bluuebunny/crossref_metadata_2025 huggingface dataset:
Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria
Authors: Brinkhoff Thorsten , Fischer Doreen , Vollmers John , Voget Sonja , Beardsley Christine , Thole Sebastian , Mussmann Marc , Kunze Brigitte , Wagner-Döbler Irene , Daniel Rolf , Simon Meinhard
Published: December 2011

Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2 m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this cluster was only detected on aggregates up to a few meters above the sediment surface, but never in the fraction of free-living bacteria. A quantitative real-time PCR approach revealed that the MMC constituted up to 13% of total bacterial 16S rRNA genes in surface sediments of the North Sea. In a global survey, including sediments from the Mediterranean Sea, the Atlantic, Pacific and Indian Ocean and various climatic regions, the MMC was detected in most samples and to a water depth of 4300 m. Two fosmids of a library from sediment of the southern North Sea containing 16S rRNA genes affiliated with the MMC were sequenced. Both fosmids have a single unlinked 16S rRNA gene and no complete rRNA operon as found in most bacteria. No synteny to other myxobacterial genomes was found. The highest numbers of orthologues for both fosmids were assigned to Sorangium cellulosum and Haliangium ochraceum. Our results show that the MMC is an important and widely distributed but largely unknown component of marine sediment-associated bacterial communities.
Deep levels in H-irradiated GaAs1-xNx (x < 0.01) grown by molecular beam epitaxy
Authors: Shafi M. , Mari R. H. , Khatab A. , Henini M. , Polimeni A. , Capizzi M. , Hopkinson M.
Published: December 2011

Dilute nitride GaAs1-xNx layers have been grown by molecular beam epitaxy with nitrogen concentration ranging from 0.2% to 0.8%. These samples have been studied before and after hydrogen irradiation by using standard deep level transient spectroscopy (DLTS) and high resolution Laplace DLTS techniques. The activation energy, capture cross section and density of the electron traps have been estimated and compared with results obtained in N-free as-grown and H-irradiated bulk GaAs.
Window layer with p doped silicon oxide for high Voc thin-film silicon n-i-p solar cells
Authors: Biron Rémi , Pahud Celine , Haug Franz-Josef , Escarré Jordi , Söderström Karin , Ballif Christophe
Published: December 2011

We investigate the influence of the oxygen content in boron-doped nanocrystalline silicon oxide films (p-nc-SiOx) and introduce this material as window layer in n-i-p solar cells. The dependence of both, optical and electrical properties on the oxygen content is consistent with a bi-phase model which describes the p-nc-SiOx material as a mixture of an oxygen-rich (O-rich) phase and a silicon-rich (Si-rich) phase. We observe that increasing the oxygen content enhances the optical gap E04 while deteriorating the activation energy and the planar conductivity. These trends are ascribed to a higher volume fraction of the O-rich phase. Incorporated into n-i-p a-Si:H cells, p-nc-SiOx layers with moderate oxygen content yield open circuit voltage (Voc) up to 945 mV, which corresponds to a relative gain of 11% compared to an oxygen-free p-layer. As a similar gain is obtained on planar and on textured substrates, we attribute the increase in Voc to the higher work function of the p-nc-SiOx layer made possible by its wider band gap. These results are attained without changing the dilution ratio of the 250 nm thick intrinsic layer. We also observe an enhancement of 0.6 mA cm−2 in short circuit current density in the short wavelengths due to the higher transparency of the p-nc-SiOx layer. Finally, an initial efficiency of 9.9% for a single junction 250 nm a-Si:H n-i-p solar cell on plastic foil is achieved with the optimization of the p layer thickness, the doping ratio of the front transparent conductive oxide, and the optical properties of the back reflector.
Surfactant-driven dynamics of liquid lenses
Authors: Karapetsas George , Craster Richard V. , Matar Omar K.
Published: December 2011

Sessile liquid lenses spreading over a fluid layer, in the presence of Marangoni stresses due to surfactants, show a surprisingly wide range of interesting behaviour ranging from complete spreading of the lens, to spreading followed by retraction, to sustained pulsating oscillations. Models for the spreading process, the effects of surfactant at the moving contact line, sorption kinetics above and below the critical micelle concentration, are all incorporated into the modelling. Numerical results cast light upon the physical processes that drive these phenomena, and the regular oscillatory beating of lenses is shown to occur in specific limits.
Localization scheme for relativistic spinors
Authors: Ciupka J. , Hanrath M. , Dolg M.
Published: December 2011

A new method to determine localized complex-valued one-electron functions in the occupied space is presented. The approach allows the calculation of localized orbitals regardless of their structure and of the entries in the spinor coefficient matrix, i.e., one-, two-, and four-component Kramers-restricted or unrestricted one-electron functions with real or complex expansion coefficients. The method is applicable to localization schemes that maximize (or minimize) a functional of the occupied spinors and that use a localization operator for which a matrix representation is available. The approach relies on the approximate joint diagonalization (AJD) of several Hermitian (symmetric) matrices which is utilized in electronic signal processing. The use of AJD in this approach has the advantage that it allows a reformulation of the localization criterion on an iterative 2 × 2 pair rotating basis in an analytical closed form which has not yet been described in the literature for multi-component (complex-valued) spinors. For the one-component case, the approach delivers the same Foster-Boys or Pipek-Mezey localized orbitals that one obtains from standard quantum chemical software, whereas in the multi-component case complex-valued spinors satisfying the selected localization criterion are obtained. These localized spinors allow the formulation of local correlation methods in a multi-component relativistic framework, which was not yet available. As an example, several heavy and super-heavy element systems are calculated using a Kramers-restricted self-consistent field and relativistic two-component pseudopotentials in order to investigate the effect of spin-orbit coupling on localization.
Holmboe instability in non-Boussinesq fluids
Authors: Barros Ricardo , Choi Wooyoung
Published: December 2011

We perform the stability analysis for stratified shear flows whose density transition layer is much thinner than, and possibly, displaced with respect to, the velocity shear layer for which Holmboe instability along with the well-known Kelvin-Helmholtz (KH) instability is known to be present. Here, we provide a more complete picture of stability characteristics of stratified shear flows with taking into account the effects of non-negligible density increment for which the classical Boussinesq approximation is no longer valid. It is shown that, in addition to the Kelvin-Helmholtz and Holmboe instabilities for which two unstable modes exist, there is another instability with a single unstable mode so that the unstable waves excited by this instability mechanism propagate only in one direction. Depending on the physical parameters, this unstable mode may not be captured by the stability analysis under the Boussinesq approximation. With a better understanding of the instability mechanisms with including the non-Boussinesq effects, we could validate some of previous experimental results and provide new evidences to observations that have not been fully explained. The results are also expected to be useful in designing laboratory experiments to observe Holmboe waves and estimating their wavelengths and phase speeds.
The role of boron segregation in enhanced thermoelectric power factor of CoSi1−xBx alloys
Authors: Sun Hui , Morelli Donald T. , Kirkham Melanie J. , Meyer Harry M. , Lara-Curzio Edgar
Published: December 2011

We report on the influence of boron segregation on the thermoelectric properties of CoSi. Contrary to previous suggestions, and in stark contrast to aluminum substitution, boron does not enter the lattice on the Si site, but rather segregates to the grain boundaries in these alloys. Through a combination of x-ray diffraction, scanning electron microscope, and scanning Auger techniques, we present clear evidence of the formation of a CoB phase at the grain boundaries. Consistent with the failure of B to substitute for Si, we observe no changes in the electron concentration or the Seebeck coefficient under boron substitution. The electrical resistivity, on the other hand, displays a non-monotonic behavior with increasing boron concentration, first decreasing for small amounts of boron, before increasing at higher levels of substitution. We attribute this behavior to a combination of an initial healing effect of boron on microcracks, followed by the eventual increase in electron scattering by the secondary CoB phase at higher concentrations.
Observation of non-basal slip in semipolar InxGa1-xN/GaN heterostructures
Authors: Wu Feng , Young E. C. , Koslow I. , Hardy M. T. , Hsu P. S. , Romanov A. E. , Nakamura S. , DenBaars S. P. , Speck J. S.
Published: December 2011

In this paper, we report on observations of the operation of secondary slip systems to relieve lattice mismatch stress in semipolar InGaN/GaN heterostructures. Two-dimensional arrays of misfit dislocations were observed. Consistent with previous reports, primary relaxation occurred along the projected c direction via primary slip on the (0001) basal plane. In addition, evidence for secondary relaxation was detected in cathodoluminescence spectroscopy, high resolution x-ray diffraction, and transmission electron microscopy (TEM) studies. The secondary misfit dislocations were determined by TEM to have a-type Burgers vectors a/3 〈2¯110〉 and line directions along 〈42¯2¯3¯〉, consistent with prismatic slip on one of the m-type planes inclined with respect to the (112¯2) growth surface. Evidence of an additional slip system with approximate misfit line direction of type 〈202¯3¯〉 is also given.
Ferroelectric and electrical characterization of multiferroic BiFeO3 at the single nanoparticle level
Authors: Vasudevan R. K. , Bogle K. A. , Kumar A. , Jesse S. , Magaraggia R. , Stamps R. , Ogale S. B. , Potdar H. S. , Nagarajan V.
Published: December 2011

Ferroelectric BiFeO3 (BFO) nanoparticles deposited on epitaxial substrates of SrRuO3 (SRO) and La1−xSrxMnO3 (LSMO) were studied using band excitation piezoresponse spectroscopy (BEPS), piezoresponse force microscopy (PFM), and ferromagnetic resonance (FMR). BEPS confirms that the nanoparticles are ferroelectric in nature. Switching behavior of nanoparticle clusters were studied and showed evidence for inhomogeneous switching. The dimensionality of domains within nanoparticles was found to be fractal in nature, with a dimensionality constant of ∼1.4, on par with ferroelectric BFO thin-films under 100 nm in thickness. Ferromagnetic resonance studies indicate BFO nanoparticles only weakly affect the magnetic response of LSMO.
Measurements and simulations of shock wave generated plasma-vacuum interface
Authors: Kaganovich D. , Helle M. H. , Gordon D. F. , Ting A.
Published: December 2011

A controlled gradient gas jet was designed, constructed, and tested at the Naval Research Laboratory for the generation of high density and sharp gradient plasma regions. The gas jet uses a laser-generated shock wave to control the density gradient at the vacuum and neutral gas interface. The length scale of the laser produced plasma density gradient is fully controlled by the strength of the shock wave and can be varied continuously from100 μm for a weak shock to under 20 μm in case of strong shock wave as verified by the experimental results and simulations.
Genome-wide selection in poultry
Authors: Preisinger Rudolf
Published: December 2011

In poultry breeding programs owned by private companies, selection is done within closed populations based on comprehensive phenotypic data recording in both pure and cross line birds under standardised housing conditions. Due to sex-limited data recording, male selection for egg quality and production traits is based mainly on female sibling tests. Early selection of the most promising male within full sib families will improve the rate of genetic progress and can substantially reduce the generation interval. Several past studies, based mainly on microsatellites, have identified quantitative trait loci (QTL) for production and quality traits with only limited use in commercial programs. Genome-wide selection is still in its initial stages in which 10–40-K single nucleotide polymorphism (SNP) chips have been used so far. Due to sequencing of all major pure lines from DNA pools, a customised 600-K SNP chip has been developed for comprehensive genotyping of all commercial lines. Small-scale line-specific SNP chips will be developed afterwards in order to reduce costs for genotyping of male progeny during rearing periods. Only the most promising young males will be transferred to the breeding farm for performance testing and pedigree reproduction. Parental generation will still be genotyped with the comprehensive SNP chip and used for retraining and for imputing. The first results using 30-K SNP chips were obtained from a commercial line used for training, validation and selection, which have shown improved accuracy of prediction at a young age and so resulted in increased genetic gain. Genome-wide marker-assisted selection must prove its advantages over traditional methods including cost benefits.
The effect of sieve agitators and dispersing agent on the method of determining and expressing fineness of feed materials by sieving
Authors: Stark C. R. , Chewning C. G.
Published: December 2011

Research in both swine and poultry continue to investigate the optimal particle size for growth and gut health. Although researchers have reported the methods used to determine the particle size of the grain in a study, most reports have not provided details of the actual procedure. Although the standard method suggested adding both agitators and dispersing agents to facilitate the flow of material through the sieves there has been limited research as to whether these modifiers significantly change the particle size value. Researchers, laboratories, and feed mills that analyse samples without sieve agitators or a dispersing agent could overestimate the particle size and underestimate the distribution of the particles of a sample. Two experiments were conducted to determine the effect of adding sieve agitators and dispersing agent to the ANSI/ASAE S319.3 FEB03 ‘Method of Determining and Expressing Fineness of Feed Materials by Sieving’. The first experiment evaluated the effect of sieve agitator use and dispersing agent use on the geometric mean diameter (dgw) and geometric standard deviation (Sgw) of hammermill and roller mill corn samples. Whole corn was ground to produce samples that were classified as either coarse, medium, or fine. The second experiment evaluated the effect of sieve agitators, a dispersing agent, and the combination of agitators with a dispersing agent on dgw and Sgw of hammermill ground corn, wheat, and sorghum. The results of Expt 1 indicated that a decreased (P < 0.01) dgw resulted when agitators were added to the hammermill ground samples while a further decrease (P < 0.01) was observed due to the addition of the dispersing agent. The largest decrease in dgw was observed due to the addition of the dispersing agent. The addition of agitators to the roller mill samples only decreased the dgw of the medium grind sample. The dispersing agent decreased (P < 0.01) the dgw of roller mill samples. The addition of a dispersing agent consistently decreased the dgw of all the ground corn samples as compared with the standard method without modifiers. The results of Expt 2 were consistent with those of Expt 1 in that the addition of the dispersing agent and agitators decreased dgw values and appeared to have an additive effect in both corn and sorghum samples. The addition of a dispersing agent facilitated the flow of product through the sieves. The wider distribution (Sgw) indicated that a greater percentage of material flowed to the smaller sieves. The results of the experiments clearly showed the benefit of adding sieve agitators and a dispersing agent to facilitate the flow of material through the sieves, so that a better estimate of the micron diameter and particle size distribution could be achieved.
Integrative taxonomy demonstrates the unexpected synonymy between two predatory mite species: Cydnodromus idaeus and C. picanus (Acari:Phytoseiidae)
Authors: Tixier Marie-Stéphane , Tsolakis Haralabos , Ragusa Salvatore , Poinso Alix , Ferrero Maxime , Okassa Mireille , Kreiter Serge
Published: December 2011

Species of the mite family Phytoseiidae are well known as predators of mite pests all over the world. Their identification is thus of great interest for biological control. The specimens examined in this study belong to the species Cydnodromus idaeus (described from Brazil) and C. picanus (described from Chile). They were collected together on the same plant in Argentina. These species are mainly differentiated by the presence/absence of the dorsal solenostomes (gland openings) gd2. Some morphometric differences were observed between the Argentinian specimens and the type material of C. idaeus and C. picanus; however, they were not sufficient to support a species separation. Morphological and molecular analyses with two mtDNA (12S rRNA, CytB) and a nuclear DNA (ITS) marker showed no difference between Argentinian specimens with and without the solenostome gd2. Also, molecular differentiation between these latter specimens, C. picanus and C. idaeus, was very low, suggesting that all these individuals belong to the same species. Biological experiments confirm these results, as 75% of the progeny resulting from females with gd2 had gd2 present whereas all the descendants resulting from the females without gd2 had gd2 present too. The presence/absence of this solenostome seems thus to be variable within a species and cannot be used diagnostically. We conclude that all specimens from Argentina belong to C. idaeus and that C. picanus is a junior synonym of C. idaeus. The present results were unexpected as the presence/absence of solenostomes is used in Phytoseiidae identification keys and as one of a suite of diagnostic characters for discriminating between species. The consequences of these findings for the taxonomy of Phytoseiidae are discussed.
Immature stages of Euchirinae (Coleoptera:Scarabaeoidea): genera Cheirotonus and Propomacrus with comments on their phylogeny based on larval and adult characters
Authors: Šípek Petr , Janšta Petr , Král David
Published: December 2011

We report the discovery of the larvae of Propomacrus bimucronatus (Pallas, 1781) in their natural habitat; providing notes on their biology based on field observations and laboratory-bred specimens. We give a detailed description of Cheirotonus formosanus Ohaus, 1913 and P. cypriacus Alexis & Markis, 2002 larvae as well as a redescription of the immature stages of P. bimucronatus and present the first diagnosis of larval Euchirinae. Based on 105 morphological and ecological characters of adults and larvae in 24 taxa of Scarabaeoidea, we discuss the phylogenetic relationships of Euchirinae within the group. Our results corroborate Euchirinae monophyly, supported by two larval synapomorphic characters; however, no adult autapomorphic characters were detected. The results of 15 separate phylogenetic analyses (differing in the set of terminalia, characters and in the optimality criteria) indicate a possible sister group relationship between Euchirinae and a clade comprising Melolonthinae + Rutelinae + Dynastinae, with Cetoniinae being a sister group to the whole clade. Larval characters represent a valuable source of information for the systematics of Scarabaeoidea; however, special effort should be paid to improve the still unsatisfactory sampling of immature data.
Mid-latitude afforestation shifts general circulation and tropical precipitation
Authors: Swann Abigail L. S. , Fung Inez Y. , Chiang John C. H.
Published: December 2011

We show in climate model experiments that large-scale afforestation in northern mid-latitudes warms the Northern Hemisphere and alters global circulation patterns. An expansion of dark forests increases the absorption of solar energy and increases surface temperature, particularly in regions where the land surface is unable to compensate with latent heat flux due to water limitation. Atmospheric circulation redistributes the anomalous energy absorbed in the northern hemisphere, in particular toward the south, through altering the Hadley circulation, resulting in the northward displacement of the tropical rain bands. Precipitation decreases over parts of the Amazon basin affecting productivity and increases over the Sahel and Sahara regions in Africa. We find that the response of climate to afforestation in mid-latitudes is determined by the amount of soil moisture available to plants with the greatest warming found in water-limited regions. Mid-latitude afforestation is found to have a small impact on modeled global temperatures and on global CO
2
, but regional heating from the increase in forest cover is capable of driving unintended changes in circulation and precipitation. The ability of vegetation to affect remote circulation has implications for strategies for climate mitigation.
Treating His Imperial Majesty's Warts: British Policy towards Iran 1977–79
Authors: Posnett Edward
Published: December 2011

Analysis of British policy towards Iran during the shah's final years has tended to be the preserve of those who formulated it. In general, it has focused on the extent to which British policymakers predicted the events of the Iranian revolution (published accounts by British policymakers include: Anthony Parsons,The Pride and The Fall: Iran 1974–1979(1984); David Owen,Time to Declare(1991); Ivor Lucas,A Road To Damascus: Mainly Diplomatic Memoirs from the Middle East(1997), and “Revisiting the Decline and Fall of the Shah of Iran” (2009)). This article is different in both its sources and scope. Unlike any other published study on Anglo-Iranian relations, it relies on government records recently released in the National Archives. Instead of focusing on the British response to the Iranian revolution, it seeks to account for the strength of the shah's leverage and illustrate its consequences during one of the most important periods in Iran's history.
Analysis of yeast endocytic site formation and maturation through a regulatory transition point
Authors: Carroll Susheela Y. , Stimpson Helen E. M. , Weinberg Jasper , Toret Christopher P. , Sun Yidi , Drubin David G.
Published: December 2011

The earliest stages of endocytic site formation and the regulation of endocytic site maturation are not well understood. Here we analyzed the order in which the earliest proteins are detectable at endocytic sites in budding yeast and found that an uncharacterized protein, Pal1p/Ydr348cp, is also present at the initial stages of endocytosis. Because Ede1p (homologue of Eps15) and clathrin are the early-arriving proteins most important for cargo uptake, their roles during the early stages of endocytosis were examined more comprehensively. Ede1p is necessary for efficient recruitment of most early-arriving proteins, but not for the recruitment of the adaptor protein Yap1802p, to endocytic sites. The early-arriving proteins, as well as the later-arriving proteins Sla2p and Ent1/2p (homologues of Hip1R and epsins), were found to have longer lifetimes in CLC1-knockout yeast, which indicates that clathrin light chain facilitates the transition from the intermediate to late coat stages. Cargo also arrives during the early stages of endocytosis, and therefore its effect on endocytic machinery dynamics was investigated. Our results are consistent with a role for cargo in regulating the transition of endocytic sites from the early stages of formation to the late stages during which vesicle formation occurs.
Zonula occludens-1 and -2 regulate apical cell structure and the zonula adherens cytoskeleton in polarized epithelia
Authors: Fanning Alan S. , Van Itallie Christina M. , Anderson James M.
Published: December 2011

The structure and function of both adherens (AJ) and tight (TJ) junctions are dependent on the cortical actin cytoskeleton. The zonula occludens (ZO)-1 and -2 proteins have context-dependent interactions with both junction types and bind directly to F-actin and other cytoskeletal proteins, suggesting ZO-1 and -2 might regulate cytoskeletal activity at cell junctions. To address this hypothesis, we generated stable Madin-Darby canine kidney cell lines depleted of both ZO-1 and -2. Both paracellular permeability and the localization of TJ proteins are disrupted in ZO-1/-2–depleted cells. In addition, immunocytochemistry and electron microscopy revealed a significant expansion of the perijunctional actomyosin ring associated with the AJ. These structural changes are accompanied by a recruitment of 1-phosphomyosin light chain and Rho kinase 1, contraction of the actomyosin ring, and expansion of the apical domain. Despite these changes in the apical cytoskeleton, there are no detectable changes in cell polarity, localization of AJ proteins, or the organization of the basal and lateral actin cytoskeleton. We conclude that ZO proteins are required not only for TJ assembly but also for regulating the organization and functional activity of the apical cytoskeleton, particularly the perijunctional actomyosin ring, and we speculate that these activities are relevant both to cellular organization and epithelial morphogenesis.
Minimal cut sets in a metabolic network are elementary modes in a dual network
Authors: Ballerstein Kathrin , von Kamp Axel , Klamt Steffen , Haus Utz-Uwe
Published: December 2011

Motivation: Elementary modes (EMs) and minimal cut sets (MCSs) provide important techniques for metabolic network modeling. Whereas EMs describe minimal subnetworks that can function in steady state, MCSs are sets of reactions whose removal will disable certain network functions. Effective algorithms were developed for EM computation while calculation of MCSs is typically addressed by indirect methods requiring the computation of EMs as initial step.

Results: In this contribution, we provide a method that determines MCSs directly without calculating the EMs. We introduce a duality framework for metabolic networks where the enumeration of MCSs in the original network is reduced to identifying the EMs in a dual network. As a further extension, we propose a generalization of MCSs in metabolic networks by allowing the combination of inhomogeneous constraints on reaction rates. This framework provides a promising tool to open the concept of EMs and MCSs to a wider class of applications.

Contact:  utz-uwe.haus@math.ethz.ch; klamt@mpi-magdeburg.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Targeted MRI Contrast Agents for Pediatric Hepatobiliary Disease
Authors: Courtier Jesse L. , Perito Emily R. , Rhee Sue , Tsai Patrika , Heyman Melvin B. , MacKenzie John D.
Published: December 2011

New options are available for the magnetic resonance imaging (MRI) assessment of pediatric hepatobiliary disease. This article describes the potential utility for MRI with contrast agents tailored for hepatobiliary imaging. MRI contrast agents that preferentially target the liver may be helpful in characterizing liver masses and bile duct abnormalities in select children. The imaging approach is noninvasive and relatively rapid to perform. It also provides anatomic and functional information and is a radiation‐free alternative to other imaging strategies. This relatively new imaging procedure is placed in the context of more established imaging modalities. The pharmacokinetics, technical considerations, and potential applications of these hepatobiliary‐specific contrast agents also are discussed.
Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several novel genotypes and a largely conserved genotype constellation
Authors: Matthijnssens Jelle , Miño Samuel , Papp Hajnalka , Potgieter Christiaan , Novo Luis , Heylen Elisabeth , Zeller Mark , Garaicoechea Lorena , Badaracco Alejandra , Lengyel György , Kisfali Péter , Cullinane Ann , Collins P. J. , Ciarlet Max , O’Shea Helen , Parreño Viviana , Bányai Krisztián , Barrandeguy María , Van Ranst Marc
Published: December 2011

In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P[18], RVA/Horse-wt/IRL/03V04954/2003/G3P[12] and RVA/Horse-wt/IRL/04V2024/2004/G14P[12] from Europe; RVA/Horse-wt/ARG/E30/1993/G3P[12], RVA/Horse-wt/ARG/E403/2006/G14P[12] and RVA/Horse-wt/ARG/E4040/2008/G14P[12] from Argentina; and RVA/Horse-wt/ZAF/EqRV-SA1/2006/G14P[12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to non-equine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines.
Phenotypes of vesicular stomatitis virus mutants with mutations in the PSAP motif of the matrix protein
Authors: Obiang Linda , Raux Hélène , Ouldali Malika , Blondel Danielle , Gaudin Yves
Published: December 2011

Vesicular stomatitis virus (VSV) matrix protein (M) has a flexible amino-terminal part that recruits cellular partners. It contains a dynamin-binding site that is required for efficient virus assembly, and two motifs, 24PPPY27 and 37PSAP40, that constitute potential late domains. Late domains are present in proteins of several enveloped viruses and are involved in the ultimate step of the budding process (i.e. fission between viral and cellular membranes). In baby hamster kidney (BHK)-21 cells, it has been demonstrated that the 24PPPY27 motif binds the Nedd4 (neuronal precursor cell-expressed developmentally downregulated 4) E3 ubiquitin ligase for efficient virus budding and that the 37PSAP40 motif, although conserved among M proteins of vesiculoviruses, does not possess late-domain activity. In this study, we have re-examined the contribution of the PSAP motif to VSV budding. First, we demonstrate that VSV M indeed binds TSG101 [tumour susceptibility gene 101; a component of the ESCRT1 (endosomal sorting complex required for transport 1)] through its PSAP motif. Second, we analysed the phenotype of several recombinant mutants. We show that a double mutant with point mutations in both the PSAP and the PPPY motifs is impaired compared with a single mutant in the PPPY motif, indicating that the PSAP motif partially compensates for the lack of the PPPY motif. Mutants’ phenotypes depend on cell lines: in CERA (chicken embryo-related, Alger clone) cells, a recombinant virus with a single mutation in the PSAP motif was impaired compared with the wild type, and a mutant with a single mutation in the dynamin-binding motif was much less impaired in Vero cells than in BSR (clones of BHK-21) cells. These results have implications for the VSV budding pathway that will be discussed.
Feline Immunodeficiency Virus-Based Lentiviral Vectors: Figure 1.
Authors: Saenz Dyana T. , Barraza Román , Loewen Nils , Teo Wulin , Poeschla Eric M.
Published: December 2011

Feline immunodeficiency virus (FIV)-based lentiviral vectors are useful for introducing integrated transgenes into nondividing human cells. This article describes the production and use of advanced generation FIV vectors. Key properties are discussed in comparison to other lentiviral vectors. Additional topics include the practical implications of species-specific retroviral restriction factors and the production of nonintegrating FIV vectors.
Rapid Mounting of Adult Drosophila Structures in Hoyer’s Medium
Authors: Stern David L. , Sucena Elio
Published: December 2011

The Drosophila cuticle carries a rich array of morphological details. Thus, cuticle examination has had a central role in the history of genetics. This protocol describes a procedure for mounting adult cuticles in Hoyer’s medium, a useful mountant for both larval and adult cuticles. The medium digests soft tissues rapidly, leaving the cuticle cleared for observation. In addition, samples can be transferred directly from water to Hoyer’s medium. However, specimens mounted in Hoyer’s medium degrade over time. For example, the fine denticles on the larval dorsum are best observed soon after mounting; they begin to fade after 1 week, and can disappear completely after several months. More robust features, such as the ventral denticle belts, will persist for a longer period of time. Because adults cannot profitably be mounted whole in Hoyer’s medium, some dissection is necessary.
Isolation of DNA from Red Blood Cells in Xenopus
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M.
Published: December 2011

The amphibian Xenopus laevis is an important model organism that is particularly valuable for studies of early vertebrate development. Genomic DNA constitutes the total genetic information of an organism and it is used for Southern blotting, for determining gene structure, and for detecting the presence or absence of genes of interest. Genomic DNA can be extracted from Xenopus red blood cells, which are unlike the mammalian equivalent in that they contain nuclei. This article describes a protocol for the isolation of genomic DNA from frog red blood cells.
Magnetic Trap Construction: Figure 1.
Authors: Lionnet Timothée , Allemand Jean-François , Revyakin Andrey , Strick Terence R. , Saleh Omar A. , Bensimon David , Croquette Vincent
Published: December 2011

In recent years, techniques have been developed to study and manipulate single molecules of DNA and other biopolymers. In one such technique, the magnetic trap, a single DNA molecule is bound at one end to a glass surface and at the other to a magnetic microbead. Small magnets, whose position and rotation can be controlled, pull on and rotate the microbead. This provides a simple method to stretch and twist the molecule. The system allows one to apply and measure forces ranging from 10−3 to >100 picoNewtons (pN). In contrast to other techniques, the force measurement is absolute and does not require calibration of the sensor. This protocol describes a procedure for building and using a magnetic trap. It gives a method for constructing a microchamber suitable for magnetic tweezers studies, including antibody coating and passivation. It also describes a series of simple steps to achieve end-labeling of DNA anchoring fragments. One anchoring fragment is biotin-labeled and the other is labeled with digoxigenin. The anchoring fragments are then digested and ligated to a central DNA region containing the sequence of interest. The biotinylated DNA is adsorbed onto streptavidin-coated magnetic beads, and the DNA–bead mixture attaches specifically to the antidigoxigenin-coated surface of the microchamber.
Imaging Synaptic Vesicle Recycling by Staining and Destaining Vesicles with FM Dyes
Authors: Hoopmann Peer , Rizzoli Silvio O. , Betz William J.
Published: December 2011

The synaptic vesicle is the essential organelle of the synapse. Many approaches for studying synaptic vesicle recycling have been devised, one of which, the styryl (FM) dye, is well suited for this purpose. FM dyes reversibly stain, but do not permeate, membranes; hence they can specifically label membrane-bound organelles. Their quantum yield is drastically higher when bound to membranes than when in aqueous solution. This protocol describes the imaging of synaptic vesicle recycling by staining and destaining vesicles with FM dyes. Nerve terminals are stimulated (electrically or by depolarization with high K+) in the presence of dye, their vesicles are then allowed to recycle, and finally dye is washed from the chamber. In neuromuscular junction (NMJ) preparations, movements of the muscle must be inhibited if imaging during stimulation is desired (e.g., by application of curare, a potent acetylcholine receptor inhibitor). The main characteristics of FM dyes are also reviewed here, as are recent FM dye monitoring techniques that have been used to investigate the kinetics of synaptic vesicle fusion.
Curcumin promotes differentiation of glioma‐initiating cells by inducing autophagy
Authors: Zhuang Wenzhuo , Long Linmei , Zheng Bingxin , Ji Wenjun , Yang Neng , Zhang Qingqing , Liang Zhongqin
Published: December 2011

Glioblastoma (GBM) is a highly aggressive brain tumor characterized by increased proliferation and resistance to chemotherapy and radiotherapy. Recently, a growing body of evidence suggests that glioma‐initiating cells (GICs) are responsible for the initiation and recurrence of GBM. However, the factors determining the differential development of GICs remain poorly defined. In the present study, we show that curcumin, a natural compound with low toxicity in normal cells, significantly induced differentiation of GICs in vivo and in vitro by inducing autophagy. Moreover, curcumin also suppressed tumor formation on intracranial GICs implantation into mice. Our results suggest that autophagy plays an essential role in the regulation of GIC self‐renewal, differentiation, and tumorigenic potential, suggesting autophagy could be a promising therapeutic target in a subset of glioblastomas. This is the first evidence that curcumin has differentiating and tumor‐suppressing actions on GICs. (Cancer Sci 2012; 103: 684–690)
Using ecological niche modelling to evaluate niche stability in deep time
Authors: Stigall Alycia L.
Published: December 2011

Aim  To investigate relative niche stability in species responses to various types of environmental pressure (biotic and abiotic) on geological time‐scales using the fossil record.

Location  The case study focuses on Late Ordovician articulate brachiopods of the Cincinnati Arch in eastern North America.

Methods  Species niches were modelled for a suite of fossil brachiopod species based on five environmental variables inferred from sedimentary parameters using GARP and Maxent. Niche stability was assessed by comparison of (1) the degree of overlap of species distribution models developed for a time‐slice and those generated by projecting niche models of the previous time‐slice onto environmental layers of a second time‐slice using GARP and Maxent, (2) Schoener’s D statistic, and (3) the similarity of the contribution of each environmental parameter within Maxent niche models between adjacent time‐slices.

Results  Late Ordovician brachiopod species conserved their niches with high fidelity during intervals of gradual environmental change but responded to inter‐basinal species invasions through niche evolution. Both native and invasive species exhibited similar levels of niche evolution in the invasion and post‐invasion intervals. Niche evolution was related mostly to decreased variance within the former ecological niche parameters rather than to shifts to new ecospace.

Main conclusions  Although the species examined exhibited morphological stasis during the study interval, high levels of niche conservatism were observed only during intervals of gradual environmental change. Rapid environmental change, notably inter‐basinal species invasions, resulted in high levels of niche evolution among the focal taxa. Both native and invasive species responded with similar levels of niche evolution during the invasion interval and subsequent environmental reorganization. The assumption of complete niche conservatism frequently employed in ecological niche modelling (ENM) analyses to forecast or hindcast species geographical distributions is more likely to be accurate for climate change studies than for invasive species analyses over geological time‐scales.
On a hidden game board: the patient’s first encounter with emergency care at the emergency department
Authors: Elmqvist Carina , Fridlund Bengt , Ekebergh Margaretha
Published: December 2011

Aims and objectives.  Describe and understand the patient’s first encounter in emergency care at the emergency department, as experienced by the patient, next of kin and first providers from different professions.

Background.  The emergency department is most often described as having high levels of satisfaction with the quality of care delivered. Although the patients appreciate clinical competence, quick assessment and technical skills, a close connection between patient satisfaction and vulnerability has been shown.

Design.  A lifeworld research perspective was used in four different situations at the emergency department.

Methods.  The data consisted of 14 open‐ended interviews with patients, next of kin and first providers.

Results.  The analysis showed that narratives of the past, present and future characterises the encounter where mutual narratives form a foundation for those involved in the encounter. Five constituents further described the variations; vague rules and conflicting expectations in the encounter, an encounter with the biological body, ‘courtesy encounters’, isolated in a timeless encounter, striving for meaning in the encounter.

Discussion.  Instead of expecting the patients to know the unwritten rules of the emergency department, the first providers could give clear information about expected waiting times and what to expect in the encounter. The challenge is to make a meaningful comprehensible context for all involved which can be generated in the interpersonal encounter.

Relevance to clinical practice.  The findings highlight the importance of disclosing the rules of the game by means of giving clear information which would give possibilities for the patient to maintain control, for strengthening the nurse’s role as the patients’ advocate and for strengthening the effort for an emergency department to become more of a learning organisation.
Cord blood Tregs with stable FOXP3 expression are influenced by prenatal environment and associated with atopic dermatitis at the age of one year
Authors: Hinz D. , Bauer M. , Röder S. , Olek S. , Huehn J. , Sack U. , Borte M. , Simon J. C. , Lehmann I. , Herberth G. ,   for the LINA study group
Published: December 2011

Background:

Regulatory T cells (Tregs) with stable FOXP3 expression are characterized by a specific demethylated region in the FOXP3 gene (Treg‐specific demethylated region, TSDR). The aim of this study was to analyse the influence of prenatal factors on cord blood Treg numbers, as detected by changes in the TSDR demethylation, and the subsequent risk for allergic diseases.

Methods:

Analyses were performed within the LINA study in blood samples from pregnant women (34th gestational week) and in cord blood (n = 346 mother–child pairs). Treg numbers were detected via DNA demethylation in the FOXP3 TSDR. At age 1, total and specific IgE was measured in children's blood. In addition, maternal cytokine production (Th1/Th2/Th17) was analysed. Exposure and disease outcomes were assessed by questionnaires.

Results:

Boys had lower Treg numbers compared with girls (P < 0.001). Parental atopy history, particularly maternal hay fever and paternal asthma were related to lower Treg numbers in cord blood (adj. MR = 0.81, 95% CI = 0.68–0.97; adj. MR = 0.60, 95% CI = 0.45–0.81). Maternal cytokines (IL‐13, IL‐17E and IFN‐γ) and maternal smoking/exposure to tobacco smoke during pregnancy were also associated with decreased cord blood Treg numbers (adj. MR = 0.89, 95% CI = 0.97–1.00). Children with lower Treg numbers at birth had a higher risk to develop atopic dermatitis (adj. OR = 1.55, 95% CI = 1.00–2.41) and sensitization to food allergens (adj. OR = 1.55, 95% CI = 1.06–2.25) during the first year of life.

Conclusions:

These results indicate that both genetic and environmental factors presumably influence the development of foetal Tregs. Low cord blood Treg numbers may predict early atopic dermatitis.
Characterization and Complete Nucleotide Sequence of Two Isolates of Tomato mosaic virus
Authors: Hu Qiong , Jiang Tong , Xue Chaoyang , Zhou Xueping
Published: December 2011

Two virus isolates, designated S1 and TL, were obtained from tomato and camellia root in China, respectively, and their host ranges, symptomatology, serological reactions and complete nucleotide sequences were determined. Isolate TL systemically infected Chenopodium amaranticolor causing leaf chlorosis, but the isolate S1 induced only local necrotic lesions. The complete nucleotide sequences of S1 and TL were determined and consisted of 6384 and 6383 nucleotides (Genbank accessions AJ132845 and AJ417701), respectively. Sequence analysis revealed that both isolates have the highest nucleotide sequence identity (over 92%) with Tomato mosaic virus (ToMV), but less (80%) with other tobamoviruses. Phylogenetic analyses based on the amino acid sequences of 30‐kD and 17.5‐kD proteins also indicated that both the isolates form a cluster with the isolates of ToMV. These data suggest that S1 and TL are isolates of ToMV. The possible reasons that TL infected C. amaranticolor systemically but S1 induced only local necrotic lesions are discussed.