Looking for the vector of the latest discovered geminivirus genus, Capulavirus. [P.48]

Viral metagenomics studies based on virion-associated nucleic acid extraction, sequence-independent amplification and next generation sequencing proved to be effective for discovering three highly divergent geminiviruses in South Africa, France and Finland. Although these geminiviral sequences were isolated from different continents, hemispheres and plant families, including Euphorbia caput-medusae (Euphorbiaceae), Medicago sativa (Fabaceae) and Plantago lanceolata (Plantaginaceae), they were clustered in the same phylogenetic group and were highly divergent from all the sequences classified in the seven established geminivirus genera. Based on sequence relatedness and genome organization, these new highly divergent geminivirus species were provisionally classified in a new geminivirus genus, tentatively named "Capulavirus". To estimate the epidemiological potential of these new geminiviruses but also to confirm their classification according to the criteria defined by the International Committee on Taxonomy of Viruses, including insect vector and host range, further studies were done with two capulaviruses available in our laboratory: Euphorbia caput medusae latent virus (EcmLV) from South Africa (Bernardo et al. 2013) and a capulavirus isolated from alfalfa in France provisionally named Alfalfa leaf curl virus (ALCV) according to the symptoms observed on infected plants. ALCV may cause yield losses because the infected plants exhibited stunting and distorted growth. ALCV was detected in Camargue, Provence Alpes Côte d'Azur, Languedoc Roussillon and Midi-Pyrénées. An infectious clone of EcmLV was prepared and used to determine the host range of EcmLV and test various phloem feeding insects reared in our laboratory, for vector transmission. Potentially infectious clones are presently prepared for ALCV for similar tests. In the meantime, a naturally infected alfalfa plant was transferred to a growth chamber and used as source plant for vector transmission. Potential vectors were also collected from infected alfalfa fields for testing ALCV transmission to alfalfa seedlings prepared in insect proof conditions. (Résumé d'auteur

Development of a novel LC-MS/MS method for the detection of adulteration of South African sauvignon blanc wines with 3-alkyl-2-methoxypyrazines

Thesis (MSc (Chemistry and Polymer Science))--University of Stellenbosch, 2008.A method for the detection of adulteration of South African Sauvignon blanc wines, by enrichment with foreign sources of 3-alkyl-2-methoxypyrazenes, is described. The levels of three 3-alkyl-2-methoxypyrazenes (3-isobutyl-, 3- isopropyl- and 3-sec-butyl-2-methoxypyrazine) in South African Sauvignon blanc wines were measured with liquid chromatography-mass spectrometry. Sample preparation involved clean-up and pre-concentration by distillation followed by solvent extraction of the distillate with dichloromethane. Extracts were acidified and concentrated by evaporation and finally reconstituted to a fixed volume to affect quantitative pre-concentration of the samples. Sample extracts were separated with reversed phase liquid chromatography utilizing a phenyl-hexyl separation column. Residues were measured with liquid chromatography-mass spectrometry utilizing a tandem quadrupole mass spectrometric detector operated in multiple reaction monitoring mode for optimal trace level quantitation. Atmospheric pressure chemical ionization was utilized as electrospray ionization was found to suffer from quenching effects attributed to the sample matrix. Qualitative information was obtained from the relevant molecular ions as well as two secondary ion transitions (and one ion ratio) in each case. Recoveries obtained by the extraction procedure were better than 90% with coefficient of variance of better than 10% at concentrations from 1 to 100 ng/L. The limit of detection of the method was 0.03 ng/L and the limit of quantification 0.10 ng/L for the three analytes measured. The described LC-MS method is more sensitive for the determination of 3-alkyl-2-methoxypyrazines in wine than GC methods reported for the same purpose. From the experimental data, a set of parameters were established to discriminate adulterated South African Sauvignon blanc wines. It was demonstrated that the 3-isobutyl-2-methoxypyrazine concentration, despite showing considerable variance, was confined to a relatively narrow range spanning approximately two orders of magnitude (0.20 to 22 ng/L). A clear indication of possible maximum values for this compound in South African Sauvignon blanc wines was obtained from the analysis of a large number of samples (577), spanning most relevant wine producing regions and representing vintages 2003 to 2006. It was also demonstrated that South African Sauvignon blanc wines contain the major 3- alkyl-2-methoxypyrazenes in reasonably distinct relative amounts and that the said ratios of abundance may be used to elucidate authenticity. The expected effect of adulteration with green pepper extracts or some synthetic preparations on the 3-isobutyl-2-methoxypyrazine concentration as well as the relative abundances were also determined by characterizing the corresponding profiles in green peppers and some synthetic flavor preparations. Two adulterated samples in the dataset were identified by both outlined criteria. A limited number of wines of other cultivars were also analyzed. The results represent the most complete and accurate data on the 3-alkyl-2-methoxypyrazine content of South African Sauvignon blanc wines to date. A publication covering the work presented in this thesis is currently in preparation

Coreference resolution in clinical discharge summaries, progress notes, surgical and pathology reports: a unified lexical approach

We developed a lexical rule-based system that uses a unified approach to resolving coreference across a wide variety of clinical records comprising discharge summaries, progress notes, pathology, radiology and surgical reports from two corpora (Ontology Development and Information Extraction (ODIE) and i2b2/VA) provided for the fifth i2b2/VA shared task. Taking the unweighted mean between 4 coreference metrics, validation of the system against the i2b2/VA corpus attained an overall F-score of 87.7% across all mention classes, with a maximum of 93.1% for coreference of persons, and a minimum of 77.2% for coreference of tests. For the ODIE corpus the overall F-score across all mention classes was 79.4%, with a maximum of 82.0% for coreference of persons and a minimum of 13.1% for coreference of diagnostic reagents. For the ODIE corpus our results are comparable to the mean reported inter-annotator agreement with the gold standard. We discuss the four categories of errors we identified, and how these might be addressed. The system uses a number of reusable modules and techniques that may be of benefit to the research community

Er doped oxide nanoparticles in silica based optical fibres

Erbium doped materials are of great interest in optical telecommunications due to the Er3+ intra-4f emission at 1.54 ?m. Erbium doped fibre amplifiers (EDFA) were developed in silica glass because of the low losses at this wavelength and the reliability of this glass. Developments of new rare earth doped fibre amplifiers aim to control their spectroscopic properties including shape and width of the gain curve and optical quantum efficiency. Standard silica glass modifiers, such as aluminium, result in very good properties in current EDFA. However, for more drastic spectroscopic changes, more important modifications of the rare earth ions local environment are required. To address this aim, we present a fibre fabrication route creating rare earth doped calcia?silica or calcia?phosphosilica nanoparticles embedded in silica glass. By adding alkaline earth elements such as calcium, in low concentration, one can obtain a glass with an immisci- bility gap so that phase separation occurs with an appropriate heat treatment. We investigated the role of two elements: calcium and phosphorus (a standard silica modifier). Scanning electron microscopy shows that nanoparticles are only observed when calcium is incorporated. The size of the particles is determined to be around 50 nm in preform samples. The nature of these particles depends on phosphorus content: without P, electron diffraction shows that the particles are amorphous whilst they are partially crystalline when phosphorus is added. In addition through use of energy dispersive x-ray techniques, we have shown that erbium ions are located in the nanoparticles

Classification of affine operators up to biregular conjugacy

Let f(x)=Ax+b and g(x)=Cx+d be two affine operators given by n-by-n matrices A and C and vectors b and d over a field F. They are said to be biregularly conjugate if hf=gh for some bijection h: F^n-->F^n being biregular, this means that the coordinate functions of h and h^{-1} are polynomials. Over an algebraically closed field of characteristic 0, we obtain necessary and sufficient conditions of biregular conjugacy of affine operators and give a canonical form of an affine operator up to biregular conjugacy. These results for bijective affine operators were obtained by J.Blanc [Conjugacy classes of affine automorphisms of K^n and linear automorphisms of P^n in the Cremona groups, Manuscripta Math. 119 (2006) 225-241]