Non-clinical isolates bring new findings on enterococcal virulence

Dissertation presented to obtain the PhD degree in Biology

Influence of abiotic stress factors on VOCs emission from Portuguese rice paddy fields: relation with increased climate change

Dissertação para obtenção do Grau de Mestre em Engenharia do Ambiente Perfil de Gestão de Sistemas Ambientais

Impact of different irrigation strategies on grapes and wine quality of four grapevine cultivars (Vitis sp.) in cool climate conditions. An investigation into the relationships among ABA, water status, grape cultivar and wine quality

Niagara Peninsula of Ontario is the largest viticultural area in Canada. Although it is considered to be a cool and wet region, in the last decade many water stress events occurred during the growing seasons with negative effects on grape and wine quality. This study was initiated to understand and develop the best strategies for water management in vineyards and those that might contribute to grape maturity advancement. The irrigation trials investigated the impact of time of initiation (fruit set, lag phase and veraison), water replacement level based on theoretical loss through crop evapotranspiration (ETc; 100,50 and 25%) and different irrigation strategies [partial root zone drying (PRD) versus regulated deficit irrigation (RD!)] on grape composition and wine sensory profiles. The irrigation experiments were conducted in a commercial vineyard (Lambert Vineyards Inc.) located in Niagara-on-the-Lake, Ontario, from 2005 through 2009. The two experiments that tested the combination of different water regimes and irrigation time initiation were set up in a randomized block design as follows: Baco noir - three replicates x 10 treatments [(25%, 50% and 100% of ETc) x (initiation at fruit set, lag phase and veraison) + control]; Chardonnay - three replicates x seven treatments [(25%, 50% and 100% of ETc) x (initiation at fruit set and veraison) + control]. The experiments that tested different irrigation strategies were set up on two cultivars as follows: Sauvignon blanc - four replicates x four treatments [control, fully irrigated (100% ETc), PRD (100% ETc) and RDI (25% ETc)]; Cabemet Sauvignon - four replicates x five treatments [control, fully irrigated (100% ETc), PRD (100% ETc), RDI (50% ETc) and RDI (25% ETc)]. The controls in each experiment were nonirrigated. The irrigation treatments were compared for many variables related to soil water status, vine physiology, berry composition, wine sensory profile, and hormone composition [(abscisic acid (ABA) and its catabolites]. Soil moisture profile was mostly affected by irrigation treatments between 20 and 60 em depth depending on the grapevine cultivar and the regime of water applied. Overall soil moisture was consistently higher throughout the season in 100 and 50% ETc compare to the control. Transpiration rates and leaf temperature as well as shoot growth rate were the most sensitive variables to soil water status. Drip irrigation associated with RDI treatments (50% ETc and 25% ETc) had the most beneficial effects on vine physiology, fruit composition and wine varietal typicity, mainly by maintaining a balance between vegetative and reproductive parts of the vine. Neither the control nor the 100 ETc had overall a positive effect on grape composition and wine sensory typicity. The time of irrigation initiation affected the vine physiology and grape quality, the most positive effect was found in treatments initiated at lag phase and veraison. RDI treatments were overall more consistent in their positive effect on grape composition and wine varietal typicity comparing to PRD treatment. The greatest difference between non-irrigated and irrigated vines in most of the variables studied was found in 2007, the driest and hottest season of the experimental period. Soil water status had a greater and more consistent effect on red grapevine cultivars rather than on white winegrape cultivars. To understand the relationships among soil and plant water status, plant physiology and the hormonal profiles associated with it, abscisic acid (ABA) and its catabolites [phaseic acid (PA), dihydrophaseic acid (DPA), 7-hydroxy-ABA (TOH-ABA), 8' -hydroxy-ABA, neophaseic acid and abscisic acid glucose ester (ABA-GE)] were analyzed in leaves and berries from the Baco noir and Chardonnay irrigation trials over two growing seasons. ABA and some of its catabolites accurately described the water status in the vines. Endogenous ABA and some of its catabolites were strongly affected in Baco noir and Chardonnay by both the water regime (i.e. ET level) and timing of irrigation initiation. Chardonnay grapevines produced less ABA in both leaves and berries compared to Baco noir, which indicated that ABA synthesis is also cultivar dependant. ABA-GE was the main catabolite in treatments with high water deficits, while PA and DPA were higher in treatments with high water status, suggesting that the vine produced more ABA-GE under water deficits to maintain rapid control of the stomata. These differences between irrigation treatments with respect to ABA and catabolites were particularly noticeable in the dry 2007 season. Two trials using exogenous ABA investigated the effect of different concentrations of ABA and organs targeted for spraying, on grape maturation and berry composition of Cabemet Sauvignon grapevines, in two cool and wet seasons (2008-2009). The fIrst experiment consisted of three replicates x three treatments [(150 and 300 mg/L, both applications only on clusters) + untreated control] while the second experiment consisted in three replicates x four treatments [(full canopy, only clusters, and only leaves sprayed with 300 ppm ABA) + untreated control]. Exogenous ABA was effective in hastening veraison, and improving the composition of Cabemet Sauvignon. Ability of ABA to control the timing of grape berry maturation was dependant on both solution concentration and the target organ. ABA affected not only fruit composition but also yield components. Berries treated with ABA had lower weight and higher skin dry mass, which constitutes qualitative aspects desired in the wine grapes. Temporal advancement of ripening through hormonal control can lead to earlier fruit maturation, which is a distinct advantage in cooler areas or areas with a high risk of early frost occurrence. Exogenous ABA could provide considerable benefits to wine industry in terms of grape composition, wine style and schedule activities in the winery, particularly in wet and cool years. These trials provide the ftrst comprehensive data in eastern North America on the response of important hybrid and Vitis vinifera winegrape cultivars to irrigation management. Results from this study additionally might be a forward step in understanding the ABA metabolism, and its relationship with water status. Future research should be focused on ftnding the ABA threshold required to trigger the ripening process, and how this process could be controlled in cool climates.

Développement du chant et profil d'amusie congénitale chez l'enfant

La musique est universelle et le chant est le moyen d’expression musicale le plus accessible à tous. Les enfants chantent spontanément entre un an et un an et demi (Ostwald, 1973). Pourtant, le développement de cette habileté est très peu étudié en neuropsychologie et ce, malgré le fait qu’elle représente une immense source d’informations sur le traitement de la musique par le cerveau. Les études proposées ici visaient à mieux comprendre le développement normal et pathologique des fonctions perceptives et vocales. Dans un premier temps, une étude sur le chant normal chez les enfants de 6 à 11 ans est présentée. Le développement du chant de 79 enfants d’âge scolaire y est analysé de manière systématique et objective. Cette étude se penche plus particulièrement sur l’influence de l’âge ainsi que d’autres facteurs (le genre, la perception musicale, la présence de paroles et la présence d’un accompagnement vocal) sur la qualité du chant. Les jeunes participants ont chanté une chanson familière dans différentes conditions, soit avec et sans paroles, après un modèle ainsi qu’à l’unisson avec ce dernier. Suite à l’analyse acoustique des performances, différentes variables mélodiques et rythmiques telles que le nombre d’erreurs d’intervalles, le nombre d’erreurs de contours, la taille des déviations d’intervalles, le nombre d’erreurs rythmiques, la taille des déviations temporelles et le tempo, ont été calculés. Les résultats montrent que certaines habiletés de base liées au chant se développent toujours après 6 ans. Toutefois, le rythme est maîtrisé plus tôt, et les enfants d’âges scolaires réussissent parfois mieux que les adultes sur le plan rythmique. De plus, il est plus difficile pour les enfants de chanter avec des ii paroles que sur une syllabe et chanter à l’unisson représente un défi plus grand que chanter après un modèle. Par ailleurs, le nombre d’erreurs de contours, d’intervalles et de rythme, de même que la taille des erreurs rythmiques, sont liés à nos mesures de perception musicale. La seconde étude présente le premier cas documenté d’amusie congénitale chez l’enfant. Elle implique l’analyse de la perception musicale et du chant d’une fillette de 10 ans nous ayant été référée par son directeur de chorale. De sévères déficits ont été relevés chez elle et un diagnostic d’amusie congénitale fut posé. En effet, ses résultats aux tests visant à évaluer sa perception musicale indiquent d’importantes difficultés tant sur le plan de la discrimination des différences mélodiques et rythmiques, qu’au niveau de la mémoire des mélodies. La fillette présente des lacunes claires quant à la perception des fines différences de hauteurs. L’analyse des réponses cérébrales en potentiels évoqués suggère que l’enfant souffre de déficits situés tôt au cours des processus de traitement auditif, tel que démontré par l’absence de négativité de discordance (MMN). Le chant de la jeune fille est lui aussi déficitaire, particulièrement en ce qui concerne le nombre d’erreurs d’intervalles et leurs tailles. En conclusion, nos études montrent que les aptitudes pour le chant sont toujours en développement au cours des premières années de scolarisation. Ce développement peut être entravé par la présence d’un déficit lié spécifiquement à la perception musicale. Pour la première fois, l’amusie congénitale, sera décrite chez l’enfant.

Longitud cervical como predictor de exito en induccion de trabajo de parto en nuliparas

La inducción del trabajo de parto ha demostrado aumentar simultáneamente las tasas de cesárea, especialmente en nulíparas con cérvix clínicamente desfavorables. Ya que la valoración clínica del cérvix es un método subjetivo, aunque ampliamente utilizado, el objetivo del presente estudio fue determinar la utilidad de la medición ecográfica de la longitud cervical comparándola con el puntaje de Bishop, en la predicción del éxito de la inducción del parto en las pacientes nulíparas en el servicio de Obstetricia del Hospital Universitario Clínica San Rafael, Bogotá. Materiales y métodos: Se realizó un estudio observacional, evaluando una cohorte prospectiva de 80 gestantes a quienes se les realizó valoración ultrasonográfica y clínica del cérvix antes de iniciar la inducción del trabajo de parto. Resultados: El análisis bivariado demostró que las pacientes con longitud cervical >20mm tienen 1.57 veces la probabilidad de tener parto por cesárea (RR 1.57 IC95% 1.03-2.39 p <0.05). De manera similar las pacientes con puntaje de Bishop 0 a 3 tienen 2.33 veces la probabilidad de tener parto por cesárea (RR 2.33 IC95% 1.28-4.23 p <0.05). La regresión logística binaria demostró que la edad materna y la longitud cervical fueron los únicos parámetros independientes con significancia estadística para predecir el éxito de la inducción. Conclusiones: La medición ecográfica de la longitud cervical tiene mayor utilidad que la valoración clínica del cérvix en la predicción del éxito de la inducción del parto en nulíparas.

La evoluci??n hist??rica de los conceptos cient??ficos como prerrequisito para comprender su significado actual : el caso de la cantidad de sustancia y el mol

Resumen basado en la publicaci??n

Estudio de las comunidades microbianas de embutidos fermentados ligeramente acidificados mediante técnicas moleculares. Estandarización, seguridad y mejora tecnológica.

Los embutidos fermentados ligeramente acidificados son un grupo de productos tradicionales mediterráneos, caracterizados por un pH superior a 5,3. Para un control eficiente de la seguridad microbiológica de los embutidos se necesitan técnicas rápidas para la identificación y recuento de los microorganismos patógenos a estudiar. En el presente trabajo, se desarrolló una técnica para la enumeración de L. monocytogenes que combinó el método del número más probable y la identificación mediante PCR específica. Para la detección de Salmonella spp. y L. monocytogenes se desarrolló un sistema de PCR-multiplex que permitió la identificación de ambos patógenos de forma simultánea en una sola reacción. El estudio de la calidad microbiológica de los embutidos fermentados ligeramente acidificados se completó con la caracterización de las comunidades microbianas más importantes en estos productos. Se identificaron a nivel de especie los aislados de bacterias del ácido láctico (BAL), de enterococos y de cocos gram-positivos catalasa-positivos (CGC+). Posteriormente se realizó una tipificación molecular de los mismos mediante RAPD y análisis del perfil plasmídico y se estudiaron las principales características de interés higiénico-sanitario y tecnológico de las cepas. Mediante PCR se identificó Lactobacillus sakei como la especie predominante (74%), seguida por Lactobacillus curvatus (21,2%). La actividad aminoácido-descarboxilasa se asoció a la especie L. curvatus (el 66% de los aislados presentaron esta actividad). La identificación de los enterococos se realizó mediante PCR-multiplex y por secuenciación del gen sodA. Enterococcus faecium fue la especie de enterococos predominante (51,9%) seguida por Enterococcus faecalis (14,2%). Todas las cepas de E. faecalis presentaron genes asociados a factores de virulencia. E. faecalis presentó mayor resistencia a antibióticos que el resto de las especies de enterococos estudiadas. Tan sólo una cepa de E. faecium presentó el genotipo vanA (que confiere resistencia de alto nivel a la vancomicina). La identificación de los aislados de CGC+ (mediante PCR específica y amplificación de la región intergénica 16S-23S ARNr) demostró que Staphylococcus xylosus es la especie predominante en los embutidos fermentados ligeramente acidificados (80,8%). La amina biógena más común en los CGC+ fue la feniletilamina, producida por un 10,8% de aislados. Un pequeño porcentaje de aislados fueron mecA+ (4,6%), presentando además resistencia a múltiples antibióticos. El potencial enterotoxigénico de las cepas de CGC+ fue muy reducido (3,3% de los aislados), detectándose únicamente el gen entC. El estudio pormenorizado de las comunidades bacterianas de interés permitió la selección de 2 cepas de L. sakei y 2 cepas de S. xylosus con características tecnológicas e higiénico-sanitarias óptimas. Para evaluar su efectividad como cultivos iniciadores se elaboraron dos tipos de embutidos ligeramente ácidos, chorizo y fuet, inoculados con microorganismos patógenos (Salmonella spp., L. monocytogenes y S. aureus). El uso de cultivos iniciadores permitió el control de L. monocytogenes, Enterobacteriaceae y Enterococcus así como del contenido en aminas biógenas. Los recuentos de Salmonella spp. disminuyeron de forma significante durante la maduración de los embutidos, independientemente del uso de cultivos iniciadores. El uso del tratamiento de alta presión (400 MPa) en los embutidos madurados consiguió la ausencia de Salmonella spp. en los lotes tratados.

A model of seed dormancy in wild oats (Avena fatua) for investigating genotype x environment interactions

Dormancy is an adaptive trait in seed populations that helps ensure that seed germination is distributed over time and occurs in environmental conditions suitable for seedling growth. Several genes.. associated with seed dormancy in various plant species, have been integrated into a hypothetical dormancy model for Avena fatua L. (wild oats). Generally, the synthesis of, and sensitivity to, abscisic acid (ABA) during imbibition determines whether genes similar to those during maturation are expressed leading to a maintenance of dormancy during extended imbibition. Alternatively, there may be a shift towards expression of genes associated with gibberellins leading to germination. Environmental factors during maturation, after-ripening and imbibition are likely to interact with the genotype to affect gene expression and hence whether or not a seed germinates. In spite of the difficulties of working on a hexaploid species, A. fatua was selected for study because of its worldwide importance as a weed. Dormant and non-dormant genotypes of this species were also available. Gene expression studies are being carried out on three A.fatua genotypes produced tinder different environmental conditions to investigate the role of specific genes in dormancy and genotype X environment interactions in relation to dormancy.

The phenology and potential for self-pollination of two Australian monoecious fig species

In this preliminary study, the reproductive phenology of two monoecious fig species, Ficus racemosa and F. rubiginosa, was examined in tropical Australia. Syconia (inflorescences) occurred on both species all year round, but pre-floral and interfloral syconia were much commoner than the wasp-receptive and wasp-emitting phases in both species. The temporal overlap of the wasp-receptive and wasp-emitting phases on a single tree indicated that self-pollination was possible in both species and that pollinators may sometimes persist through multiple generations on one tree. This sexual phase overlap was commoner in F. rubiginosa than in F racemosa. The two species also differed in their general within-tree asynchrony, with a higher diversity of phases on F. rubiginosa than on F. racemosa. The time from syconium initiation to ripening was very similar in F. rubiginosa (mean = 48.51 days) and F. racemosa (mean = 43.53 days). However, there was much more variation within and between trees for F. rubiginosa. In addition, the wasp-receptive phase was found to last up to 5 days (rnean = 4.38) in F. rubiginosa. Such longevity should contribute substantially to local pollinator population persistence. Future work should use genetic studies to determine whether self-pollination is common in these fig species.

A molecular and structural characterization of senescing Arabidopsis siliques and comparison of transcriptional profiles with senescing petals and leaves

Senescence of plant organs is a genetically controlled process that regulates cell death to facilitate nutrient recovery and recycling, and frequently precedes, or is concomitant with, ripening of reproductive structures. In Arabidopsis thaliana, the seeds are contained within a silique, which is itself a photosynthetic organ in the early stages of development and undergoes a programme of senescence prior to dehiscence. A transcriptional analysis of the silique wall was undertaken to identify changes in gene expression during senescence and to correlate these events with ultrastructural changes. The study revealed that the most highly up-regulated genes in senescing silique wall tissues encoded seed storage proteins, and the significance of this finding is discussed. Global transcription profiles of senescing siliques were compared with those from senescing Arabidopsis leaf or petal tissues using microarray datasets and metabolic pathway analysis software (MapMan). In all three tissues, members of NAC and WRKY transcription factor families were up-regulated, but components of the shikimate and cell-wall biosynthetic pathways were down-regulated during senescence. Expression of genes encoding ethylene biosynthesis and action showed more similarity between senescing siliques and petals than between senescing siliques and leaves. Genes involved in autophagy were highly expressed in the late stages of death of all plant tissues studied, but not always during the preceding remobilization phase of senescence. Analyses showed that, during senescence, silique wall tissues exhibited more transcriptional features in common with petals than with leaves. The shared and distinct regulatory events associated with senescence in the three organs are evaluated and discussed.

Evaluation of Serpa cheese proteolysis by nitrogen content and capillary zone electrophoresis

Proteolysis of Serpa cheese produced traditionally (B) and semi-industrially (C) was evaluated for the first time by determination of nitrogen content and capillary zone electrophoresis (CZE). A citrate dispersion of cheese was fractionated to determine the nitrogen in pH 4.4, trichloroacetic and phosphotungstic acid soluble fractions (pH 4.4-SN, TCA-SN and PTA-SN, respectively). The pH 4.4-SN was significantly higher for B ( P < 0.001), while TCA-SN was significantly higher for C ( P < 0.001). PTA-SN was also higher for C but at 60 days ripening no significant difference was found between B and C. Degradation of alpha(s1) - and beta-caseins evaluated by CZE was in good agreement with the maturation index (pH 4.4-SN/TN).

Textural and microstructural properties of urfa cheese (a white-brined Turkish cheese)

The texture and microstructure of white-brined cheeses similar to urfa (a traditional Turkish cheese) were studied. One batch of cheeses was made in the traditional manner and one batch was made from ultrafiltered (UF) milk. Samples from each batch were either ripened in brine after production or scalded in whey for 3 min at 90degreesC prior to ripening. The results showed only marginal differences in the ripening profiles of both batches of unscalded cheeses, but scalding slowed down the extent of proteolysis in both batches. The scalded cheeses had a firmer texture than the unscalded ones, and the unscalded UF cheese had a more 'springy' body than the unscalded traditional cheese. Overall, scalding resulted in a more homogeneous structure, but the unscalded UF cheese had a close texture that resembled the scalded samples. It was concluded that, with respect to texture and structure, cheeses made with UF milk do not need to be scalded after production.

Influence of harvest date and crop yield on the fatty acid composition of virgin olive oils from cv. Picual

In this study was analyzed the effect of crop year and harvesting time on the fatty acid composition of cv. Picual virgin olive oil. The study was carried out during the fruit ripening period for three crop seasons. The mean fatty acid composition of Picual oils was determined. The oils contained palmitic acid (11.9%), oleic acid (79.3%), and linoleic acid (2.95%). The content of palmitic acid and saturated fatty acids decreased during fruit ripening while oleic and linoleic acids increased. The amount of stearic and linolenic acids decreased. The amount of saturated acids, palmitic and stearic, and the polyunsaturated acids linoleic and linolenic was dependent on the time of harvest, whereas the amount of oleic acid varied with the crop year. The differences observed between crop years for both palmitic and linoleic acid may be explained by the differences in the temperature during oil biosynthesis and by the amount of summer rainfall for oleic acid content. A significant relationship was observed between the MUFA/PUFA ratio and the oxidative stability measured by the Rancimat method.

Effect of chymosin and salt reduction on the quality of ultrafiltrated white-salted cheese

This study demonstrated that both chymosin and salt-in-moisture (SM) were important factors for proteolysis in the manufacture of ultrafiltrated white-salted cheese, with significant effects on water-soluble nitrogen and nitrogen soluble in trichloroacetic acid. In contrast, the levels of free amino acids were not significantly affected by chymosin and salt treatments. The cheeses made using high levels of chymosin with low SM had lower levels of residual α(s1)- and β-casein at the end of ripening. On texture profile analysis, the hardness and fracturability of the cheeses significantly increased with SM and decreased during ripening. Increases in chymosin significantly contributed to the overall weakening of the structure throughout ripening. Bitter flavour was detected after 12 weeks in the cheese made with the higher chymosin level and lower SM, which could be the result of accumulation of γ-casein fractions. The sensory data indicated that the hedonic responses for low chymosin with low SM cheeses were good and acceptable in flavour, which may be due to the moderate levels of proteolysis products.