This thesis presents an overview of the research activities undertaken during my PhD under the supervision of Dr. F. Iza from the School of Electronic, Electrical and Systems Engineering and Dr. B. Buckley from the Chemistry Department at Loughborough University. The thesis is divided as follows. The first chapter of the thesis presents an introduction to plasma and chemical probes as well as the motivation for developing fluorescent probes for plasma characterisation. Analytical techniques used during this work to analyse chemical substances are described in the second chapter. Results and discussions from the experiments are discussed in chapters 3 to 7. Conclusions and future work are presented in chapter 8. In chapter 9, experimental data is presented. In the last century, plasma has attracted the attention of numerous researchers. Due to the wide-range of applications of this ionised gas, people from different fields have focused their effort on studying plasma. Low-temperature plasmas have received growing attention in the last 50 years when the development in cold plasma devices made them more controllable. Plasma played (and continues to play) a critical role in the fabrication process of integrated circuits and recent advances in the generation of low-temperature atmospheric-pressure plasmas have resulted in the emergence of new applications including treatment of temperature sensitive surfaces and biological targets. During the first months at Loughborough I worked on the ozonolysis of various alkenes with air plasmas. This allowed me to familiarised myself with plasma as this was new to me and get a feeling of some of the challenges lying ahead. Nonetheless, the data I obtained was encouraging and I presented the results of batch and flow plasma-based ozonolysis of alkenes at the Technological Plasma Workshop held in Manchester in January 2012. Once I had familiarised myself with the plasma system, I worked on synthesising fluorescent probes to detect ozone, one of the many reactive species that are typically generated in oxygen containing plasmas. Details of the experiments conducted to date and most significant findings are discussed in this thesis.

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第17541号 / 工博第3700号 / 新制||工||1563(附属図書館) / 30307 / 京都大学大学院工学研究科都市環境工学専攻 / (主査)教授 清水 芳久, 教授 田中 宏明, 教授 米田 稔 / 学位規則第4条第1項該当

Over the past several decades the phenomenon of luminescence (divided into fluorescence and phosphorescence) has received great attention in the field of biological science. This quest has motivated scientists for a variety of applications, including fluorescence imaging. Fluorescence microscopy techniques that provide unique advantages, such as high spatial resolution and superior sensitivity, have been regarded as attractive tools in biophotonics. With the progress of ultrafast laser sources, two-photon absorption (2PA), in which a molecule absorbs two photons simultaneously, has opened possibilities of using it for various applications. Two-photon fluorescence microscopy (2PFM), which affords deeper tissue penetration and excellent three-dimensional (3D) images, is now being widely employed for bioimaging. This dissertation focuses on the design, synthesis, and photophysical characterization of new fluorophores, as well as desirable applications. Chapter 1 gives an account of a brief introduction of luminescence and 2PA, as well as their utilities in biological applications. In chapter 2, a series of new BODIPY derivatives are presented along with their comprehensive linear and nonlinear characteristics. They exhibited excellent photophysical properties including large extinction coefficients, high fluorescence quantum yields, good photostability, and reasonable two-photon absorption cross sections. Two promising compounds were further evaluated as NIR fluorescent probes in one-photon and two-photon fluorescence imaging. Chapter 3 provides the design, synthesis, and photophysical characterization of two BODIPY dyes. In order to assess the potential of using the dye as a fluorescent probe, Lysotracker Red, a commercial lysosomal marker, was investigated for comparison purposes. The results indicate that figure of merit of both compounds were three orders of magnitude higher than that of Lysotracker Red. With an eye towards applications, one of the compounds was encapsulated in silica-based nanoparticles for in vitro and ex vivo one-photon and two-photon fluorescence imaging, in which the surface of the nanoparticle was modified with RGD peptides for specific targeting. The nanoprobe exhibited good biocompatibility and highly selective RGD-mediated uptake in ?V?3 integrin-overexpressing cancers, while maintaining efficient fluorescence quantum yield and high photostability. In chapter 4, the synthesis and photophysical properties of a novel photosensitizer with heavy atoms (halogen) were presented. The dye exhibited low fluorescence quantum yield, resulting in high singlet oxygen generation quantum yield. In vitro photodynamic studies demonstrated that photosensitization of the agent can induce cellular damage, subsequently leading to cell death by a necrotic cell death mechanism, supporting the therapeutic potential of using the agent for photodynamic therapy.

Chemical sensors capable of detecting a specific atom or molecule under various conditions have been utilized in biological and environmental analyses. Fluorescence based sensors are particularly advantageous in these studies because of their high sensitivity, relative ease in handling, and low technical costs. This dissertation focuses on the detection of two analytes, H+ and hypochlorous acid, which are of interest in biology because the presence of abnormal quantities of these analytes may be indicative of disease. We have established a new platform for which sensitive changes in various regions of pH can be detected using fluorescence. The aminomethylrhodamine (AMR) scaffold is highly versatile, i.e. the pH range in which the sensor is active can be tuned by introducing different substituents on the amine moiety. Overall this systematic approach to the design of pH sensitive fluorophores has allowed for a library of compounds that are responsive over a broad range of pH (pH 3 - 10) by simply changing the substituent on the amino group. We report the synthesis and characterization of a silicon analog of rhodamine for the fluorescence based detection of hypochlorous acid. This fluorophore exhibits a 90 nm bathochromic shift in its absorption and emission, relative to its oxygen counterpart. Hypochlorous acid is a biological agent linked to certain diseases. Therefore, the longer wavelength properties of the this far-red fluorescent sensor will be of significant benefit to imaging experiments of this analyte in biological media and tissue due to its spectral proximity of the so called NIR optical window. Furthermore, the novel synthetic methodology of this sensor possesses a key intermediate, which could potentially lead to future fluorescence based sensors. The characterization of a fluorescent probe designed for the detection of hypochlorous acid (HOCl) using a silicon analog of fluorescein (SiF) was also reported. Over a range of pHs, the probe reacts with a stoichiometric amount of HOCl resulting in a mixture of two pH dependent fluorescent species, a SiF disulfide product and a SiF sulfonate product. The unique colorometric properties of the individual SiF fluorophores were utilized to perform simultaneous detection of HOCl and pH. When an excess of HOCl is present, the SiF fluorophores become chlorinated, via an intermediate halohydrin, resulting in a more pH independent and red-shifted fluorophore. Finally, an attempt was made at developing a pH responsive photodynamic therapy agent. This system was designed to target the relatively low extracellular pH found around tumors. A di-bromohydroxymethylrhodamine system was synthesized and the photophysical properties were characterized. This system absorbs weakly under acidic conditions (ca. pH 3), however was shown to be a moderate photosensitizer under acidic conditions.

In the first study, a new µ-HPLC column was developed using a monolithic silica gel as a column substrate for chiral separation by covalently modifying with (S, S)-Whelk-O1 chiral selector. The monolithic stationary phase was generated through a sol-gel process and prepared in situ in a 100 µm i.d. fused silica capillary tubing. The chromatographic performance was characterized in terms of retention factor, column efficiency, enantioselectivity and resolution, as well as the kinetics parameters affecting the separation. Comparison with a commercial particle packed HPLC column demonstrates a promising enantioselective resolving ability of the monolithic Whelk-O1 capillary column. The second project focuses on characterization of fluorescent sensor for zinc detection. In this work, we have examined the photophysical properties of the fluorescent probe sensor that has been developed in our laboratory for Zn2+ recognition via a photo-induced electron transfer (PET) sensing mechanism. To characterize the fundamental function of sensor, response curves have been conducted, using acetone/methanol (199:1), 1,4-dioxane, acetone, methanol and aqueous buffer as the solvent system. Similar to prior work from our group, the sensor was found to respond selectively to Zn2+ ions with fluorescence enhancement. The fluorescence properties and binding response were evaluated in the presence of water and a Lewis base, which we found to have a marked effect on the fluorescence signal. The selectivity of the sensor for Zn2+ was also observed and compared to other divalent metal such as Ca2+, Mg2+, Cu2+ and Hg2+ with the goal of learning fundamental information on the system that can aid in the development of future PET based sensors.

Bacterial quorum sensing is regarded as a novel target for the design of antimicrobials. Based on lead structures identified from HTS, 39 analogues have been synthesized and evaluated in Vibrio haveyi. Potent inhibitors with IC50 values at single-digit micromolar concentrations for AI-2 mediated quorum sensing have been identified. On the second project, post-synthesis modifications of DNA provide easy functionalizations for expanded applications such as aptamer selection. A CBT-modified thymidine analogue (CBT-TTP) has been synthesized and used for enzymatic incorporation into DNA. Post-synthesis modifications through condensation with 1,2-aminothiol for installation of a boronic acid moiety or a fluorophore have been achieved. On the third project, H2S has been recognized as an important gasotransmitter and its concentration is relevant to a variety of diseases. A novel fluorescent probe (DNS-Az) has been developed for quantitation of H2S in aqueous solutions. This probe has been used to measure H2S concentrations in the blood.

Low density surface sites are believed to play an important role in processes occurring on oxide surfaces, including catalysis and particle and film nucleation. However, our understanding of the role and chemical nature of such sites play in these processes is limited by the inability to experimentally detect minority surface sites in many oxide systems. The research performed for this dissertation is focused on developing a surface science technique utilizing fluorescent molecules to titrate specific surface sites on planar fused silica surfaces in an ultra-high vacuum (UHV) environment. High sensitivity (low detection limit) is achieved by using derivatives of perylene, a high quantum yield fluorophore. High specificity is attained by employing perylene derivatives with functional groups designed to react chemically with and titrate various sites. In addition to titrating the well-studied hydroxyl sites with perylene-3-methanol (density ~ 10¹⁴ cm⁻²), which is used to establish the technique, the detection of strained siloxane sites (~ 10¹² cm⁻²), ) with perylene-3-methanamine and oxygen vacancy sites (~ 10¹¹ cm⁻²), ) with 3-vinyl perylene is demonstrated. Particle nucleation on oxides is suspected to involve defects that trap adatoms and form critical nuclei. Using this technique, the possible role strained siloxane and oxygen vacancy sites play in trapping adatoms during the nucleation of Ge nanoparticles on silica surfaces is examined. / text

Le monoxyde d’azote (NO), un neurotransmetteur important en biologie, a attiré l’attention ces dernières années pour son rôle majeur joué dans l’apparition d’une myriade de maladies telles que certains cancers, diabètes etc. Comprendre les mécanismes biologiques liés à la production du NO pourrait aboutir à la découverte de nouveaux moyens thérapeutiques. Cependant, le fonctionnement de l’enzyme qui produit le monoxyde d’azote, la NO-Synthase, n’est pas complétement élucidé. Dans ce but, des approches biomimétiques peuvent apporter une solution. Les microréacteurs ou proto-cellules, enveloppes imitant sommairement la compartimentation cellulaire sont un outil de choix, permettant de répliquer un environnement contrôlé où les concentrations et distances de réactions sont proches d’une cellule, permettant ainsi d’étudier le fonctionnement de la NO-Synthase. Cette thèse présente trois problématiques qui ont pour but de développer un tel microréacteur encapsulant la NO-Synthase : (1) la libération contrôlé d’espèces réactives déclenchée par un stimulus lumineux, (2) le suivi de l’activité de l’enzyme par des sondes fluorescentes et (3) le contrôle de la réaction enzymatique dans l’espace et dans le temps. Deux systèmes ont été étudiés pour libérer de manière contrôlée des espèces: la première consiste à déstabiliser des nano polymersomes par photo-clivage du copolymère qui le constitue. Le deuxième système est basé sur une rapide augmentation de la pression osmotique par irradiation à l’intérieur des polymersomes, induisant un éclatement de ceux-ci et la libération d’espèces encapsulées. La deuxième problématique abordée est le suivi de l’activité enzymatique au moyen de sondes hydrophobes et hydrophiles fluorescentes qui détectent le monoxyde d’azote à différent endroits du microréacteur. Le dernier point abordé est l’étude des microréacteur et la libération contrôlé en leur sein. / Nitric oxide (NO) has been identified as an important chemical messenger in cells and living organisms. Understanding the mechanism involved in NO production by NO-synthase is of fundamental importance. Mimicking basic cell functions by encapsulating NO-synthase in a controlled and confined cell like environment, could help provide information about the enzyme. Polymersomes resulting from the self-assembly of amphiphilic block copolymers were used as the synthetic cell like microreactor. To this end, three major challenges were addressed in this thesis: (1) controlling species release and concentration inside the microreactor, (2) measuring the enzyme response by NO detection and (3) controlling enzymatic reactions in space and time inside a microreactor. Light was used as the exogenous stimulus to induce release; its application is instantaneous, non-invasive and easy to control spatially and temporally. Two different ways to release species via light excitation were explored. The first strategy involves destabilization of nanopolymersomes by block separation, induced by copolymer photocleavage. The second strategy was to induce fast osmotic pressure increase of the polymersomes internal medium, resulting in bursting and species release. In order to monitor NO production by NO-synthase in different parts of the microreactor, hydrophobic and hydrophilic fluorescent NO probes have been synthesized and studied showing excellent correlation with NO concentration. The release of species inside microreactor was finally achieved in order to control enzymatic reaction.

In this work, we studied two yeast ABC transporters, Pdr10p and Pdr15p. At the time of assignment of this thesis, it was believed that these proteins contribute to the yeast MDR phenotype (PDR) on the grounds of their high homology to another yeast MDR protein, Pdr5p. In order to study these pumps, two sets of isogenic null-mutant strains were prepared with all possible combinations of gene deletions. We report that both of the studied proteins are very important in sus- taining the normal plasma membrane microenvironment for the most abundant, and essential, yeast plasma membrane protein, H+ -ATPase and so influence the membrane potential. Pdr10p and Pdr15p thus play an as yet unknown role in reg- ulation of the activity of this enzyme. Furthermore, we report that deletion of the genes coding for these proteins severely reduces the ability of the H+ -ATPase to be activated by the protonophore CCCP which is a weak acid. Studies performed with immunosuppressant FK506 further show that this compound reduces the viability of S. cerevisiae mutant strain PLY643 lacking genes coding for Pdr5p, Snq2p and Yor1p. Further deletion of Pdr10p and Pdr15p does not increase the lethality of this compound. Neither CCCP nor FK506 are substrates of the stud- ied pumps. 1

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21668号 / 医博第4474号 / 新制||医||1035(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 松田 道行, 教授 萩原 正敏, 教授 安達 泰治 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM