Arsenic (As) is a problem with rice production systems throughout the world as high As concentrations are reported in rice grains originating from several parts of the world. This characteristic is mainly due to the flooded conditions utilized in rice culture. We hypothesized that the soluble As concentrations in the rice rhizosphere can be decreased by growing rice more aerobically through intermittent flooding. Intermittent water management practices might also change microbial populations in the rice rhizosphere that might potentially impact As chemistry and bioavailability. Two field-scale experiments were conducted over two years to study the impact of intermittent and continuous flooding on As speciation and microbial populations in the rice rhizosphere. As levels and speciation in the rhizosphere soil, root-plaque and pore-water were determined using a high performance liquid chromatography-inductively coupled plasmamass spectroscopy (HPLC-ICP-MS). The microbial populations were assessed from the rhizosphere soil and root-plaque samples using quantitative polymerase chain reaction (qPCR) and 16S rRNA sequencing. Pore-water and root-plaque total-As concentrations significantly decreased in the intermittent compared to the continuous flood plots. Inorganic arsenite (iAsIII) was predominant in pore-water and inorganic arsenate (iAsV) in root-plaque and soil. Rootplaque sequestered significantly higher levels of As (almost tenfold higher) than the adjacent rhizosphere soil. Grain As concentrations also decreased by 35 to 45 percent in the intermittent compared to the continuously flooded plots. Organic As species, monomethyl and dimethyl arsenate were detected in the rhizosphere with relative increases and decreases among the treatments. Bacteria were the predominant group (91 to 94 percent and 48 to 78 percent of total community in root-plaque and rhizosphere soils, respectively). Archaea were also a major component of rhizosphere soil with their populations being higher under continuous flooding. The relative abundance of iron-reducing bacteria was around 3 to 6 percent of the total community in root-plaque and around 6 to 6 percent in soil, with significantly lower abundance in the intermittent compared to the continuously flooded plots. Results of these studies demonstrated that intermittent flooding could be a potential management option to reduce grain As in rice cultivated on fields with moderate to high As concentrations.

As part of a larger quantitative microbial risk assessment (QMRA) study, the raw water intakes of 8 different drinking water treatment plants in Ontario were sampled for rotavirus. Group A rotavirus was detected and semi-quantified via RT-qPCR. Rotavirus was detected in 6 of 8 drinking water treatment plant raw water intakes at various sampling times during a 2 year period at estimated quantities of 0 – 513 viral genome copies/L water. As hypothesized, the virus counts showed a seasonal tendency with significant detection most likely to occur during the spring months and a correlation with turbidity measurements. To our knowledge this is the first study exploring the presence of rotavirus in Ontario source waters. With new proposed changes to the Health Canada guidelines regarding the viruses in drinking water, data on the presence of rotavirus in source waters is required for assessment of risk to public health. / Kingsclear First Nation

No description available.

Lamprey adults may be parasitic or non-parasitic, but the genetic basis of life history type is unknown. Although external differences between types are not apparent until metamorphosis, previous studies have suggested histological differences during ovarian differentiation. This study examined potential differences between parasitic chestnut lamprey Ichthyomyzon castaneus and non-parasitic northern brook lamprey I. fossor before, during, and after ovarian differentiation, using histological examination of the gonad, quantitative reverse-transcriptase PCR, and RNA sequencing. There were no observable differences in the timing or nature of ovarian differentiation. However, there was evidence of differential expression of individual genes associated with growth, apoptosis, and fecundity and of sets of genes associated with energy and lipid metabolism. The sequence resources developed in this project will be useful for future examination of the genetic basis of lamprey life history type and of the genes controlling sex differentiation in these ancient vertebrates.

La microflore des raisins est importante d'un point de vue technologique car elle conditionne en partie la qualité du vin. Or, la diversité des flores fongiques présentes sur baies de raisin ainsi que leur potentiel de contamination du produit final ne sont pas encore pleinement connus. Dans ce cadre, la caractérisation des flores fongiques cultivables présentes sur baies de raisin a été réalisée par PCR ITS-RFLP. 41 espèces de moisissures différentes sur les 43 étudiées appartenant à 11 genres différents ont été caractérisées de façon fiable. Seules les espèces Penicillium thomii et Penicillium glabrum ont présenté le même profil. Ainsi 96.3% des souches étudiées ont été caractérisées avec au maximum 4 enzymes de restriction et 41.5% des souches ont pu l'être avec seulement 2 enzymes de restriction. Ces résultats ont permis d'enrichir les bases de données, moyennement pourvues en séquences ITS caractéristiques de genres ou d'espèces de moisissures présentes sur baies de raisin. De plus, une étude exhaustive des moisissures présentes sur baies de raisin en Bourgogne a permis, par PCR ITS-RFLP, d'identifier 199 souches au niveau de l'espèce et ce quelque soit le genre. Penicillium spinulosum est l'espèce majoritaire isolée pour le millésime 2008 en Bourgogne. Parallèlement, la quantification de Botrytis cinerea, choisi comme micro-organisme modèle, a été réalisée par qPCR. La technique qPCR décrite dans ce travail présente (i) une bonne sensibilté avec une limite de détection de 6.4 pg d'ADN correspondant à 540 spores, (ii) l'originalité de travailler en échantillons naturellement contaminés et la fiabilité d'utiliser un standard interne. L'évaluation de l'efficacité de différentes stratégies de traitements anti-Botrytis a confirmé l'importance de la prophylaxie (effeuillage) dans la lutte contre Botrytis cinerea.

Lamprey adults may be parasitic or non-parasitic, but the genetic basis of life history type is unknown. Although external differences between types are not apparent until metamorphosis, previous studies have suggested histological differences during ovarian differentiation. This study examined potential differences between parasitic chestnut lamprey Ichthyomyzon castaneus and non-parasitic northern brook lamprey I. fossor before, during, and after ovarian differentiation, using histological examination of the gonad, quantitative reverse-transcriptase PCR, and RNA sequencing. There were no observable differences in the timing or nature of ovarian differentiation. However, there was evidence of differential expression of individual genes associated with growth, apoptosis, and fecundity and of sets of genes associated with energy and lipid metabolism. The sequence resources developed in this project will be useful for future examination of the genetic basis of lamprey life history type and of the genes controlling sex differentiation in these ancient vertebrates.

L'objet de cette thèse fut d'utiliser l'avantage qu'offre la microfluidique couplée à la thermique, pour fabriquer des dispositifs de contrôle de température sur des projets/applications distincts en vue de leur valorisation. En biologie moléculaire, par la réalisation d'une PCR quantitative rapide, pour la détection d'agents pathogènes. Nous avons réalisé une nouvelle plateforme de détection d'agent pathogène capable de faire 30 cycles d'amplifications en moins de trois minutes. Nous avons également illustré la capacité du dispositif à quantifier par fluorescence en temps réel des agents simulant de l'Anthrax et d'Ebola. 7 minutes et 7 minutes 30 secondes suffisent pour amplifier/détecter ces bactéries et virus. Nous avons également prouvé qu'à ces vitesses ce dispositif rapide de qPCR/RT-qPCR ne dégradait pas l'efficacité, la spécificité et les cycles seuils de détection. Nous avons également démontré que la sensibilité du dispositif était de 100 copies d'Adn initiale. En biologie cellulaire, Nous avons réalisé un dispositif " universel " de contrôle dynamique de température pour l'imagerie cellulaire haute résolution. Ce dispositif de contrôle dynamique de température, permet l'étude spatiotemporelle de mécanismes cellulaires sous microscope haute résolution grâce à l'utilisation de mutant thermosensibles. De nombreuses validations biologiques ont ainsi été réalisées sur notre dispositif dont l'objet final est la commercialisation. / The purpose of this work is to take advantage of micro fabrication combined with heat and mass transfer to build potential commercialized temperature control devices in several domain. In molecular biology, for molecular pathogenesis detection we made a new PCR device able to able to perform 30 amplifications cycles in less than 3 minutes. We also demonstrated that our platform was able to quantify with fluorescence the presence of Ebola and Anthrax simulant agents. Respectively 7 minutes and 7 minutes 30 secondes are required to detect the virus and bacteria. In cellular biology we have made a universal temperature control for live cell imaging. It device allow to perform spacio-temporal study of cell mecanisms due to is fast ability to shift from a temperature to another in less than 10 seconds. Many biological validations have been performed. Thank to his universal adaptation to microscope we have also decided to commercialize this device by creating a new start-up.

Common wheat ( Triticum aestivum L.) is the most commonly grown cereal in the world. In this time wheat genotypes with different colour of kernels have become more important not only to enhance food sources, but also for its importance as a function food, which provides health-promoting substances. Anthocyanins, flavonoid substances in nature, are responsible for the different pigmented caryopsis of common wheat. Pigments formed in anthocyanin biosynthetic pathway are stored in different parts of the caryopsis. Purple pigments are accumulated in the pericarp and blue pigments are accumulated in the aleurone layer of the caryopsis. In this work we use spring forms of common wheat with white endosperm (Novosibirskaya 67), with purple pericarp (ANK - 28B and Abissinskaya Arraseita), and with blue aleurone layer (UC66049 and Tschermaks Blaukörniger Sommerweizen) from Agrotest fyto Kroměříž, s.r.o. collection. Total RNA from this genotypes was isolated using a phenol-chloroform extraction. Total RNA was transcribed into cDNA by reverse transcription. Based on the obtained PCR products sequences were obtained candidate gene sequences for dihydroflavonol-4-reductase (95-100% similarity) and anthocyanidinsynthase (90% similarity). The variability among genotypes in this study was due to single nucleotide polymorphisms and indels. The obtained candidate sequences were localized in the wheat genome and after that was studied gene expression of DFR gene by using qPCR.

The thesis deals with localization and quantification of Sphaerospora molnari (Myxozoa) in common carp (Cyprinus carpio). Sphaerospora molnari is microscopic endoparasite which attacks various tissues and organs, preferentially parasitizing intracellularly (histozoic type) in a carp fry. In this work, we studied the course of parasite infection in the various tissues and organs of the host (blood, gills, skin, kidney, liver, and muscle) in laboratory conditions. The course of infection was detected using qPCR.

Dentre as oito espécies do gênero Listeria, a única transmitida por alimentos, patogênica para humanos, é a Listeria monocytogenes. De grande preocupação para a indústria alimentícia, este microrganismo pode ser encontrado em diversas superfícies de plantas processadoras de alimentos, sendo capaz de se aderir e formar persistentes biofilmes. No presente trabalho, foi estudada a influência da concentração de glicose e do tempo de incubação na formação de biofilme por uma cepa de L. monocytogenes, sorotipo 1/2a, cultivada em três diferentes temperaturas, 7°C, 25°C e 37°C, através de planejamento experimental utilizando a Metodologia de Superfície de Resposta. As duas variáveis testadas, para os intervalos estudados, foram significativas (p<0,05) na formação de biofilme somente na temperatura de 37°C e, tanto concentrações de glicose tendendo a zero combinadas com tempos de incubação próximos a 26 h, como maiores concentrações de glicose combinadas com menores tempos de incubação, dentro da faixa de estudo aplicada, representaram boas condições para a formação de biofilme. Foi também realizada a análise transcricional de genes relacionados à formação de biofilme e virulência em duas cepas de L. monocytogenes, sorotipos 1/2a e 4b, cultivadas a 7°C e 37°C (condição controle), pela técnica de PCR quantitativo em tempo real (RT-qPCR). Para ambas as cepas, os genes sigB, prfA, luxS, sufS, sufU, ltrC e flaA apresentaram transcrição significativamente aumentada (p<0,05) a 7°C, em comparação aos resultados para a condição de cultivo a 37°C, enquanto que o gene hly não variou significativamente a sua transcrição entre as duas temperaturas. O gene actA foi mais transcrito a 7°C para a cepa denominada 55, do sorotipo 1/2a, enquanto que não variou significativamente a sua transcrição entre as duas condições de crescimento para a cepa denominada 47, do sorotipo 4b. No entanto, para a cepa 55, o gene degU não demonstrou diferença estatisticamente significativa entre seus níveis de transcrição nas duas temperaturas estudadas, mas para a cepa 47, apresentou transcrição significativamente aumentada a 7°C. Interessantemente, a presença do gene agrA não foi detectada na cepa 47, e os seus níveis de transcrição foram menores a 7°C para a cepa 55. Estes resultados demonstram que os dois sorotipos estudados, responsáveis por muitos dos casos humanos de listeriose, apresentam mecanismos moleculares diferentes, nas temperaturas de 7°C e 37°C. / Among the eight species of genus Listeria, the only transmitted by food, pathogenic for humans, is Listeria monocytogenes. Of great concern to the food industry, this microorganism can be found in various areas of food processing plants, being able to adhere and form persistent biofilms. In the present work, the influence of glucose concentration and incubation time on biofilm formation by a strain of L. monocytogenes, serotype 1/2a, grown in three different temperatures, 7°C, 25°C and 37°C, have been studied, through an experimental design using the Response Surface Methodology. The two variables tested, for the studied intervals, were significant (p<0,05) in the biofilm formation only at a temperature of 37°C and, both glucose concentrations tending to zero combined with incubation times near to 26 h, and higher glucose concentrations combined with lower incubation times, within the applied range study, represented good conditions for biofilm formation. Transcriptional analysis of genes related to biofilm formation and virulence in two strains of L. monocytogenes, serotypes 1/2a and 4b, grown at 7°C and 37°C (control condition), was also performed, by real-time quantitative PCR (RT-qPCR). For both strains, sigB, prfA, luxS, sufS, sufU, ltrC and flaA genes showed significantly increased transcription (p<0,05) at 7°C, in comparison with results for the growth condition at 37°C, whereas hly gene did not varied significantly its transcription between the two temperatures. The actA gene was more transcribed at 7°C for the 55 strain, serotype 1/2a, while did not varied significantly its transcription between the two growth conditions for the 47 strain, serotype 4b. However, for 55 strain, the degU gene did not showed statistically significant difference for its transcription levels between the two studied temperatures, but for 47 strain, presented significantly increased transcription at 7°C. Interestingly, the presence of agrA gene was not detected in 47 strain, and its transcription levels were lower at 7°C for 55 strain. These results demonstrate that the two studied serotypes, responsible for many of the human listeriosis cases, have different molecular mechanisms, at temperatures of 7 and 37°C.