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Granulomatous colitis in dogs can be associated with infection of the colonic mucosa by invasive strains of

Granulomatous colitis in dogs can be associated with infection of the colonic mucosa by invasive strains of Escherichia coli. To date, fluorescence in situ hybridization (FISH) is the gold-standard method to assess intramucosal and intracellular bacterial invasion. However, FISH requires expensive fluorescence microscopy equipment and is therefore not widely available. We investigated the use of immunohistochemistry (IHC) as an alternative method to detect invasive E. coli in dogs with granulomatous colitis. Archived paraffin-embedded blocks were selected from 26 dogs with colitis, in which FISH had been performed by an outside laboratory. Using a polyclonal antibody, IHC for E. coli was performed on sections cut from the same blocks, and the presence of invasive E. coli was recorded. All 11 specimens in which FISH had detected E. coli were also positive on IHC, with strong immunolabeling in the cytoplasm of macrophages and extracellularly in the lamina propria; all 15 specimens that were negative for invasive bacteria on FISH were also negative on IHC. We found that IHC is a sensitive technique for the detection of invasive E. coli in dogs with granulomatous colitis.

The sulfonation of aniline was made, for the first time, using an ohmic heating reactor to produce sulfanilic acid, a compound of great economic interest. High heating rate, low thermal inertia and high selectivity are key advantages of this process.

Tomato severe rugose virus (ToSRV) is predominant among the more than 20 tomato-infecting begomoviruses reported in Brazil after the invasion of Bemisia tabaci Middle East-Asia Minor 1 (= biotype B) in the early 1990s. ToSRV is currently detected in association and/or displacing other begomoviruses in major tomato-producing areas. The prevalence of ToSRV across many ecogeographical regions is yet elusive. This peculiar ToSRV feature can be partially explained by its large number of alternative hosts, including those not yet characterized. Here, isolates of ToSRV were characterized in four new natural hosts, including Pachyrhizus erosus (Fabaceae), Solanum betaceum (section Pachyphylla, Solanaceae), S. torvum (section Torva, Solanaceae), and Oxalis latifolia (Oxalidaceae family). These results reinforce the notion that the wide host range of ToSRV may play relevant biological and epidemiological roles in explaining the geographical dispersion and large frequency of this virus in tomato crops in the Neotropics.

Metagenomic approaches in conjunction with high-throughput sequencing (HTS) have been employed for the discovery of novel plant-associated viral species, including members of the Geminiviridae family. In the present work, the HTS strategy allowed for the identification of genetically divergent tomato-associated geminivirus 1 (TaGV1) isolates from tomato and table beet in Brasilia-DF, Brazil. The complete genomes of these novel isolates displayed 2573 nucleotides in length (recovered by Sanger sequencing) with 83% identity to previously reported TaGV1 isolates and ≈ 63% identity with a range of capulaviruses. Phylogenetic analyses of all the available TaGV1 isolates, using either their complete genomes or Rep gene (C1:C2) sequences, indicated the genus Capulavirus as the closest group, whereas the CP (V1) gene information indicated the closest relationship with members of the genus Topocuvirus. Southern hybridization confirmed the TaGV1 association with one out of five and two out of 15 original field-collected table beet and tomato leaf samples, respectively. Leaf curling and overall size reduction were observed in two out of seven Nicotiana benthamiana plants in biolistic inoculation assays with an infectious TaGV1 clone (obtained from one novel isolate from tomato). However, no systemic infection was detected in the inoculated tomato and table beet seedlings. Additional infectivity assays with a new set of table beet and tomato accessions as well as a large number of indicator plants are needed to establish the host range of these new TaGV1 isolates.

Megacoelomyces (type species: Megacoelomyces sanchezii), an ascomycete asexual morph infecting Myrcia fenzliana (Myrtaceae) from the Brazilian Cerrado, is described as a new genus in the Phaeosphaeriaceae (Pleosporales, Dothideomycetes, Ascomycota), based on multilocus phylogeny (three nuclear ribosomal DNA and two protein-coding genes) in addition to morphological (light and scanning electron microscopy) and ecological data.

Tomato yellow vein streak virus (ToYVSV) and tomato golden vein virus (TGVV) are begomoviruses reported infecting tomatoes and other hosts across South America. However, their close phylogenetic relationship has generated uncertainties about their taxonomic status and nomenclature. In fact, genomic DNA-A identity levels of isolates reported with an identical virus name may range from 89-100%. In view of the potential inaccuracy regarding the classification status of these viruses (strains vs. distinct species), we carried out a comprehensive set of analyses employing all 45 available isolates with complete DNA-A sequences with either ToYVSV or TGVV designation. Two clear-cut clusters were identified and they were consistent with the current criteria for Begomovirus species demarcation. Moreover, our reappraisal confirmed a large array of misnamed isolates and recognized a distinctive set of virus species-specific genomic, biological, and ecological features. Hence, the present work gives support to the notion that these viruses are closely-related, but they are distinct and valid Begomovirus species. From the breeding standpoint, this information will be useful in guiding germplasm screening strategies searching for sources of large-spectrum resistance to isolates of both viruses.

Made available in DSpace on 2020-12-12T02:18:41Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 Yield losses due to Groundnut ringspot virus – GRSV (genus Orthotospovirus) infection have been observed across major peanut (Arachis hypogaea L.) growing areas in Brazil. However, effective management systems capable of minimizing GRSV damage are not yet available. The aim of the present study was to verify the effectiveness of the pyraclostrobin (a strobilurin fungicide reported as a potential activator of natural, large–spectrum plant defense mechanisms) in the management of GRSV in peanuts. Two independent field experiments were carried out in commercial peanut areas with a natural occurrence of GRSV. A completely randomized block design was used with a 5 × 2 factorial scheme, including four replicates, five peanut cultivars (‘Runner IAC 886’, ‘IAC OL4’, ‘IAC 503’, ‘IAC 505’, and ‘Granoleico’) and two treatments (with and without pyraclostrobin application). At 80 and 100 days after sowing, visual disease severity scores and the number of infected plants were evaluated, followed by virus quantification in the leaf tissues and yield. The cultivars ‘Granoleico’ and ‘IAC 503’ displayed the highest levels of GRSV susceptibility. Pyraclostrobin was found to be effective in reducing the number of GRSV–infected plants, as well as in attenuating disease severity. In addition, pyraclostrobin was able to promote significant yield increase. Even though the mechanism(s) of pyraclostrobin action against GRSV remain elusive, this fungicide can be regarded as a potential component for viral disease management programs in peanuts. Apta Polo Regional Centro Norte, Rodovia Washington Luis, Km 372, C. Postal 24, CEP 15830-000 Universidade de Brasília, UnB Embrapa Hortaliças Departamento de Produção Vegetal FCAV/Unesp Instituto Taquaritinguense de Ensino Superior–ITES Centro de Grãos e Fibras IAC Departamento de Produção Vegetal FCAV/Unesp

We report the first full-length genome of a Bougainvillea chlorotic vein banding virus, isolate BCVBV-UNB-01, causing leaf yellowing in a Bougainvillea spectabilis from Brasilia, Brazil. The genome, recovered using high throughput sequencing (Illumina HiSeq) and Sanger, consisted of 8665 nucleotides and four typical badnavirus ORFs: ORF I with 456 nt in length, ORF II with 432 nt, ORF III with 6636 nt and ORF IV with 594 nt. Phylogenetic analysis using Bayesian inference of the 1228 bp of the RT + RNase H region along other 35 badnaviruses clustered isolate BCVBV-UNB-01 with BCVBV accession (NC011592) from Taiwan. The accurately aligned region of 1228 bp using Sequence Demarcation Tool (SDT) software, confirmed this result, evidencing a robust identification. In addition, further studies involving biological characteristics, distribution and diversity of BCVBV in Brazil will be conducted in an attempt for better understanding the role of interactions among virus, plant and vector.

The paper presents an overview of the design status of the Radial Neutron Camera (RNC), that, together with the Vertical Neutron Camera, will provide, through reconstruction techniques applied to the measured line-integrated neutron fluxes, the time resolved measurement of the ITER neutron and α-source profile (i.e. neutron emissivity, neutrons emitted per unit time and volume). The RNC is composed of two subsystems, the In-Port RNC and Ex-Port RNC located, respectively, inside and outside the Plug of Equatorial Port #01. The In-Port subsystem is in a more advanced design stage since it has recently undergone the Final Design Review in the ITER procurement process. The paper describes the diagnostic layout, the interfaces, the measurement capabilities and the main challenges in its realization. Prototyping and testing of neutron detectors and electronics components were carried out and led to the choice of the component solutions that can match the environmental and operational constraints in terms radiation hardness, high temperature and electromagnetic compatibility. The performance of the RNC in terms of neutron emissivity measurement capability was assessed through 1D and 2D reconstruction analysis. It is proven that the neutron emissivity can be reconstructed in real-time within the measurement requirements: 10% accuracy, 10 ms time resolution and a/10 (a = plasma minor radius) space resolution.

International audience; N2O and CO2 can be formed in the interstellar space and in ices on the surface of outer solar system bodies, such as Pluto and Triton. Energetic ions can simulate the energy transfer processes that occur by cosmic ray irradiation of interstellar ices, comets, and icy solar system bodies. Proceeding systematic research, pure nitrous oxide (N2O) ice, and nitrous oxide and carbon dioxide (CO2) ice mixture were irradiated at 11 K with MeV-nitrogen (N+) and -xenon (Xe23+) ion beams. The chemical and physical effects induced by ion irradiation on the N2O ice and the N2O:CO2 ice mixture are compared. The formation and dissociation cross sections scale with the electronic stopping power (Se) roughly as σ ∼ a Sen, where n ∼ 3/2. The n power law is helpful for predicting the N2O formation and dissociation cross-sections for other ion beam projectiles and energies; these predictions will allow estimating the effects of the entire cosmic ray radiation field.

Maize striate mosaic virus (MSMV; genus Mastrevirus) has been previously reported in association with maize in Brazil. Here, we recovered the complete genome of a novel MSMV isolate from sugarcane via high-throughput sequencing. PCR assays with MSMV specific-primers confirmed the presence of this virus in sugarcane. To our knowledge, this is the first worldwide report of MSMV on sugarcane.

In a systematic field survey for plant-infecting viruses, leaf tissues were collected from trees showing virus-like symptoms in Brazil. After viral enrichment, total RNA was extracted and sequenced using the MiSeq platform (Illumina). Two nearly full-length picorna-like genomes of 9534 and 8158 nucleotides were found associated with Hovenia dulcis (Rhamnaceae family). Based upon their genomic information, specific primers were synthetized and used in RT-PCR assays to identify plants hosting the viral sequences. The larger contig was tentatively named as Hovenia dulcis-associated virus 1 (HDaV1), and it exhibited low nucleotide and amino acid identities with Picornavirales species. The smaller contig was related to insect-associated members of the Dicistroviridae family but exhibited a distinct genome organization with three non-overlapping open reading frames (ORFs), and it was tentatively named as Hovenia dulcis-associated virus 2 (HDaV2). Phylogenetic analysis using the amino acid sequence of RNA-dependent RNA polymerase (RdRp) revealed that HDaV1 and HDaV2 clustered in distinct groups, and both viruses were tentatively assigned as new members of the order Picornavirales. HDaV2 was assigned as a novel species in the Dicistroviridae family. The 5&prime, ends of both viruses are incomplete. In addition, a nucleotide composition analysis (NCA) revealed that HDaV1 and HDaV2 have similarities with invertebrate-infecting viruses, suggesting that the primary host(s) of these novel virus species remains to be discovered.

A complex of begomoviruses (Geminiviridae) can cause severe tomato yield losses in the neotropics. Here, next-generation sequencing was employed for large-scale assessment of single-stranded (ss)DNA virus diversity in tomatoes either harboring or lacking the large-spectrum begomovirus tolerance Ty-1 gene. Individual leaf samples exhibiting begomovirus-like symptoms (n = 107) were field-collected, circular DNA-enriched, subdivided into pools (with and without Ty-1), and Illumina-sequenced. Virus-specific PCR and Sanger dideoxy sequencing validations confirmed 15 distinct ssDNA virus/subviral agents (occurring mainly in mixed infections), which highlight the potential drawbacks of employing virus-specific resistance in tomato breeding. More viruses (14 versus 6 species) were observed in tomatoes without the Ty-1 gene. A gemycircularvirus (Genomoviridae), a new alpha-satellite, and two novel Begomovirus species were identified exclusively in samples without the Ty-1 gene. A novel begomovirus was found only in the Ty-1 pool, being the only species associated with severe symptoms in Ty-1 plants in our survey. Our work is the first step towards the elucidation of the potential begomovirus adaptation to Ty-1 and its specific filtering effects on a subset of ssDNA viral/subviral agents.

Neutron/gamma discrimination techniques are widely applied in scintillator-based neutron diagnostics for present nuclear fusion tokamak experiments (e.g. JET – Neutron Camera and compact neutron spectrometer) and will also be necessary for neutron diagnostics of up-coming machines (e.g. ITER Radial Neutron Camera). Neutron/gamma discrimination in scintillators relies on the fact that the detectors output pulses have different shapes depending on the impinging particle; several discrimination techniques are described in literature such as the charge-integration, curve-fitting and pattern recognition [1]. This paper aims at describing a new technique for neutron/gamma discrimination in scintillators based on trapezoidal filtering, which targets Field Programmable Gate Array (FPGA) implementation due to its recursive nature. Furthermore its capability to restore the baseline of each detected pulse and the fact that the output signals are shorter than the correspondent incoming pulses, points this technique as a promising solution for applications in high count rate conditions. First results coming from the application of a real-time FPGA implementation of the trapezoidal filter to simulated neutron/gamma data including pile-up events and to real scintillator data will be presented.

This paper describes the high-priority testing activities supporting the ITER radial neutron camera (RNC) design, performed by a consortium of European institutes within a framework contract placed by fusion for energy, the ITER European Domestic Agency. The main role of the RNC is to measure the uncollided 14- and 2.5-MeV neutrons from deuterium-tritium and deuterium-deuterium fusion reactions through an array of flux monitors/spectrometers located in collimated lines of sight viewing the plasma through the ITER equatorial port plug #1. The line-integrated neutron fluxes will be used to evaluate, through reconstruction techniques, the radial profile of the neutrons emitted per unit time and volume (neutron emissivity) and, therefore, the neutron yield and the alpha particles' birth profile. The activity of high-priority testing is dedicated to the preparation and the design of experimental test environment, the conduction of appropriate tests and reporting of test results for the high-priority prototypes, clarifying or verifying the expected key function and system behavior, and enhancing learning on specific issues (potential showstoppers). © 1973-2012 IEEE.

Snap and common beans (Phaseolus vulgaris L.) are severely affected by Bean golden mosaic virus (BGMV) infection, so far the only begomovirus reported on these crops in Brazil (1). Samples of snap and common beans colonized by the whitefly Bemisia tabaci biotype B and displaying golden mosaic, chlorotic spots, and leaf distortion were collected in three production regions in Goiás State (Goianápolis, Luziânia, and Itaberaí) between 2003 and 2007. Total DNA extracted from leaf samples was used as template in PCR assays using universal primers targeting conserved regions of the DNA-A and DNA-B genomes (3). Begomovirus-specific amplicons were observed only with DNA template from symptomatic plants. Two single amplicons were observed for both genomic segments, indicating the presence of bipartite species in all samples. Sequence analysis of four isolates (named as GO-176, GO-260, GO-354, and GO-368) obtained from common bean samples indicated identity levels of approximately 95% with the DNA-A segment of BGMV (GenBank Accession No. FJ665283). However, the complete DNA-A sequence (GenBank Accession No. HM357459.1) of the GO-060 isolate (from a symptomatic snap bean plant collected in Goianápolis) displayed 76% identity with BGMV (GenBank Accession No. FJ665283) and 95% identity with the DNA-A of a Sida micrantha mosaic virus (SimMV) isolate (GenBank Accession No. EU908733.1) reported to be infecting okra (Abelmoschus esculentus L.) and 94.8% with a SimMV isolate reported to be infecting soybean (GenBank Accession No. FJ686693) in Brazil (2). Koch's postulates were fulfilled for the isolate GO-060 by inoculating a set of soybean and bean accessions via a biolistic approach. The ratio of positive PCR amplicons per total of inoculated plants were 15 of 16 for snap bean cv. Trepador, 9 of 10 for snap bean cv. Fartura, 18 of 24 for common bean cv. Olate Pinto, and 19 of 25 for common bean cv. Carioca. The isolate was also able to infect eight of nine soybean ‘Doko’ plants. Sequence analysis using symptomatic leaf samples (15 days after inoculation) confirmed SimMV as the causal agent. To our knowledge, this is the first report of a SimMV isolate infecting P. vulgaris. This virus is apparently fast expanding its host range from Malvaceae to Solanaceae species and leguminous hosts after the introduction of B. tabaci biotype B (2). More extensive surveys are necessary to access the current epidemiological importance of SimMV in both snap and common beans in Brazil. References: (1) J.C. Faria and D. P. Maxwell. Phytopathology 89:262, 1999. (2) F. R. Fernandes et al. Arch. Virol. 154:1567, 2009. (3) M. R. Rojas et al. Plant Dis. 77:340, 1993.

The ITER project demanding operating conditions, as well as other enabling experiments in relevant fusion projects, present new challenges to the diagnostics, control and instrumentation. The most critical requirements relate to the high acquisition rates (up to some gigasample per second), high physical event rate (up to several megaevents per second), need to handle enormous quantities of data in long experimental pulses (up to 30 minutes) and highly complex control and diagnostic algorithms. Radiation hardness of all equipment involved must also be taken into account for high magnetic fields as well as neutron irradiation in the fusion devices port cells. The implementation of state-of-the-art designs were tested both with in-house built prototypes and complete systems installed in the major international fusion experiments. The main technologies used include Advanced Telecommunications Computing Architecture (ATCA), high speed electronic devices for signal digitization, complex real-time algorithms for physics analysis, control and data compression implemented in high-performance computing using field-programmable gate arrays and multicore processor architectures. The control and data acquisition group at Instituto de Plasmas e Fusao Nuclear (Instituto Superior Tecnico - Lisboa) has conducted several projects and studies for the development of reliable high-performance processing tools and instrumentation for the diagnostics and control of fusion devices capable of complying with the most demanding requirements.

The Radial Neutron Camera (RNC) diagnostic is a neutron detection system with multiple collimators aiming at characterizing the neutron emission that will be produced by the ITER tokamak. The RNC plays a primary role for basic and advanced plasma control measurements and acts as backup for system machine protection measurements. During the RNC system level design phase the following real-time data processing algorithms were developed to assess RNC data throughput needs and measurement performances: (i) real-time data compression block (ii) real-time calculation of the neutron emissivity radial profile, based on Tikhonov regularization, starting from the line-integrated measurements, the line-of-sight geometry and using the magnetic flux information [1] (iii) real-time calculation of the neutron emissivity profile using a-priori trained neural networks, the line-integrated measurements and the magnetic flux information (the best output from different neural networks being evaluated by a figure of merit that maps the neutron emissivity profile to the original line-integrated measurements) [2] . This paper presents results for the processing times of the various algorithms and their minimum control cycle for different conditions, such as number of lines of sight, number of magnetic flux surfaces and measurement error on the line integrated RNC measurements.

The new multichannel X-mode reflectometer installed on ASDEX Upgrade measures the plasma density profile evolution at different positions in front of the ICRF antenna. The reflectometer operates in the extended U-band (40–68 GHz) microwave region, measuring density profiles up to 2 × 1019 m−3 with magnetic fields between 1.5 T and 2.7 T. In this heterodyne reflectometer architecture, the signal reflected by the plasma is down-shifted and quadrature detectors demodulate its in-phase and quadrature (IQ) components. In this work we analysed the acquired IQ signals from the different reflectometer antennas, and describe the waveguide dispersion calibration and filtering of the raw signal. The effect of spurious reflections, such as the multiple reflections from the ICRF antenna metal straps, are analysed and taken into account on the data processing software. In high plasma density and high magnetic field scenarios, both the lower and upper X-mode cut off frequencies are detected in the probing range. The first fringe (FF) reflection of the upper cut off indicates the start of the plasma signal and must be determined robustly to reduce density profile errors. Existing FF estimation algorithms based on signal amplitude and spectral information may still fail in the presence of both upper and lower cut off reflections.

Securing economically and ecologically significant molluscs, as our oceans warm and acidify due to climate change, is a global priority. South eastern Australia receives warm water in a strengthening East Australia Current and so resident species are vulnerable to elevated temperature and marine heat waves. This study tested whether oysters pre exposed to elevated temperature or heat stress enhances resilience to ocean warming later in life. Two Australian species, the flat oyster,Ostrea angasi,and the Sydney rock oyster,Saccostrea glomerata, were given a mild dose of warm water or “heat shock” stress in the laboratory and then transferred to elevated temperature conditions where we used the thermal outfall from power generation as a proxy to investigate the impacts of ocean warming. Shell growth, condition index, lipid content and profile and survival of oysters was impacted by elevated temperature in the field, with flat oysters being more impacted than Sydney rock oysters. Flat oysters grew faster than Sydney rock oysters at ambient temperature, but were more sensitive to elevated temperature. Early exposure to heat stress did little to ameliorate the negative effects of increased temperature, although the survival of heat shocked flat oysters was greater than non-heat shocked oysters. Further investigations are required to determine if early exposure to heat stress can act to inoculate oysters to future stress and overall enhance resilience of oysters to ocean warming.

ObjectivesTo evaluate the surgical techniques, approaches, audiological outcomes and complications of endoscopic stapes surgery.MethodsSystematic searches of the literature were performed in PubMed, Web of Science and Scopus databases, to identify studies of patients who underwent stapes surgery using endoscopic approaches and studies reporting objective post-operative hearing outcomes. The following information was extracted: surgery duration, complications, surgical technique and audiometric results.ResultsFourteen studies were selected for appraisal, which included a total of 282 ears subjected to endoscopic stapes surgery. Endoscopic stapes surgery seems to provide adequate visualisation of the middle-ear structures, thereby allowing less invasive surgery and potentially equivalent audiological outcomes as compared with a traditional microscopic approach. Other advantages of endoscopic stapes surgery include decreased surgery time, a reduced need for drilling, and auditory results comparable to those of microscopic techniques.ConclusionStudies have shown that endoscopic stapes surgery has similar surgical and functional advantages as compared with microscopic surgery.

)3 Acetylene, C2H2, has been observed in the interstellar medium, mostly around young stellar objects, as well as in molecular clouds and cometary comae, representing an important species of astrophysical interest. In this work, we present a laboratory study of the C2H2 radiolysis at 45 K for three different beams and energies: 1.0 MeV H+ and He+, and 1.0 and 1.5 MeV N+ beams. Fourier transform infrared spectroscopy was used for monitoring the molecular changes induced by the ion processing. Two different sample thicknesses were irradiated; for the thicker one, implantation had occurred. Spectra and absorbance evolutions for the thin and thick films are qualitatively different. Four C2H2 bands are observed at 3225, 1954, 1392, and 763 cm−1. The C2H2 compaction and apparent destruction cross-sections are determined. For the case of the H+ beam, the compaction cross-section dominates. Concerning molecular synthesis by irradiation, New product bands were not observed in the thin ice irradiations; for the thicker film ice, the daughter species CH4, C2H4, C3H6, and C4H4 have been identified and their destruction and formation cross-sections determined. The apparent destruction cross-section was found to be a function of the electronic stopping power (Se) as σd ∝ S$_\mathrm{ e}^{3/2}$. The half-life of the C2H2 bombarded by galactic cosmic rays is estimated. The current findings are a contribution to the understanding of how the molecules synthesized upon irradiation of Interstellar and outer Solar system ices participate to the molecular enrichment and to the physicochemical evolution of the Universe.

Securing economically and ecologically significant molluscs, as our oceans warm due to climate change, is a global priority. South eastern Australia receives warm water in a strengthening East Australia Current and so resident species are vulnerable to elevated temperature and marine heat waves. This study tested whether prior exposure to elevated temperature can enhance resilience of oysters to ocean warming. Two Australian species, the flat oyster, Ostrea angasi, and the Sydney rock oyster, Saccostrea glomerata, were obtained as adults and "heat shocked" by exposure to a dose of warm water in the laboratory. Oysters were then transferred to elevated seawater temperature conditions where the thermal outfall from power generation was used as a proxy to investigate the impacts of ocean warming. Shell growth, condition index, lipid content and survival of flat oysters and condition of Sydney rock oysters were all significantly reduced by elevated seawater temperature in the field. Flat oysters grew faster than Sydney rock oysters at ambient temperature, but their growth and survival was more sensitive to elevated temperature. "Stress inoculation" by heat shock did little to ameliorate the negative effects of increased temperature, although the survival of heat-shocked flat oysters was greater than non-heat shocked oysters. Further investigations are required to determine if early exposure to heat stress can enhance resilience of oysters to ocean warming.

An important instrumental development work has been done in the last two decades in the field of neutron and gamma ray spectroscopic measurements of magnetic confinement plasmas. Starting from the present state of the art instrumentation installed at JET, this paper reviews the recent development that has been carried out within the EUROFUSION programme for the forthcoming high power JET D and DT campaign. This development was dedicated to the realization of new compact neutron and gamma-ray spectrometers which combine very high energy resolution (typically better than 5%) and MHz counting rate capabilities allowing for time resolution in the 10 ms time scale. One of the advantages offered by the compact dimensions of these spectrometers is to make possible their use in multiple sight-line camera configurations, such as for future burning plasma reactors (ITER and DEMO). New compact neutron spectrometers based on single crystal diamond detectors have been developed and installed at JET for measurements of the 14 MeV neutron spectrum. Measurements on a portable DT neutron generator have shown that neutron spectroscopy of the accelerated beam ions at unprecedented energy resolution (∼1% at 14 MeV) is possible, which opens up new opportunities for diagnosing DT plasmas. For what concerns gamma ray measurements, the JET gamma ray camera has been recently upgraded with new compact spectrometers based on a LaBr3 scintillator coupled to Silicon Photomultiplier with the dual aim to improve the spectroscopic and rate capabilities of the detectors. The upgrade camera system will reconstruct the spatial gamma ray emissivity from the plasma in the MeV energy range at MHz counting rates and energy resolution in the 2-4% range. This will allow physics studies of gamma rays produced by the interaction of fast ions with impurities in the plasma and bremsstrahlung emission from runaway electrons.

Across the globe, restoration efforts are stemming the loss of native oyster reefs and the ecosystem services they provide, but these efforts will need to consider climate change in order to be sustainable. South-eastern Australia is the focus of restoring the once abundant oyster Ostrea angasi. This region is also a climate change ‘hot spot’ where the ocean is warming rapidly, with the potential to be exacerbated by marine heatwaves and coastal acidification. In this study, the impact of near-future (~2050) elevated temperature and pCO2 on O. angasi was determined and considered in context with concerns for the long-term sustainability of oyster reef restoration efforts. Oysters were exposed to ambient and elevated pCO2 concentrations (mean ± SE: 408 ± 19.8 and 1070 ± 53.4 μatm) and ambient and elevated temperatures (22.78 ± 0.17 and 25.73 ± 0.21°C) for 10 wk in outdoor flow-through mesocosms. Shell growth, condition index, standard metabolic rate (SMR), extracellular pH and survival were measured. Elevated temperature caused high mortality (36%) and decreased the condition of oysters (33%). Elevated pCO2 increased SMR almost 4-fold and lowered the extracellular pH of O. angasi by a mean 0.29 pH units. In combination, elevated pCO2 and temperature ameliorated effects on SMR and survivorship of oysters. O. angasi appears to be living near the limits of its thermal tolerance. Restoration projects will need to account for the temperature sensitivity of this species and its changing habitat to ‘climate proof’ long-term restoration efforts.

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The Ty-1 locus confers tolerance to monopartite and bipartite Begomovirus spp. (genus Begomovirus, family Geminiviridae) and this phenotype is improved in homozygous tomato lines. However, the gene Mi (Meloidogyne spp. resistance) is in repulsion phase linkage with Ty-1, which hampers the large-scale development of multiresistant inbred lines. Seventy-one Solanum (section Lycopersicon) accessions were whitefly inoculated with the bipartite Begomovirus sp. Tomato rugose mosaic virus (ToRMV) and simultaneously infested with a mixture of Meloidogyne incognita and M. javanica under greenhouse conditions in Brazil. Accessions were then transplanted into a nematode-infested field with natural ToRMV infection. A severity index was used to evaluate ToRMV reaction. Nematode evaluation was done by counting the number of galls per root system. Seventeen accessions with Meloidogyne spp. and ToRMV resistance were selected and evaluated in Spain against three monopartite Begomovirus spp. associated with the tomato yellow leaf curl virus disease, using infectious clones. Systemic infection was monitored by DNA hybridization. Five S. peruvianum accessions (PI-306811, PI-365951, LA-1609, LA-2553, and CNPH-1194) displayed nematode and broad-spectrum resistance to all Begomovirus spp. tested in both continents. From the breeding standpoint, accessions combining resistance to Meloidogyne spp. and to bipartite and monopartite Begomovirus spp. would be useful for the development of elite lines expressing all traits in homozygous condition.

Sweet potato chlorotic stunt virus (SPCSV; genus Crinivirus, family Closteroviridae), is an economically important pathogen of sweet potato. In the present work, the nucleotide sequences of two RNA segments of SPCSV (isolate SPCSV-UNB-01) were determined by MiSeq Illumina sequencing of samples of sweet potato plants grafted onto Ipomoea setosa. A comparative analysis of the genome organization of SPCSV-UNB-01 and other SPCSV sequences showed that RNA1 was lacking p22, and p5.1 and that p5.2. was absent in RNA2, indicating a unique genomic pattern. SPCSV-UNB-01 contained longer p6 and p5 regions, with little similarity to orthologous sequences. Sequence comparison did not reveal any previously identified functional domains within these open reading frames (ORFs). No recombination or rearrangement events were detected. Phylogenetic analysis suggested the possibility of separate entries of SPCSV into South America based on the genetic distance between SPCSV-UNB-01 and the Peruvian isolate m2-47. Samples from northeastern Brazil (State of Pernambuco) were positive for SPCSV when tested using specific primers for the major coat protein (CP) gene. This is the first full-length genome sequence of SPCSV-UNB-01 from Brazil.

In several nuclear applications, scintillators, coupled with a photomultiplier and pulse amplifier, are used in order to detect high energy particles, i.e. neutrons and gamma rays. The different particles incident on the scintillator produce electrical pulses having different shape; moreover, the amplitude of these signals is related to the particles energy. The electrical pulses of the scintillator chain are acquired by digital systems that, generally, perform a triggered acquisition consisting of a stream of pulse windows. The aim of this study is the development of a simplified clustering algorithm able to produce reference patterns in compliance with the pattern recognition algorithm based on the matched filter technique, starting from a stream of pulses generated by particles having different energy and type. This paper contains a general description of the clustering algorithm and of the main customizations performed for the scintillator signals. In order to test in real case the efficiency, the algorithm has been applied on the data acquired during a radiation test performed at Frascati Neutron Generator for Stilbene scintillator. The results show that this algorithm works properly, deriving the centroids of the clusters representing the neutron and gamma shapes, together with their occurrences in the analysed data stream.

For the future JET deuterium-tritium (DT) campaigns numerous gamma-ray diagnostics, in particular the JET Gamma-ray Camera (GC) and the JET Gamma-ray Spectrometer (GS), were upgraded in the last few years. The upgrade of GC and GS included replacement of detector modules in order to allow operation at expected high count rate of ∼0.5 Mcps on the scintillator front surface of 506 mm2 for each GC crystal and 7 squared inches for GS as well as to improve energy resolution to equal or better than 5% at gamma-ray energy above 1.1 MeV for both diagnostics. Within the JET4 Enhancements Project, performance of a number of photodetectors including multi-pixel photon counter (MPPC), PIN diode and photomultiplier tube (PMT) connected to scintillators was investigated. Upgraded detector modules are based on fast scintillators with a decay time of about 20 ns, LaBr3:Ce and CeBr3, coupled to MPPC and PMT for GC and GS, respectively. Results on energy resolution obtained with upgraded diagnostics, already installed at JET, are presented and compared to those collected in laboratory conditions.

The ITER Radial Neutron Camera (RNC) Data Acquisition (DAQ) prototype is based on the PCIe protocol as the interface to be used between the I/O unit and the host computer, allowing the scalability of the final RNC DAQ system. The prototype architecture comprises two digitizer modules with two channels in each, installed in the host computer and the maximum produced data throughput is up to 1.6 GB/s per board, allowing a sustainable 2 MHz peak event to cope with the long plasma discharges, up to half an hour. The Linux Device Driver provides the interface between the hardware and the host applications running on a high-performance computer, which receives the acquired data through the Direct Memory Access (DMA) channels. The preliminary tests show that the Linux kernel miss some hardware interrupts when the time between interrupts is in the microsecond scale, which implies data loss if a traditional read technique based on interrupt handling is implemented. The direct usage of the polling mechanisms to retrieve the data is not suitable as the variable event rate over the same discharge does not allow to define an optimal fixed-time to retrieve data and identify missing data packets. This contribution presents the architecture, implementation and test of a different device driver approach using the polling mechanism which improves the performance and reliability. This allows the device driver to automatically check and transfer missing data blocks, recovering the data losses transparently for the host applications. The performance results for tests with different event data rates and duration up to an hour are also presented.

A new bipartite begomovirus (family Geminiviridae) was detected on cowpea (Vigna unguiculata) plants exhibiting bright golden mosaic symptoms on leaves under field conditions in Brazil. Complete consensus sequences of DNA-A and DNA-B components of an isolate of the virus (PE?088) were obtained by nanopore sequencing and confirmed by Sanger sequencing. The genome components presented the typical genomic organization of New World (NW) begomoviruses. Pairwise sequence comparisons revealed low levels of identity with other begomovirus species previously reported infecting cowpea around the world. Phylogenetic analysis using complete sequences of DNA-A components revealed that the closest relatives of PE?088 (85-87% nucleotide sequence identities) were three legume-infecting begomoviruses from Brazil: bean golden mosaic virus, macroptilium common mosaic virus and macroptilium yellow vein virus. According to the current classification criteria, PE?088 represents a new species in the genus Begomovirus, tentatively named as cowpea bright yellow mosaic virus (CoBYMV). Made available in DSpace on 2020-02-13T18:16:37Z (GMT). No. of bitstreams: 1 NanoporesequencingofanovelbipartiteNewWorldbegomovirusinfectingcowpea.2019.pdf: 698810 bytes, checksum: 04996c44ec3b021cc5633c257679e0b6 (MD5) Previous issue date: 2019