Magnetic particles with active functional groups offer numerous advantages for use in μ-TAS (Micro Total Analytical Systems). The functional site allows chemical binding of the particle with the target species in the fluid sample. Selection of the functional group establishes the target molecule and vice versa under assumptions of highly specific biding. The particles hence act as mobile reaction substrates with high surface to volume ratios owing to their small size. The concept of action at a distance allows their use as agents for separation in microchannels based on relatively simple design. It is possible to manipulate magnetic particles and bound target species using an externally applied magnetic field. Hence, the particles can be effectively separated from the flow of a carrier fluid. Magnetic fields create dipolar interactions causing the particles to form interesting structures and aggregates. Depending upon the applied field, the microstructure evolution of the aggregate is interesting in its own right, e.g. related to improvements in material properties and bottom-up self assembly. The shape of the aggregates can be determined a priori if the interaction between the particles is well characterized. The dominant competing forces that influence magnetic particle dynamics in a flow are magnetic and viscous. There are a number of physical parameters such as viscosity, magnetic susceptibility, fluid velocity, etc. which are varied to study their individual effects. Initially dilute suspensions are studied experimentally and numerically using a particle based dynamics approach. Once established, a force model for particle interaction is investigated for concentrated suspensions. A Lagrangian particle tracking algorithm that returns positions of the particles is used for this work that focuses on studying the dynamics of these particles. A mathematical model is proposed and investigated for functionalization between magnetic and non-magnetic particles. Having characterized the collection of magnetic particles, the effect of relative concentrations is investigated on the collection of the non-magnetic species. / Ph. D.

The thesis has been focused on testing of micromethod of DNA isolation from leaves, fruits and fruit products. Jams were selected for the analysis of plant DNA in technologically processed foods. Plant leaves, fruits, and jams were homogenized using plastic copist in a lysis buffer containing 2% cetyltrimethylammonium bromide (CTAB) with 2.5M sodium chloride (NaCl). Microisolation of plant DNA was performed using poly(hydroxyethylmethacrylate-co-glycidylmethacrylate) – P(HEMA-co-GMA)microparticles. Isolated the DNA concentration and purity were assessed by UV light aborbance using a spectrophotometer. After that, amplification of the DNA was tested in PCR. Primers specific for plant ribosomal DNA: 18S_for a 5,8S_rev (PCR product - 700bp), 26S_for a 26S_rev (PCR product - 220 bp), 18S_for a 18¬S_rev (PCR product - 263 bp) were used. The PCR conditions were optimized and the effect of the amplicon length on its detection was followed. PCR products were detected by agarose gel electrophoresis. It was shown that DNA isolated from almost all of leaves using magnetic particles was in PCR-ready quality in contrary to the fruits. DNA amplified in PCR with primers giving short PCR products was isolated from almost all tested jams. The method must be optimalised, yet.

The thesis were focused on the optimalization of micromethod for isolation of DNA in quality for polymerase chain reaction (PCR) using magnetic microparticles from plant food products. There were chosen a red beetroot (fresh, frozen, dried and sterilized) for the analysis and food products containing red beetroot. Different approaches of processing of homogenates were compared and optimized. The homogenates were prepared in lysis buffer with cetyltrimethylammonium bromide (CTAB) with different amounts of NaCl with or without addition of organic extraction agents chloroform-octanol and isopropanol. Microisolation of DNA was performed using magnetic particles P(GMA). The concentration of NaCl and polyethylene glycol (PEG) 6000 in separation mixtures was tested. The influence on quantity and purity of isolated DNA was compared and the optimum amounts of NaCl in CTAB buffer and optimal concentration of PEG 6000 in separation mixtures were compared. The optimized separation mixture for the DNA isolation from red beetroot was applied to food products containing red beetroot. Amplifiability of DNA was tested in conventional PCR using specific primers for plant DNA. PCR products of length 700 bp were detected by agarose gel electrophoresis.

Different species of genus Bifidobacterium are part of human and animal intestinal flora. These bacteria have benefit effects and therefore they are used in foods and pharmaceutical products as probiotics. Cheese is now suitable as a probiotic matrix except yoghurts and fermentated milks. This diploma thesis was focused on optimalization of DNA isolation from bacteria of genus Bifidobacterium. Magnetic microparticles (P(HEMA-co¬-GMA)) were used for DNA isolation in presence of 8% polyethyleneglycol PEG 6000 and 5 M sodium chloride. Phenol extraction weas also used as an isolation method. Isolated DNA was used for amplification in domain, genus and species specific PCRs. Optimized method was tested for detection of bacteria of genus Bifidobacterium in experimentaly prepared probiotic cheeses. These cheeses contained potential probiotic bacteria from Laktoflóra collection. Bacteria were identified into species using species specific PCR. Species Bifidobacterium animalis was identified in all samples of probiotic cheeses.

The aim of the work was testing of two types of magnetic mikrosheres functionalised with –COOH groups for the isolation of bacterial DNA. Isolation of DNA was carried out from crude lysates of cells prepared from pure culture of Lactobacillus paracassei RL-10 in the presence of binding buffer with 2 M NaCl and 16% PEG 6000. The influence of RNA degradation by enzyme RNase A on the amount of isolated DNA was investigated. It was estimated that RNA degradation affects the amount of DNA isolated. The amount of DNA depended on the type of microparticles. Higher amounts of DNA were isolated using particles with higher content of carboxyl groups. DNA applicable in PCR was isolated using both types of microsheres. In next part of the work, microparticles functionalised with –NH2 groups were used to DNA isolation using electrostatic forces. It was shown that buffer with lower pH is suitable for DNA adsorption onto magnetic microparticles.

This thesis deals with the isolation of probiotic DNA from meat products and its assesment by PCR methods. In this thesis is developed homogenization of samples of sausages with kopist, preparation of sausage cells lysates and isolation of DNA by using of magnetic microparticles. The DNA was isolated from sausage lysates by using magnetic microparticles. Isolated DNA was further amplified in genus and spesies-specific PCR methods. In tested products was proven presence of DNA of domain Bacteria, type Lactobacillus and Bifidobacterium. In one product was proven presence of species Lactobacillus acidophilus and Bifidobacterium animalis.

The thesis has been focused on testing of micromethod of DNA isolation using magnetic particles from thermic-managed food products in a quality suitable for polymerase chain reaction (PCR). Currant jams were selected for the analysis. These were homogenized using plastic copist and stomacher in lysis buffer with cetyltrimethylammonium bromide (CTAB). The effect of chloroform-octanol and isopropanol in the preparation of homogenates was tested. Homogenates were used for DNA isolation by magnetic particles. Rough fraction of DNA was purified by binding on the magnetic particles after centrifugation of the CTAB complexes with proteins, polyphenols and polysaccharides. Two types of magnetic particles were tested: microparticles of poly(hydroxyethylmethacrylate-co-glycidylmethacrylate) - P(HEMA-co-GMA) and nanoparticles of iron oxides covered by poly(L-lysine) - PLL. Isolated DNA was analyzed spectrophotometrically - it was assessed its concentration and contamination by polyphenols and proteins. After that, amplification of the DNA was tested in PCR. Primers specific for plant ribosomal DNA were used. PCR products of expected length 700 bp were detected by agarose gel electrophoresis. It was shown that DNA isolated from currant jams using magnetic particles was in PCR-ready quality.

Résumé : Cette thèse porte sur l’élaboration d’un outil de capture d’ADN permettant d’identifier une mutation génétique (SNP) grâce à la formation de sandwichs avec des particules de carboxylatex biofonctionnalisées avec des oligonucléotides couplée à une détection de la fluorescence. Le modèle biologique choisi pour ce projet est le génotypage plaquettaire et plus particulièrement la recherche du gène biallélique HPA-1. Le principal objectif de ce travail a été d’optimiser un outil de capture préalablement développé dans l’équipe (Trévisan, 2011) afin de réduire le nombre d’étapes et de simplifier la mise en œuvre globale du test en modifiant les interactions moléculaires utilisée pour capturer l’ADN cible et en utilisant des particules fluorescentes comme élément de détection. En présence d’ADN cible, des sandwichs sont formés entre les particules fluorescentes et les particules magnétiques biofonctionnalisées. Ces sandwichs sont purifiés par séparation magnétique et la fluorescence est détectée par trois méthodes : la cytométrie en flux, l’imagerie de fluorescence et l’Evareader (détection par ondes évanescentes). Dans un premier temps, les paramètres de fonctionnalisation chimique et biologique des différentes particules (magnétiques et fluorescentes) ont été déterminés et optimisés ainsi que les conditions d’hybridation pour la capture de l’ADN cible. Ensuite, la formation des sandwichs et leur détection ont été suivies par des mesures de fluorescence en utilisant trois méthodes différentes : la cytométrie en flux, l’imagerie de fluorescence et l’Evareader (capteur à ondes évanescentes). Les résultats obtenus avec les différentes méthodes de détection sont concordants et montrent que l’outil de capture d’ADN développé permet de capturer la cible synthétique (oligonucléotide) HPA-1 en réduisant le temps d’analyse de 45 min. Dans nos conditions, le test permet de discriminer l’allèle a de l’allèle b du gène HPA-1 qui ne diffère que d’un nucléotide. Le rapport des signaux de fluorescence issus du sandwich spécifique et du sandwich non spécifique est d’environ 2,5 à 3. Ce rapport devra être amélioré par la suite, en optimisant les conditions de formation des sandwichs. La prochaine étape consistera à optimiser le système de capture d’ADN développé pour gagner en spécificité et déterminer la limite de détection du test. Ce test devra également être validé avec des échantillons biologiques. A plus long terme, la fluorescence pourra être détectée par un photodétecteur miniaturisé actuellement développé à l’Université de Sherbrooke. Des études préliminaires présentées dans ce manuscrit montrent les potentialités de ce nouveau transducteur. // Abstract : This thesis is about the development of a new assay to capture DNA. This assay is based on the formation of sandwiches between biofunctionnalized with oligonucleotides carboxylatex microparticles combined with fluorescence detection. It should be able to discriminate single nucleotide polymorphism (SNP). This assay is designed to be applied to platelet genotyping for the research of the gene HPA-1. The main goal of this work was to improve an assay previously developed (Trévisan, 2011) by INL and EFS Rhône-Alpes. The objectives are to reduce the number of steps and to simplify the test. To do so, the molecular interactions used in order to capture target DNA are modified and fluorescent microparticles are used for the detection. In the presence of target DNA, sandwiches are formed between both biofunctionnalized fluorescent and magnetic particles. Those sandwiches are purified through magnetic separation. Then, fluorescence is detected by three methods: flow cytometry, fluorescence imaging and Evareader (detection with an evanescent wave). First, chemical and biological parameters for the functionalization of the different particles (magnetic and fluorescent) are determined. The conditions for the capture of target DNA were optimized. Then, the formation and the detection of the sandwiches were estimated by measuring the fluorescence using three different methods: flow cytometry, fluorescence imaging and Evareader. The results obtained with the three methods are consistent. They show that the new system enables to capture synthetic target (oligonucleotide) HPA-1 with a reduction of total time analysis of 45 min. In our conditions, SNP can be discriminated for HPA-1 gene. For this discrimination, the fluorescence signal ratio about 2.5 to 3. This ratio should be improved by optimizing the conditions of sandwiches formation. Next step will consist in the optimization of the system developed to capture DNA in order to gain specificity and to determine the limit of detection. This test should also be validated with biological samples. In the long term, fluorescence could be detected by a miniaturized photodetector developed in the University of Sherbrook. Preliminary studies presented in this manuscript show the potentialities of this new transducer.

Cette thèse porte sur l’élaboration d’un outil de capture d’ADN permettant d’identifier une mutation génétique (SNP) grâce à la formation de sandwichs avec des particules de carboxylatex biofonctionnalisées avec des oligonucléotides couplée à une détection de la fluorescence. Le modèle biologique choisi pour ce projet est le génotypage plaquettaire et plus particulièrement la recherche du gène biallélique HPA-1. Le principal objectif de ce travail a été d’optimiser un outil de capture préalablement développé dans l’équipe (Trévisan, 2011) afin de réduire le nombre d’étapes et de simplifier la mise en oeuvre globale du test en modifiant les interactions moléculaires utilisée pour capturer l’ADN cible et en utilisant des particules fluorescentes comme élément de détection. En présence d’ADN cible, des sandwichs sont formés entre les particules fluorescentes et les particules magnétiques biofonctionnalisées. Ces sandwichs sont purifiés par séparation magnétique et la fluorescence est détectée par trois méthodes : la cytométrie en flux, l’imagerie de fluorescence et l’Evareader (détection par ondes évanescentes). Dans un premier temps, les paramètres de fonctionnalisation chimique et biologique des différentes particules (magnétiques et fluorescentes) ont été déterminés et optimisés ainsi que les conditions d’hybridation pour la capture de l’ADN cible. Ensuite, la formation des sandwichs et leur détection ont été suivies par des mesures de fluorescence en utilisant trois méthodes différentes : la cytométrie en flux, l’imagerie de fluorescence et l’Evareader (capteur à ondes évanescentes). Les résultats obtenus avec les différentes méthodes de détection sont concordants et montrent que l’outil de capture d’ADN développé permet de capturer la cible synthétique (oligonucléotide) HPA-1 en réduisant le temps d’analyse de 45 min. Dans nos conditions, le test permet de discriminer l’allèle a de l’allèle b du gène HPA-1 qui ne diffère que d’un nucléotide. Le rapport des signaux de fluorescence issus du sandwich spécifique et du sandwich non spécifique est d’environ 2,5 à 3. Ce rapport devra être amélioré par la suite, en optimisant les conditions de formation des sandwichs. La prochaine étape consistera à optimiser le système de capture d’ADN développé pour gagner en spécificité et déterminer la limite de détection du test. Ce test devra également être validé avec des échantillons biologiques. A plus long terme, la fluorescence pourra être détectée par un photodétecteur miniaturisé actuellement développé à l’Université de Sherbrooke. Des études préliminaires présentées dans ce manuscrit montrent les potentialités de ce nouveau transducteur. / This thesis is about the development of a new assay to capture DNA. This assay is based on the formation of sandwiches between biofunctionnalized with oligonucleotides carboxylatex microparticles combined with fluorescence detection. It should be able to discriminate single nucleotide polymorphism (SNP). This assay is designed to be applied to platelet genotyping for the research of the gene HPA-1. The main goal of this work was to improve an assay previously developed (Trévisan, 2011) by INL and EFS Rhône-Alpes. The objectives are to reduce the number of steps and to simplify the test. To do so, the molecular interactions used in order to capture target DNA are modified and fluorescent microparticles are used for the detection. In the presence of target DNA, sandwiches are formed between both biofunctionnalized fluorescent and magnetic particles. Those sandwiches are purified through magnetic separation. Then, fluorescence is detected by three methods: flow cytometry, fluorescence imaging and Evareader (detection with an evanescent wave). First, chemical and biological parameters for the functionalization of the different particles (magnetic and fluorescent) are determined. The conditions for the capture of target DNA were optimized. Then, the formation and the detection of the sandwiches were estimated by measuring the fluorescence using three different methods: flow cytometry, fluorescence imaging and Evareader. The results obtained with the three methods are consistent. They show that the new system enables to capture synthetic target (oligonucleotide) HPA-1 with a reduction of total time analysis of 45 min. In our conditions, SNP can be discriminated for HPA-1 gene. For this discrimination, the fluorescence signal ratio about 2.5 to 3. This ratio should be improved by optimizing the conditions of sandwiches formation. Next step will consist in the optimization of the system developed to capture DNA in order to gain specificity and to determine the limit of detection. This test should also be validated with biological samples. In the long term, fluorescence could be detected by a miniaturized photodetector developed in the University of Sherbrook. Preliminary studies presented in this manuscript show the potentialities of this new transducer.

This thesis is interested in isolation and identification of probiotic bacteria in three different probiotic products using polymerase chain reaction (PCR). DNA in quality suitable for PCR was isolated from crude lysates using three different types of magnetic microparticles and phenol extraction. Identification genera and species of probiotic bacteria was proven using genus and species specific PCRs. Results were in accordance with data presented by manufacturers.