No description available.

Suppression of genes involved in DNA repair, tumor suppression and detoxification through epigenetic modifications has been implicated in the etiology of cancer. As such analysis of promoter methylation patterns in genes frequently down regulated in breast cancer in non-cancerous subjects may serve as an indicator of breast cancer risk. CpG-island hypermethylation of single genes has been detected in cells isolated from nipple aspirate and ductal lavage, yet both isolation methods yield insufficient cells to complete an extensive analysis on any one donor sample. As an alternative we have turned to magnetic separation of human mammary epithelial cells from breast milk. Initial studies with these cells, which are detailed in chapter one, show that a breast milk sample provides sufficient epithelial cells to isolate high quality RNA for gene expression analyses or genomic DNA for methylation analysis of multiple genes. Using quantitative RT-PCR of RNA collected from these samples we detected differences in the mRNA levels for six genes known to be down regulated in breast cancers: BRCA1, p16, CDH1, TMS-1, GSTPi, and SFRP1. Additionally using methyl-specific PCR (MSP) we assayed for a small panel of genes frequently methylated in cancer and found them to be unmethylated in the few breast milk samples examined. However, given the small number of CpG sites which can be assayed by the MSP technique it is not surprising that methylation was not detected in disease-free subjects. With methods for collecting breast milk samples and processing them for genetic material established we turned to a more comprehensive study of DNA methylation in larger population of donors which is detailed in chapter two. Utilizing a highly sensitive and highly quantitative methylation analysis technique known as Pyrosequencing we examined age-related methylation patterns for RASSF1A, TMS-1, CDH1, SFRP1, GSTPi, and CRBP1 in genomic DNA purified from exfoliated epithelial cells magnetically enriched from breast milk (n=111) and whether the protective effects conveyed by early pregnancy could be partly due to decreases in DNA hypermethylation. Although firm answers about early pregnancy were inconclusive based on our sample pool, this body of work lays down a solid foundation for future studies.

No description available.

The main aim of this study is to combine the sol-gel technology and renewable surface flow injection analysis (RS-FIA) techniques for iron speciation and determination. Thus the home-made FIA system, which consists of 2 syringe pumps and 3 multi-position selection valves, is modified with two flow cells (magnetic cell and jet ring cell) in order to be suitable for renewable surface flow injection technique. All the computer programs used for flow injection analysis are modified to control the whole system automatically. Two different types of solid phase extraction materials are used for the speciation of iron in aqueous systems. Magnetic beads coated with primary amino groups are utilized for the determination of Fe (III). The magnetic bead reactor is created within the flowing stream by retaining the magnetic beads with a home-made electromagnet. The elution cycle for Fe (III) is done with 0.1 M EDTA solution and determined on-line by transferring to an atomic absorption spectrometer. The spent beads are collected off-line and regenerated. For the preconcentration of Fe (II), ferrozine doped sol-gel beads are prepared as reactive and disposable surfaces. These beads are handled by the system equipped with a jet ring cell which is connected on-line to a portable UV-VIS fiber optic spectrometer. Amino sol-gel and ferrozine-doped sol-gel beads are prepared using sol-gel technology and characterized by using surface techniques. Their performances in preconcentration and speciation of iron and the influence of different experimental parameters such as pH, the sequence of reagents, reactor lengths and reaction periods on the flow system are investigated. Renewable surface flow injection analysis is performed by either bead injection or sequential bead injection methods.

En dépit de leur importance, la caractérisation des communautés bactériennes dans l’environnement reste encore très incomplète. Les principales raisons sont, d’une part, la difficulté d’appréhender la totalité de la communauté bactérienne quand plus de 99% des bactéries demeurent récalcitrantes à la culture in vitro et ne peuvent donc être étudiées par les approches classiques de microbiologie. D’autre part, la métagénomique, censée contourner cette méthode de culture en s’intéressant à l’ensemble des génomes extraits des milieux d’études, demeure elle aussi imparfaite du fait de limitations techniques (biais d’extraction de l'ADN, de clonage, de PCR, de séquençage et d’assemblage des génomes etc.) et conceptuelles, inhérentes à la complexité et l’hétérogénéité des environnements. Pour compenser les limites de chacune de ces techniques, des méthodes de tri cellulaire appliquées en conjonction avec les deux premières pourraient aider à un meilleur décryptage de la diversité microbienne. Basée sur la sélection spécifique (taxonomique et/ou fonctionnelle) et l’isolement direct des cellules bactériennes ciblées à partir d’un échantillon environnemental complexe, l’étude est restreinte à une population spécifique, voire à une cellule isolée. Pourront alors être appliquées les approches classiques de mise en culture ou d’extraction de l’ADN pour une étude restreinte à l’ADN ou l’ARN, leur répétition sur les différentes populations devant à terme (lointain) approcher l’exhaustivité. C’est dans ce contexte que s’est positionné ce travail de thèse visant dans un premier temps à mettre au point un nouvel outil de tri cellulaire basé sur l’intégration de micro-aimants permanents dans un canal microfluidique. A partir de ce système de tri magnétique miniaturisé, offrant de nombreux avantages (dispositif portable, peu coûteux, nécessitant de faibles volumes réactionnels et potentiellement intégrable en « laboratoire sur puce »), une technique d’isolement sélectif de cellules bactériennes marquées magnétiquement a alors été développée. Ciblées sur des critères taxonomiques après hybridation in situ avec des sondes d’acides nucléiques biotinylés complémentaires d’une région spécifique du gène 23S rRNA, des cellules bactériennes ont été marquées magnétiquement après réaction de la sonde avec des nanoparticules magnétiques fonctionnalisées par des molécules de streptavidine. Les premiers résultats montrent l’établissement d’une méthode de tri suffisamment spécifique et sensible pour piéger les cellules marquées diluées (0,04%) au sein d’une suspension, à des niveaux compatibles avec l’isolement futur de populations d’intérêt à partir de communautés d’environnements complexes. Sur un principe comparable, l’approche a été adaptée à l’étude des transferts horizontaux de gènes in situ. Les applications d’un tri cellulaire grâce au marquage par des nanoparticules magnétiques et l’emploi de micro-aimants intégrés dans des microsystèmes fluidiques semblent donc très prometteuses pour le développement de la microbiologie environnementale. / Despite their importance, bacterial communities in the environment remain poorly characterized. On the one hand, it is difficult to gain knowledge of the community as a whole because over 99% of bacteria are recalcitrant to in vitro culture, rendering classic microbiological approaches imposible to carry out. On the other hand, metagenomics, which can be used to circumvent culture-based approaches by extracting all the genomes from a given environment, is also problematic given the associated technical limitations (biases related to DNA extraction, cloning, PCR, genome sequencing and assembling etc.), and conceptual difficulties related to the complexity and the homogeneity of the environments. In order to overcome some of the limitations of these approaches, bacterial cell selection methods have been developed and can be used to improve our understanding of microbial diversity. Based on taxonomic and/or functional selection and the direct isolation of bacterial cells from an environmental sample, bacterial cell selection can be used to reduce microbial community complexity by targeting specific populations, or even an isolated cell. A variety of classic approaches such as cultivation or DNA/RNA extraction can then be carried out. This cycle can theoretically be repeated until all members of the community are characterized. The aim of this doctoral thesis was to design a novel cell selection tool based on the permanent integration of micro-magnets into a microfluidic canal. In conjunction with a new miniaturized magnetic selection system that provides several advantages over larger systems (portable, low cost, requiring smaller reaction volumes and can be potentially integrated on “laboratory on a chip” systems), a method for selective bacterial cell isolation using magnetic labeling was developed. The bacterial cells were targeted based on taxonomic criteria; biotin-labeled probes were developed for a specific region of the 23S rRNA gene. Following in situ hybridization with the probes, baceterial cells were labeled with streptavidin-functionalized magnetic nanoparticles. First results showed that the tool was specific and sensitive enough to trap labeled and diluted (0,04%) cells from a suspension at levels that are comparible to populations of interest found in complex environmental communities. This tool has also been adapted to study in situ horizontal gene transfer as well. The application of a cellular selection tool that labels targets with magnetic nanoparticles coupled to fluidic microsystems with integrated nano-magnets looks very promising for future studiesin environmental microbiology.