This research has successfully developed a multiple fluorescence detection method for high throughput capillary electrophoresis detection using a digitally-modulated light source and a spectrum detection system. A commercial available LCD (liquid crystal device) projector is adoped to replace the spacially-filttered light source (Hg lamp) in a conventional fluorescence microscopy. The LCD projector can be digitally controlled by a computer to create the three primary colors of RGB (red, green, and blue) for fluorescence excitation in the analytes. The emitted light from the fluorescent samples is then collected using a UV-VIS-NIR spectrometer through a ultimode fiber. Delicate optical components, such as filter wheel or acousto-optic filtering system, for filtering different excitation light sources can be excluded with this simple and novel approach. In addition, the desired wavelength for the excitation light can be selected quickly and smoothly without vibration problems come with the mechanical optical components. Three fluorescent dyes (Atto 647N, Rhodamine B, Fluorescein) with different excitation and emission wavelength has been used to demonstrate the proposed digitally-modulated light source system for high throughput CE system. The optimal operation conditions for obtaining best detection signal-to-noise ratio for different fluorescence dyes are firstly determined. In addition, the current study proposes a mixed-color light (visually in purple) composed of two specific primary lights (red and blue) to simultaneously excite a mixed sample composed of two fluorescent dyes (Atto 647N and FITC). Separation and detection of the mixed fluoresce samples using a single excitation illumination using the proposed digital-modulated CE system is successfully demonstrated. Finally, a single-strand DNA biosample is used to confirmed the proposed system is feasible of adopting in the bio-analytical applications. The technique proposed in this study has shown its potential to be a high throughput CE detection system.

The objective of this thesis work is to increase the functionality of optical fibers for possible applications in life-sciences. Optical fibers are a promising technology for use in biology and medicine. They are low-costwaveguides, flexible and have a small cross-section. They can guide high-power light with low loss in a micrometer core-size. These features make fibers attractive for minimally-invasive,in-vivostudies. The backwards guidance of the optical signal allows for real-time monitoring of the distance to the scattering targets and to study the environment through Raman scattering and fluorescence excitation. The longitudinal holes introduced in the fibers can be used,for instance,for delivery of medicine to a specific regionof a body. They could even be used for the extractionof species considered interesting for further analysis, for example, studyingcells that may be cancer-related. This thesis deals with four main topics. First, a demonstration is presented of the combination of high-power light guidance for ablation, low-power light reflectometry for positioning, and for liquid retrieval in a single fiber. It was found that in order to exploit the microfluidic possibilities available in optical fibers with holes, one needs to be able to combine fluids and light in a fiber without hindering the low-loss light guidance and the fluid flow. Secondly, one should also be able to couple light into the liquids and backout again. This is the subject of another paper in the present thesis. It was also observed that laser excitation through a fiber for the collection of a low-intensity fluorescence signal was often affected by the luminescence noise createdby the primary-coating of the fiber. This problem makes it difficult to measure low light-levels, for example, from single-cells. Athirdpaper in this thesis then describes a novel approach to reduce the luminescence from the polymer coating of the fiber, with the use of a nanometer-thick carbon layer on the cladding surface. Finally, exploiting some of the results described earlier, an optical fiber with longitudinal holes is used for the excitation, identification and for the collection of particles considered being of interest. The excitation light is guided in the fiber, the identification is performed by choosing the fluorescent particles with the appropriate wavelength, and, when a particle of interest is sufficiently near the fiber-tip, the suction system is activated for collection of the particle with good specificity. It is believed that the work described in this thesis could open the doors for applications in life-sciences and the future use of optical fibers for in-vivo studies. / <p>QC 20140516</p>

MicroRNAs (miRNAs) are a class of small, single-stranded, non-protein coding RNA molecules that regulate cellular messenger RNA (mRNA) and protein levels by binding to specific mRNAs. Aberrant miRNA expression has been shown to be implicated in several diseases, including cancer. Extracellular miRNAs have been found to circulate in the bloodstream and some of their levels have been associated with different diseases. Furthermore, they hold promise as tissue- and blood-based biomarkers for cancer classification and prognostication. Blood-based biomarkers are attractive for cancer screening due to their minimal invasiveness, relatively low cost and ease of reproducibility. New miRNA analysis techniques will add toward the understanding of their biological functions. In this thesis, I investigate the utility of capillary electrophoresis (CE) and mass spectrometry (MS) for analysis of miRNAs through proof-of-concept experiments. In the fi rst part of this work, we developed a Protein-Facilitated Affinity Capillary Electrophoresis (ProFACE) assay for rapid quantification of miRNA levels in blood serum (see List of publications (6)). We also implemented a capillary electrophoresis with laser induced fluorescence detection (CE-LIF) method with online sample pre-concentration for detection of endogenous microRNAs in human serum and cancer cells. 3' modification of miRNA is a physiological and common post-transcriptional event that shows selectivity for specific miRNAs and is observed across species. Recent studies have shown that post-transcriptional addition of nucleotides to the 3' end of miRNAs is a mechanism for miRNA activity regulation. For example, such modifications in plants and C. elegans influence miRNA stability. In humans, effects on miRNA stability and on mRNA target repression have both been observed. Thus, there is a need for miRNA detection techniques which are direct and multiplexed, require minimal sample preparation and provide qualitative information regarding these modifications. We developed a multiplexed miRNA detection technique based on capillary electrophoresis coupled on line with electrospray ionization mass spectrometry (CE-ESI-MS). This method allowed a label-free, direct detection of multiple miRNAs extracted from cancer serum as well as their post-transcriptional modifications with a high mass accuracy.

In this study, reversed phase HPLC with dual UV photodiode (PDA) and fluorescence (FL) detection were used to investigate copper complexes with fulvic, caffeic, vanillic, salicylic, and adipic acids. Application of the RE method provided valuable information on the retention behavior and spectral characteristics of FA and model compounds. Even though the method was only applicable to VA, the use of the PDA detector allowed the UV-V is scanning of the separated peaks. This allowed the comparison between the UV-Vis spectra of uncomplexed species. The overall results provide an experimental framework for validation of the proposed Cu-humate interaction models.

京都大学 / 新制・課程博士 / 博士(工学) / 甲第23513号 / 工博第4925号 / 新制||工||1769(附属図書館) / 京都大学大学院工学研究科材料化学専攻 / (主査)教授 大塚 浩二, 教授 松原 誠二郎, 教授 秋吉 一成 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

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Les acides nucléiques simple-Brins contenant des répétitions de guanines peuvent former des structures secondaires non canoniques dites G-Quadruplexes, composées de plusieurs couches de quartets de guanine. Malgré de nombreuses études in vivo, les preuves de présence de structures quadruplexes in vivo restent indirectes. L’objectif de ce travail était la recherche de sondes fluorescentes capables de signaler la présence d'ADN quadruplex et détecter sa structure (topologie).Deux séries de sondes fluorescentes ont été envisagées et préparées : les colorants styryles (majoritairement distyryles) et les dérivés PDC-Coumarines. La conception de ces deux séries est basée sur l’échafaudage bisquinolinium pyrido¬dicarboxamide (PDC-360A), un ligand sélectif ayant une bonne affinité vis-À-Vis des structures d’ADN quadruplexes, mais qui est non-Fluorescent. En s’inspirant de cette molécule et du motif styryle, connu pour ses propriétés spectroscopiques, nous avons préparé une librairie de colorants distyryles. Une deuxième série, les dérivés PDC-Coumarine, est synthétisée afin d’introduire la propriété fluorescente de la coumarine dans le PDC par une liaison covalente.Les propriétés de colorant de ces deux librairies (65 composés) ont été étudiées en présence de nombreuses structures d’ADN (quadruplex et duplex) en utilisant un criblage par fluorescence sur microplaques et des méthodes de titration. Nos résultats montrent que certains colorants synthétisés possèdent une haute réponse fluorimétrique (facteur d’augmentation de fluorescence de 200 à 600) vis-À-Vis de différentes structures d’ADN et d’ARN quadruplex, ayant une très faible réponse fluorimétrique vis-À-Vis de l’ADN duplex. Cela permet de marquer sélectivement l’ADN quadruplex dans la solution ou sur les gels d’électrophorèse. Ces résultats représentent une première étape vers l’utilisation de ces sondes dans un contexte biologique, par exemple dans l’imagerie de fluorescence. / Single-Stranded nucleic acids containing guanine repeats can form non-Canonical secondary structures called G-Quadruplexes. These structures are composed of several guanine quartets, maintained by hydrogen bonds and metal cations (K+ or Na+) coordinated between G-Quartets. In spite of being well-Studied in vitro, the evidence for the presence of quadruplex DNA structures in vivo remains mainly indirect. The objective of this work was research of fluorescent probes that can signal the presence of quadruplex DNA and detect its structure (topology).Two series of fluorescent probes were considered and prepared: styryls dyes (mostly distyryls) and PDC-Coumarin derivatives. The design of these two series is based on the molecular scaffold of bisquinolinium pyridodicarboxamide (PDC-360A), a selective ligand with good affinity for quadruplex DNA structures but which is not fluorescent. Inspired by this molecule and the styryl motif, which is known for its spectroscopic properties, we considered a library of distyryles dyes. A second series, the PDC-Coumarin derivatives, was developed to introduce the fluorescence property of coumarin in the PDC by a covalent link. The properties of dyes of these two libraries (65 compounds) were studied in the presence of a number of DNA structures (quadruplex and duplex) by a fluorescent screening using microplate and titration methods. Our results show that some of synthesized dyes display high fluorescence response (i.e. fluorescence increase factor from 200 to 600) for different quadruplex DNA and RNA structures, while having a very low fluorimetric response for duplex DNA. This allows a selective visualization of quadruplex DNA in solution or in electrophoresis gel. These results represent the first steps towards the use of these probes in a biological context, for example in fluorescence imaging

Ergovaline is produced by the endophyte Neotyphodium coenophialum (Morgan-Jones and Gams) in tall fescue (Schedonorus arundinacea (Schreb.) Dumort. = Festuca arundinacea Schreb.) and is blamed for a multitude of costly livestock disorders. Testing of pastures is common in both research and on farm situations. Since ergovaline is known to be unstable and affected by many variables, the objective of this study was to determine the effect of sample handling and storage on the stability of this compound. Homogeneous milled tall fescue sub-samples were analyzed for ergovaline concentration using HPLC after a range of sample handling procedures or storage. Ergovaline was unstable in milled material after 24 hours in storage, regardless of temperature. The decrease in ergovaline after 24 hours ranged from 17 to 60%. These results show that tall fescue sample handling and storage have a significant effect on ergovaline concentrations. In conclusion, accurate laboratory analysis of ergovaline content may require that samples be transported immediately to the laboratory on ice for immediate analysis. Most laboratories are not equipped for same day analysis, therefore researchers and producers should acknowledge that laboratory ergovaline results may be lower than the actual content in the field.

Un « Nanonet », acronyme pour « NANOstructured NETwork », est défini comme un réseau de nanostructures unidimensionnelles à fort facteur de forme et aléatoirement orientées sur un substrat. Dans ce travail de thèse, une étude approfondie de nanonets à base de nanofils de silicium est présentée en vue d'une intégration dans des capteurs d'ADN. Une méthode de fabrication simple de ces réseaux a tout été d'abord développée afin d'obtenir des nanonets homogènes et reproductibles. La surface des nanofils a ensuite été fonctionnalisée afin de permettre la détection de l'hybridation de l'ADN par fluorescence. Les capteurs ainsi réalisés présentent une excellente sélectivité et une meilleure limite de sensibilité que des substrats plans. Les propriétés électriques des nanonets de silicium ont également été étudiées ce qui a mené à la description des mécanismes de conduction de ces réseaux. Ainsi, il a été démontré que le comportement électrique de ces structures est dominé par les nombreuses jonctions nanofil-nanofil et suit la théorie de la percolation électrique. De plus, une procédure d'optimisation de ces jonctions a finalement permis de stabiliser les propriétés électriques des nanonets de silicium.Ces réseaux possèdent donc des propriétés remarquables provenant des constituants individuels, les nanofils, qui présentent une surface spécifique élevée, mais également de leur structure en réseaux aléatoires offrant la possibilité de les manipuler simplement et à bas coût à l'échelle macroscopique. Ces travaux ouvrent la voie à l'intégration des nanonets de silicium dans des capteurs d'ADN reposant sur la détection électrique. / A "nanonet", acronym for "NANOstructured NETwork", is defined as a network of one-dimensional nanostructures with high aspect ratio and randomly oriented on a substrate. In this work, a comprehensive study of nanonets based on silicon nanowires is presented for integration into DNA sensors. First, a simple method for the network fabrication has been developed in order to obtain homogeneous and reproducible nanonets. Then, the nanowire surface has been functionalized, so that the DNA hybridization detection is possible by fluorescence. The elaborated sensors exhibit excellent selectivity and a better sensitivity limit than planar substrates. The electrical properties of the silicon nanonets have also been investigated which resulted in the description of the conduction mechanisms of these networks. It has been shown that the electrical behaviour of such structures is ruled by the numerous nanowire-nanowire junctions and follows the electrical percolation theory. Moreover, an optimization procedure of these junctions has allowed stabilizing the electrical properties of silicon nanonets.Therefore, these networks have attractive characteristics which arise from the individual components, the nanowires with a high specific surface, but also from the structural properties of the network itself which can be simply manipulated, at a low cost, on macroscopic scales. This work paves the way for the integration of silicon nanonets into DNA sensors based on electrical detection.