrile convulsion, income and information about febrile convulsion. Among the significant variables, uncertainty was the dominant contributing factor (p < 0·001).

Conclusions.  Anxiety in mothers of children with febrile convulsion was especially related to uncertainty, so health care providers can reduce anxiety through decreasing uncertainty.

Relevance to clinical practice.  For interventions to decrease maternal anxiety, provision of information and psychosocial support are needed for parents of hospitalised children with febrile convulsions.
Secondary prevention and learning needs post percutaneous coronary intervention (PCI): perspectives of both patients and nurses
Authors: Kilonzo Brid , O’Connell Rhona
Published: March 2011

Aims and objectives.  To evaluate the learning needs of patients post percutaneous coronary intervention from the perspective of both patients’ and cardiac nurses’.

Background.  Increasing numbers of patients with cardiovascular disease are managed using postpercutaneous transluminal coronary angioplasty. This paper presents findings of a study which explored the cardiac learning needs of these patients.

Design.  Descriptive survey from one cardiac unit where approximately 30 post percutaneous coronary intervention were performed per month.

Methods.  Self‐report data were provided by patients using an adaptation of the Nursing Information and Support scale for health‐related quality of life informational needs. This scale includes physical, psychosocial, emotional and disease‐specific dimensions. The questionnaire was also provided to cardiac nurses. Statistical tests applied were Spearman’s Correlation and the Mann–Whitney U test.

Results.  Patients (n = 33) and nurses (n = 13) completed the questionnaire. Disease‐specific items, physical action, psychosocial and emotional information were the categories that patients found most important. Cardiac nurses perceived physical action as least important and focused more on psychosocial and emotional issues. Individual items revealed the patients particularly valued their interaction with the nurses.

Conclusions.  Patients appear to be more concerned with their immediate state and disease rather than their psychosocial or emotional state. Mean rankings within scales demonstrate the value patients place on the nurse–patient relationship and the time needed for this.

Relevance to clinical practice.  Findings may be helpful to nurses who wish to addresses secondary prevention issues with patients’ post percutaneous coronary intervention who experience short hospital stays.