Contribution of the Type VI Secretion System Encoded in SPI-19 to Chicken Colonization by Salmonella enterica Serotypes Gallinarum and Enteritidis

Salmonella Gallinarum is a pathogen with a host range specific to poultry, while Salmonella Enteritidis is a broad host range pathogen that colonizes poultry sub-clinically but is a leading cause of gastrointestinal salmonellosis in humans and many other species. Despite recent advances in our understanding of the complex interplay between Salmonella and their hosts, the molecular basis of host range restriction and unique pathobiology of Gallinarum remain largely unknown. Type VI Secretion System (T6SS) represents a new paradigm of protein secretion that is critical for the pathogenesis of many Gram-negative bacteria. We recently identified a putative T6SS in the Salmonella Pathogenicity Island 19 (SPI-19) of Gallinarum. In Enteritidis, SPI-19 is a degenerate element that has lost most of the T6SS functions encoded in the island. In this work, we studied the contribution of SPI-19 to the colonization of Salmonella Gallinarum strain 287/91 in chickens. Non-polar deletion mutants of SPI-19 and the clpV gene, an essential T6SS component, colonized the ileum, ceca, liver and spleen of White Leghorn chicks poorly compared to the wild-type strain after oral inoculation. Return of SPI-19 to the ΔSPI-19 mutant, using VEX-Capture, complemented this colonization defect. In contrast, transfer of SPI-19 from Gallinarum to Enteritidis resulted in transient increase in the colonization of the ileum, liver and spleen at day 1 post-infection, but at days 3 and 5 post-infection a strong colonization defect of the gut and internal organs of the experimentally infected chickens was observed. Our data indicate that SPI-19 and the T6SS encoded in this region contribute to the colonization of the gastrointestinal tract and internal organs of chickens by Salmonella Gallinarum and suggest that degradation of SPI-19 T6SS in Salmonella Enteritidis conferred an advantage in colonization of the avian host

Fungal Planet description sheets: 1042-1111

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.) from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa. Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae. UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis. USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.) on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.) from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes

History on organotin compounds, from snails to humans

Organotin compounds are industrial chemicals used as biocides, polyvinyl chloride stabilizers and industrial catalysts for the manufacture of silicone and polyurethane foams. Despite multiple applications, organotin notoriety is due to tributyltin, a potent biocide used in antifouling paints. Because of the intensive use of tributyltin for the protection of ships’ hulls, tributyltin has been largely released into waters, resulting in adverse and even bizarre effects on aquatic organisms, such as imposex in gastropods. However, organotins include other compounds such as tributyltin derivatives, phenyltins and octyltins. Organotin use in plastics, silicone and foams results in their occurrence almost everywhere, e.g., clothes, toys, wallpaper, food containers, household piping and medical devices. Hence, humans are exposed to organotins not solely through ingestion of contaminated seafood but also through direct contact with treated products and by inhalation and ingestion of dust. As a consequence, organotins have been detected in human samples. Toxicity data reveal that organotins are endocrine disruptors, immunotoxicants, carcinogens and obesogens. Here, we review the levels, fate and effects of organotin compounds toward wildlife and humans, starting with a description of organotin applications, with particular incidence in antifouling paints. The global contamination of the marine environment and the deleterious effects of tributyltin onto nontarget organisms are addressed, with particular attention to the imposex phenomenon. The restrictions on tributyltin use in antifouling paints are also described alongside with the new regulations for organotins in consumer products. The sources and pathways of organotins in the environment are discussed, studies in human exposure are presented, and future research is proposed

Direct gyrokinetic comparison of pedestal transport in JET with carbon and ITER-like walls

This paper compares the gyrokinetic instabilities and transport in two representative JET pedestals, one (pulse 78697) from the JET configuration with a carbon wall (C) and another (pulse 92432) from after the installation of JET's ITER-like Wall (ILW). The discharges were selected for a comparison of JET-ILW and JET-C discharges with good confinement at high current (3 MA, corresponding also to low rho(*)) and retain the distinguishing features of JET-C and JET-ILW, notably, decreased pedestal top temperature for JET-ILW. A comparison of the profiles and heating power reveals a stark qualitative difference between the discharges: the JET-ILW pulse (92432) requires twice the heating power, at a gas rate of 1.9 x 10(22) e s(-1), to sustain roughly half the temperature gradient of the JET-C pulse (78697), operated at zero gas rate. This points to heat transport as a central component of the dynamics limiting the JET-ILW pedestal and reinforces the following emerging JET-ILW pedestal transport paradigm, which is proposed for further examination by both theory and experiment. ILW conditions modify the density pedestal in ways that decrease the normalized pedestal density gradient a/L-n, often via an outward shift in relation to the temperature pedestal. This is attributable to some combination of direct metal wall effects and the need for increased fueling to mitigate tungsten contamination. The modification to the density profile increases eta = L-n/L-T, thereby producing more robust ion temperature gradient (ITG) and electron temperature gradient driven instability. The decreased pedestal gradients for JET-ILW (92432) also result in a strongly reduced E x B shear rate, further enhancing the ion scale turbulence. Collectively, these effects limit the pedestal temperature and demand more heating power to achieve good pedestal performance. Our simulations, consistent with basic theoretical arguments, find higher ITG turbulence, stronger stiffness, and higher pedestal transport in the ILW plasma at lower rho(*)

Long-lived coupled peeling ballooning modes preceding ELMs on JET

In some JET discharges, type-I edge localised modes (ELMs) are preceded by a class of low-frequency oscillations (Perez et al 2004 Nucl. Fusion 44 609). While in many cases the ELM is triggered during the growth phase of this oscillation, it is also observed that this type of oscillation can saturate and last for several tens of ms until an ELM occurs. In order to identify the nature of these modes, a wide pre-ELM oscillation database, including detailed pedestal profile information, has been assembled and analysed in terms of MHD stability parameters. The existence domain of these pre-ELM oscillations and the statistical distribution of toroidal mode numbers (n) up to n = 16 have been mapped in ballooning alpha (alpha(ball)) and either edge current density (J(edge)) or pedestal collisionality (nu(ee,ped)*) coordinates and compared to linear MHD stability predictions. The pre-ELM oscillations are reliably observed when the J/alpha ratio is high enough for the pedestal to access the coupled peeling-ballooning (PB) domain (aka stability nose). Conversely, when the pedestal is found to be in or near the high-n ballooning domain (which is at low J/alpha ratio), ELMs are usually triggered promptly, i.e. with no detectable pre-ELM oscillations, or with pre-ELM oscillations only observable on ECE whose n appears to be too high to be resolved by the magnetics. Individual discharges can sometimes exhibit a fairly wide range of pre-ELM mode numbers, but for a wider database, the statistical n-number domains are found to be well ordered along the J - alpha stability boundary and behave as expected from PB theory: the higher the J/alpha ratio, the lower the mode's measured n tends to be. Within the measurement uncertainties, the measured n is usually found to be compatible with the most unstable n predicted by the linear stability code MISHKA1. These results confirm the earlier hypothesis that these modes are coupled peeling-ballooning modes, and extend and generalise to higher-mode numbers the work by Huysmans et al (1998 Nucl. Fusion 38 179), who identified the lowest n modes as pure external kink modes. Since the destabilisation of PB modes is widely accepted to give rise to ELMs, the mode saturation and delayed ELM triggering that is sometimes observed is rather unexpected. Possibilities to reconcile the extended lifetime of these modes with current ELM models are briefly discussed, but will require further investigation

Long-lived coupled peeling ballooning modes preceding ELMs on JET

In some JET discharges, type-I edge localised modes (ELMs) are preceded by a class of low-frequency oscillations (Perez et al 2004 Nucl. Fusion 44 609). While in many cases the ELM is triggered during the growth phase of this oscillation, it is also observed that this type of oscillation can saturate and last for several tens of ms until an ELM occurs. In order to identify the nature of these modes, a wide pre-ELM oscillation database, including detailed pedestal profile information, has been assembled and analysed in terms of MHD stability parameters. The existence domain of these pre-ELM oscillations and the statistical distribution of toroidal mode numbers (n) up to n = 16 have been mapped in ballooning alpha (alpha(ball)) and either edge current density (J(edge)) or pedestal collisionality (nu(ee,ped)*) coordinates and compared to linear MHD stability predictions. The pre-ELM oscillations are reliably observed when the J/alpha ratio is high enough for the pedestal to access the coupled peeling-ballooning (PB) domain (aka stability nose). Conversely, when the pedestal is found to be in or near the high-n ballooning domain (which is at low J/alpha ratio), ELMs are usually triggered promptly, i.e. with no detectable pre-ELM oscillations, or with pre-ELM oscillations only observable on ECE whose n appears to be too high to be resolved by the magnetics. Individual discharges can sometimes exhibit a fairly wide range of pre-ELM mode numbers, but for a wider database, the statistical n-number domains are found to be well ordered along the J - alpha stability boundary and behave as expected from PB theory: the higher the J/alpha ratio, the lower the mode's measured n tends to be. Within the measurement uncertainties, the measured n is usually found to be compatible with the most unstable n predicted by the linear stability code MISHKA1. These results confirm the earlier hypothesis that these modes are coupled peeling-ballooning modes, and extend and generalise to higher-mode numbers the work by Huysmans et al (1998 Nucl. Fusion 38 179), who identified the lowest n modes as pure external kink modes. Since the destabilisation of PB modes is widely accepted to give rise to ELMs, the mode saturation and delayed ELM triggering that is sometimes observed is rather unexpected. Possibilities to reconcile the extended lifetime of these modes with current ELM models are briefly discussed, but will require further investigation

Beryllium melting and erosion on the upper dump plates in JET during three ITER-like wall campaigns

Data on erosion and melting of beryllium upper limiter tiles, so-called dump plates (DP), are presented for all three campaigns in the JET tokamak with the ITER-like wall. High-resolution images of the upper wall of JET show clear signs of flash melting on the ridge of the roofshaped tiles. The melt layers move in the poloidal direction from the inboard to the outboard tile, ending on the last DP tile with an upward going waterfall-like melt structure. Melting was caused mainly by unmitigated plasma disruptions. During three ILW campaigns, around 15% of all 12376 plasma pulses were catalogued as disruptions. Thermocouple data from the upper dump plates tiles showed a reduction in energy delivered by disruptions with fewer extreme events in the third campaign, ILW-3, in comparison to ILW-1 and ILW-2. The total Be erosion assessed via precision weighing of tiles retrieved from JET during shutdowns indicated the increasing mass loss across campaigns of up to 0.6 g from a single tile. The mass of splashed melted Be on the upper walls was also estimated using the high-resolution images of wall components taken after each campaign. The results agree with the total material loss estimated by tile weighing (similar to 130 g). Morphological and structural analysis performed on Be melt layers revealed a multilayer structure of re-solidified material composed mainly of Be and BeO with some heavy metal impurities Ni, Fe, W. IBA analysis performed across the affected tile ridge in both poloidal and toroidal direction revealed a low D concentration, in the range 1-4 x 10(17) D atoms cm(-2)