The effect of the magnetic field of the secondary star in dwarf novae

We investigate the effect of a secondary star magnetic field on the accretion disc dynamics of dwarf novae. Simulations have been carried out with a particle code and a dipolar magnetic field structure. The magnetic field acts to remove angular momentum from the disc material, increasing the inward mass flow. This makes the accretion disc more centrally condensed, causing a reduction in the recurrence time for dwarf nova outbursts. We have produced Doppler tomograms and light curves which may be compared with observations. These tomograms are significantly different from those produced in the absence of a magnetic field on the secondary. We derive an upper limit to the magnetic moment of the secondary star in UGem of mu_2<2x10^32 A m^2. The magnetic truncation of the accretion disc produces resonance phenomena similar to those seen in the superoutbursts of SUUMa systems. While these have not been observed for systems like UGem, observations of the SUUMa systems provide us with a useful diagnostic of the disc-field interaction. We are able to place an upper limit on the magnetic moment of the secondary in ZCha of mu_2<1x10^30 A m^2.

How the double spherules of infectious bronchitis virus impact our understanding of RNA virus replicative organelles

Powered by advances in electron tomography, recent studies have extended our understanding of how viruses construct "replication factories" inside infected cells. Their function, however, remains an area of speculation with important implications for human health. It is clear from these studies that whatever their purpose, organelle structure is dynamic (M. Ulasli, M. H. Verheije, C. A. de Haan, and F. Reggiori, Cell. Microbiol. 12:844-861, 2010) and intricate (K. Knoops, M. Kikkert, S. H. Worm, J. C. Zevenhoven-Dobbe, Y. van der Meer, et al., PLOS Biol. 6:e226, 2008). But by concentrating on medically important viruses, these studies have failed to take advantage of the genetic variation inherent in a family of viruses that is as diverse as the archaea, bacteria, and eukaryotes combined (C. Lauber, J. J. Goeman, M. del Carmen Parquet, P. T. Nga, E. J. Snijder, et al., PLOS Pathog. 9:e1003500, 2013). In this climate, Maier et al. (H. J. Maier, P. C. Hawes, E. M. Cottam, J. Mantell, P. Verkade, et al., mBio 4:e00801-13, 2013) explored the replicative structures formed by an avian coronavirus that appears to have diverged at an early point in coronavirus evolution and shed light on controversial aspects of viral biology.

Flow structure and near-field dispersion in arrays of building-like obstacles

Dispersion in the near-field region of localised releases in urban areas is difficult to predict because of the strong influence of individual buildings. Effects include upstream dispersion, trapping of material into building wakes and enhanced concentration fluctuations. As a result, concentration patterns are highly variable in time and mean profiles in the near field are strongly non-Gaussian. These aspects of near-field dispersion are documented by analysing data from direct numerical simulations in arrays of building-like obstacles and are related to the underlying flow structure. The mean flow structure around the buildings is found to exert a strong influence over the dispersion of material in the near field. Diverging streamlines around buildings enhance lateral dispersion. Entrainment of material into building wakes in the very near field gives rise to secondary sources, which then affect the subsequent dispersion pattern. High levels of concentration fluctuations are also found in this very near field; the fluctuation intensity is of order 2 to 5.

Secondary cyclogenesis along an occluded front leading to damaging wind gusts: windstorm Kyrill, January 2007

Windstorm Kyrill affected large parts of Europe in January 2007 and caused widespread havoc and loss of life. In this study the formation of a secondary cyclone, Kyill II, along the occluded front of the mature cyclone Kyrill and the occurrence of severe wind gusts as Kyrill II passed over Germany are investigated with the help of high-resolution regional climate model simulations. Kyrill underwent an explosive cyclogenesis south of Greenland as the storm crossed polewards of an intense upper-level jet stream. Later in its life cycle secondary cyclogenesis occurred just west of the British Isles. The formation of Kyrill II along the occluded front was associated (a) with frontolytic strain and (b) with strong diabatic heating in combination with a developing upper-level shortwave trough. Sensitivity studies with reduced latent heat release feature a similar development but a weaker secondary cyclone, revealing the importance of diabatic processes during the formation of Kyrill II. Kyrill II moved further towards Europe and its development was favored by a split jet structure aloft, which maintained the cyclone’s exceptionally deep core pressure (below 965 hPa) for at least 36 hours. The occurrence of hurricane force winds related to the strong cold front over North and Central Germany is analyzed using convection-permitting simulations. The lower troposphere exhibits conditional instability, a turbulent flow and evaporative cooling. Simulation at high spatio-temporal resolution suggests that the downward mixing of high momentum (the wind speed at 875 hPa widely exceeded 45 m s-1) accounts for widespread severe surface wind gusts, which is in agreement with observed widespread losses.

New insights into the structure of exotic nuclei using the RISING active stopper

This conference paper outlines the operation and some of the preliminary physics results using the GSI RISING active stopper. Data are presented from an experiment using combined isomer and beta‐delayed gamma‐ray spectroscopy to study low‐lying spectral and decay properties of heavy‐neutron‐rich nuclei around A∼190 produced following the relativistic projectile fragmentation of 208Pb primary beam. The response of the RISING active stopper detector is demonstrated for both the implantation of heavy secondary fragments and in‐situ decay of beta‐particles. Beta‐delayed gamma‐ray spectroscopy following decays of the neutron‐rich nucleus 194Re is presented to demonstrate the experimental performance of the set‐up. The resulting information inferred from excited states in the W and Os daughter nuclei is compared with results from Skyrme Hartree‐Fock predictions of the evolution of nuclear shape.

Genetic algorithm inversion of the average 1D crustal structure using local and regional earthquakes

Knowing the best 1D model of the crustal and upper mantle structure is useful not only for routine hypocenter determination, but also for linearized joint inversions of hypocenters and 3D crustal structure, where a good choice of the initial model can be very important. Here, we tested the combination of a simple GA inversion with the widely used HYPO71 program to find the best three-layer model (upper crust, lower crust, and upper mantle) by minimizing the overall P- and S-arrival residuals, using local and regional earthquakes in two areas of the Brazilian shield. Results from the Tocantins Province (Central Brazil) and the southern border of the Sao Francisco craton (SE Brazil) indicated an average crustal thickness of 38 and 43 km, respectively, consistent with previous estimates from receiver functions and seismic refraction lines. The GA + HYPO71 inversion produced correct Vp/Vs ratios (1.73 and 1.71, respectively), as expected from Wadati diagrams. Tests with synthetic data showed that the method is robust for the crustal thickness, Pn velocity, and Vp/Vs ratio when using events with distance up to about 400 km, despite the small number of events available (7 and 22, respectively). The velocities of the upper and lower crusts, however, are less well constrained. Interestingly, in the Tocantins Province, the GA + HYPO71 inversion showed a secondary solution (local minimum) for the average crustal thickness, besides the global minimum solution, which was caused by the existence of two distinct domains in the Central Brazil with very different crustal thicknesses. (C) 2010 Elsevier Ltd. All rights reserved.

THE ENDOPARASITE PILOSTYLES ULEI (APODANTHACEAE - CUCURBITALES) INFLUENCES WOOD STRUCTURE IN THREE HOST SPECIES OF MIMOSA

Pilostyles species (Apodanthaceae) are endoparasites in stems of the plant family Fabaceae. The body comprises masses of parenchyma in the host bark and cortex, with sinkers, comprising groups of twisted tracheal elements surrounded by parenchyma that enter the secondary xylem of the host plant. Here we report for the first time the effects of Pilostyles parasitism on host secondary xylem. We obtained healthy and parasitized stems from Mimosa foliolosa, M. maguirei and M. setosa and compared vessel element length, fiber length, vessel diameter and vessel frequency, measured through digital imaging. Also, tree height and girth were compared between healthy and parasitized M. setosa. When parasitized, plant size, vessel diameter, vessel element length and fiber length are all less than in healthy plants. Also, vessel frequency is greater and vessels are narrower in parasitized stems. These responses to parasitism are similar to those observed in stressed plants. Thus, hosts respond to the parasite by changing its wood micromorphology in favour of increased hydraulic safety.

Edge effects as the principal cause of area effects on birds in fragmented secondary forest

Bird communities in tropical forests are strongly affected by both patch area and habitat edges. The fact that both effects are intrinsically confounded in space raises questions about how these two widely reported ecological patterns interact, and whether they are independent or simply different spatial manifestations of the same phenomenon. Moreover, do small patches of secondary forest, in landscapes where the most sensitive species have gone locally extinct, exhibit similar patterns to those previously observed in fragmented and continuous primary forests? We addressed these questions by testing edge-related differences in vegetation structure and bird community composition at 31 sites in fragmented and continuous landscapes in the imperilled Atlantic forest of Brazil. Over a two-year period, birds were captured with mist nets to a standardized effort of 680 net-hours at each site (similar to 22 000 net-hours resulting in 3381 captures from 114 species). We found that the bird community in patches of secondary forest was degraded in species composition compared to primary continuous forest, but still exhibited a strong response to edge effects. In fragmented secondary forests, edge and area effects also interacted, such that the magnitude of edge to interior differences on bird community composition declined markedly with patch size. The change in bird species composition between forest interiors and edges was similar to the change in community composition between large and small patches (because species had congruent responses to edge and area), but after controlling for edge effects community composition was no longer affected by patch area. Our results show that although secondary forests hold an impoverished bird community, ecological patterns such as area and edge effects are similar to those reported for primary forests. Our data provide further evidence that edge effects are the main drivers of area effects in fragmented landscapes.

Forest structure in a mosaic of rainforest sites: The effect of fragmentation and recovery after clear cut

A variety of human-induced disturbances such as forest fragmentation and recovery after deforestation for pasture or agricultural activities have resulted in a complex landscape mosaic in the Una region of northeastern Brazil. Using a set of vegetation descriptors, we investigated the main structural changes observed in forest categories that comprise the major components of the regional landscape and searched for potential key descriptors that could be used to discriminate among different forest categories. We assessed the forest structure of five habitat categories defined as (I) interiors and (2) edges of large fragments of old-growth forest (>1000 ha), (3) interiors and (4) edges of small forest fragments (<100 ha), and (5) early secondary forests. Forest descriptors used here were: frequency of herbaceous lianas and woody climbers, number of standing dead trees, number of fallen trunks, litter depth, number of pioneer plants (early secondary and shade-intolerant species), vertical foliage stratification profile and distribution Of trees in different diameter classes. Edges and interiors of forest fragments were significantly different only in the number of standing dead trees. Secondary forests and edges of fragments showed differences in litter depth, fallen trunks and number of pioneer trees, and secondary forests were significantly different from fragment interiors in the number of standing dead trees and the number of pioneer trees. Horizontal and vertical structure evaluated via ordination analysis showed that fragment interiors, compared to secondary forests, were characterized by a greater number of medium (25-35 cm) and large (35-50 cm) trees and smaller numbers of thin trees (5-10 cm). There was great heterogeneity at the edges of small and large fragments, as these sites were distributed along almost the entire gradient. Most interiors of large and small fragments presented higher values of foliage densities at higher strata ( 15-20 m and at 20-25 m height), and lower densities at 1-5 m. All secondary forests and some fragment edge sites showed an opposite tendency. A discriminant function highlighted differences among forest categories, with transects of large fragment interiors and secondary forests representing two extremes along a disturbance gradient determined by foliage structure (densities at 15-20 m and 20-25 m), with the edges of both large and small fragments and the interiors of small fragments scattered across the gradient. The major underlying processes determining patterns of forest disturbance in the study region are discussed, highlighting the importance of forest fragments, independently of its size, as forests recovery after clear cut show a greatly distinct structure, with profound implications on fauna movements. (C) 2009 Elsevier BY. All rights reserved.

Ribosomal RNA gene insertions in the R2 site of Rhynchosciara (Diptera: Sciaridae)

Ribosomal RNA genes of most insects are interrupted by R1/R2 retrotransposons. The occurrence of R2 retrotransposons in sciarid genomes was studied by PCR and Southern blot hybridization in three Rhynchosciara species and in Trichosia pubescens. Amplification products with the expected size for non-truncated R2 elements were only obtained in Rhynchosciara americana. The rDNA in this species is located in the proximal end of the X mitotic chromosome but in the salivary gland is associated with all four polytene chromosomes. Approximately 50% of the salivary gland rDNA of most R. americana larval groups analysed had an insertion in the R2 site, while no evidence for the presence of R1 elements was found. In-situ hybridization results showed that rDNA repeat units containing R2 take part in the structure of the extrachromosomal rDNA. Also, rDNA resistance to Bal 31 digestion could be interpreted as evidence for nonlinear rDNA as part of the rDNA in the salivary gland. Insertions in the rDNA of three other sciarid species were not detected by Southern blot and in-situ hybridization, suggesting that rDNA retrotransposons are significantly under-represented in their genomes in comparison with R. americana. R2 elements apparently restricted to R. americana correlate with an increased amount of repetitive DNA in its genome in contrast to other Rhynchosciara species. The results obtained in this work together with previous results suggest that evolutionary changes in the genus Rhynchosciara occurred by differential genomic occupation not only of satellite DNA but possibly also of rDNA retrotransposons.

Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 angstrom. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP. (C) 2009 Elsevier Inc. All rights reserved.

Structure and Calcium-Binding Activity of LipL32, the Major Surface Antigen of Pathogenic Leptospira sp.

Leptospixosis, a spirochaetal zoonotic disease caused by Leptospira, has been recognized as an important emerging infectious disease. LipL32 is the major exposed outer membrane protein found exclusively in pathogenic leptospires, where it accounts for up to 75% of the total outer membrane proteins. It is highly immunogenic, and recent studies have implicated LipL32 as an extracellular matrix binding protein, interacting with collagens, fibronectin, and laminin. In order to better understand the biological role and the structural requirements for the function of this important lipoprotein, we have determined the 2.25-angstrom-resolution structure of recombinant LipL32 protein corresponding to residues 21-272 of the wild-type protein (LipL32(21-272)). The LipL32(21-272) monomer is made of a jelly-roll fold core from which several peripheral secondary structures protrude. LipL32(21-272) is structurally similar to several other jelly-roll proteins, some of which bind calcium ions and extracellular matrix proteins. Indeed, spectroscopic data (circular dichroism, intrinsic tryptophan fluorescence, and extrinsic 1-amino-2-naphthol-4-sulfonic acid fluorescence) confirmed the calcium-binding properties of LipL32(21-272). Ca(2+) binding resulted in a significant increase in the thermal stability of the protein, and binding was specific for Ca(2+) as no structural or stability perturbations were observed for Mg(2+), Zn(2+), or Cu(2+). Careful examination of the crystal lographic structure suggests the locations of putative regions that could mediate Ca(2+) binding as well as binding to other interacting host proteins, such as collagens, fibronectin, and lamixidn. (C) 2009 Elsevier Ltd. All rights reserved.

Insights into the mechanism of progressive RNA degradation by the archaeal exosome

Initially identified in yeast, the exosome has emerged as a central component of the RNA maturation and degradation machinery both in Archaea and eukaryotes. Here we describe a series of high-resolution structures of the RNase PH ring from the Pyrococcus abyssi exosome, one of them containing three 10-mer RNA strands within the exosome catalytic chamber, and report additional nucleotide interactions involving positions N5 and N7. Residues from all three Rrp41-Rrp42 heterodimers interact with a single RNA molecule, providing evidence for the functional relevance of exosome ring-like assembly in RNA processivity. Furthermore, an ADP-bound structure showed a rearrangement of nucleotide interactions at site N1, suggesting a rationale for the elimination of nucleoside diphosphate after catalysis. In combination with RNA degradation assays performed with mutants of key amino acid residues, the structural data presented here provide support for a model of exosome-mediated RNA degradation that integrates the events involving catalytic cleavage, product elimination, and RNA translocation. Finally, comparisons between the archaeal and human exosome structures provide a possible explanation for the eukaryotic exosome inability to catalyze phosphate-dependent RNA degradation.

Polyaniline/layered zirconium phosphate nanocomposites: Secondary-like doped polyaniline obtained by the layer-by-layer technique

In the present work, nanocomposites of polyaniline (PANI) and layered alpha-Zr(HPO4)(2).H2O (alpha-ZrP) were prepared using two different approaches: (i) the in situ aniline polymerization in the presence of the layered inorganic material and (ii) the layer-by-layer (LBL) assembly using an aqueous solution of the polycation emeraldine salt (ES-PANI) and a dispersion of exfoliated negative slabs of alpha-ZrP. These materials were characterized spectroscopically using mainly resonance Raman scattering at four exciting radiations and electronic absorption in the UV-VIS-NIR region. Structural and textural characterizations were carried out using powder X-ray diffraction (XRD) and scanning electron microscopy (SEM). The polymer obtained by the in situ aniline polymerization is located primarily in the external surface of the inorganic material although aniline monomers were intercalated between alpha-ZrP interlayer regions before oxidative polymerization. Through resonance Raman spectroscopy, it was observed that the formed polymer has semiquinone units (ES-PANI) and also azo bonds (-N = N-), showing that this method results in a polymer with a different structure from the usual ""head-to-tail"" ES-PANI. The LBL assembly of pre-formed ES-PANI and exfoliated alpha-ZrP particles produces homogeneous films with reproducible deposition from layer to layer, up to 20 bilayers. Resonance Raman (lambda(0) = 632.8 nm) spectrum of PANI/ZrP LBL film shows an enhancement in the intensity of the polaronic band at 1333 cm(-1) (nu C-N center dot+) and the decrease of the band intensity at 1485 cm(-1) compared to bulk ES-PANI. Its UV-VIS-NIR spectrum presents an absorption tail in the NIR region assigned to delocalized free charge carrier. These spectroscopic features are characteristic of highly conductive secondary doped PANI suggesting that polymeric chains in PANI/ZrP LBL film have a more extended conformation than in bulk ES-PANI.

Identification of a bisegmented double-stranded RNA virus (picobirnavirus) in calf faeces

To determine the incidence of rotavirus infection among dairy herds in the State of Sdo Paulo, Brazil, 576 faecal samples obtained from calves aged 1-45 days with and without diarrhoea, reared on 63 dairy cattle farms, were analyzed. Polyacrylamide gel electrophoresis (PAGE) identified 28 samples positive for group A rotavirus, while four samples, two diarrhoeic and two non-diarrhoeic, showed a bisegmented genome with a typical picobirnavirus pattern. Electron microscopy revealed spherical virus particles with a diameter of 37 nm and without a defined surface structure. The present study is the first report of a bisegmented virus identified in cattle in Brazil. (C) 2003 Elsevier B.V. Ltd. All rights reserved.