The development of novel chiral tethers for controlling intramolecular aryl-aryl coupling and their application in the synthesis of gomisin M1 and analogues

The primary focus of this thesis was the development of a novel chiral tether that could be used to control axial chirality around a newly formed aryl-aryl bond, and the extension of this methodology to the model synthesis of gomisin M1. In chapter 1, a review detailing the use of chiral tethers in the synthesis of atropisomers is discussed. The use of a variety of chiral molecules including 1,2-diols, 1,3-diols and other diol-based tethers, as well as amine-based and miscellaneous tethers are detailed. In chapter 2, the rationale behind the design of our novel molecular tethers, along with the subsequent synthesis of three chiral 1,3-diol-based tethers, is outlined. The method by which the enantiopurity of these diols was determined is also reviewed. This chapter also includes the attempted Mitsunobu and intramolecular couplings in the model synthesis of BINOL. Chapter 3 discusses the synthesis of suitable aryl halide substrates, and their employment in the attempted tether-controlled asymmetric model synthesis of gomisin M1. A comprehensive investigation into the attempted intramolecular biaryl coupling of these tethered substrates is also included. The non-stereoselective model synthesis of gomisin M1 is outlined in chapter 4. The installation of the desired biaryl linkage and the subsequent attempted intramolecular McMurry couplings are discussed. The impact of different protecting groups in the molecule on the intramolecular McMurry reaction is also outlined. Chapter 5 details the full experimental procedures, including spectroscopic and analytical data for the compounds prepared during this research.

Development and Application of a Multi-dimensional Strategy for Measuring Fidelity of Implementation of a Districtwide Intervention

This symposium describes a multi-dimensional strategy to examine fidelity of implementation in an authentic school district context. An existing large-district peer mentoring program provides an example. The presentation will address development of a logic model to articulate a theory of change; collaborative creation of a data set aligned with essential concepts and research questions; identification of independent, dependent, and covariate variables; issues related to use of big data that include conditioning and transformation of data prior to analysis; operationalization of a strategy to capture fidelity of implementation data from all stakeholders; and ways in which fidelity indicators might be used.

Development and application of sensitive genome-wide platforms to study the genetic and epigenetic (DNA methylation) makeup of gametes and early bovine embryos

Pour ce projet, nous avons développé une plateforme pour l’analyse pangénomique de la méthylation de l’ADN chez le bovin qui est compatible avec des échantillons de petites tailles. Cet outil est utilisé pour étudier les caractéristiques génétiques et épigénétiques (méthylation de l’ADN) des gamètes soumis aux procédures de procréation médicalement assisitée et des embryons précoces. Dans un premier temps, une plateforme d’analyse de biopuces spécifiques pour l’étude de la méthylation de l’ADN chez l’espèce bovine a été développée. Cette plateforme a ensuite été optimisée pour produire des analyses pangénomiques de méthylation de l’ADN fiables et reproductibles à partir d’échantillons de très petites tailles telle que les embryons précoces (≥ 10 ng d’ADN a été utilisé, ce qui correspond à 10 blastocystes en expansion). En outre, cet outil a permis d’évaluer de façon simultanée la méthylation de l’ADN et le transcriptome dans le même échantillon, fournissant ainsi une image complète des profils génétiques et épigénétiques (méthylation de l’ADN). Comme preuve de concept, les profils comparatifs de méthylation de l’ADN spermatique et de blastocystes bovins ont été analysés au niveau de l’ensemble du génome. Dans un deuxième temps, grâce à cette plateforme, les profils globaux de méthylation de l’ADN de taureaux jumeaux monozygotes (MZ) ont été analysés. Malgré qu’ils sont génétiquement identiques, les taureaux jumeaux MZ ont des descendants avec des performances différentes. Par conséquent, l’hypothèse que le profil de méthylation de l’ADN spermatique de taureaux jumeaux MZ est différent a été émise. Dans notre étude, des différences significatives entre les jumeaux MZ au niveau des caractéristiques de la semence ainsi que de la méthylation de l’ADN ont été trouvées, chacune pouvant contribuer à l’obtention de performances divergentes incongrues des filles engendrées par ces jumeaux MZ. Dans la troisième partie de ce projet, la même plateforme a été utilisée pour découvrir les impacts d’une supplémentation à forte concentration en donneur de méthyle universel sur les embryons précoces bovins. La supplémentation avec de grandes quantités d’acide folique (AF) a été largement utilisée et recommandée chez les femmes enceintes pour sa capacité bien établie à prévenir les malformations du tube neural chez les enfants. Cependant, plus récemment, plusieurs études ont rapporté des effets indésirables de l’AF utilisé à des concentrations élevées, non seulement sur le développement de l’embryon, mais aussi chez les adultes. Au niveau cellulaire, l’AF entre dans le métabolisme monocarboné, la seule voie de production de S-adénosyl méthionine (SAM), un donneur universel de groupements méthyles pour une grande variété de biomolécules, y compris l’ADN. Par conséquent, pour résoudre cette controverse, une forte dose de SAM a été utilisée pour traiter des embryons produits in vitro chez le bovin. Ceci a non seulement permis d’influencer le phénotype des embryons précoces, mais aussi d’avoir un impact sur le transcriptome et le méthylome de l’ADN. En somme, le projet en cours a permis le développement d’une plateforme d’analyse de la méthylation de l’ADN à l’échelle du génome entier chez le bovin à coût raisonnable et facile à utiliser qui est compatible avec les embryons précoces. De plus, puisque c’est l’une des premières études de ce genre en biologie de la reproduction bovine, ce projet avait trois objectifs qui a donné plusieurs nouveaux résultats, incluant les profils comparatifs de méthylation de l’ADN au niveau : i) blastocystes versus spermatozoïdes ; ii) semence de taureaux jumeaux MZ et iii) embryons précoces traités à de fortes doses de SAM versus des embryons précoces non traités.

Development of Zirconia based phosphors for application in lighting and as luminescent bioprobes

The strong progress evidenced in photonic and optoelectronic areas, accompanied by an exponential development in the nanoscience and nanotechnology, gave rise to an increasing demand for efficient luminescent materials with more and more exigent characteristics. In this field, wide band gap hosts doped with lanthanide ions represent a class of luminescent materials with a strong technological importance. Within wide band gap material, zirconia owns a combination of physical and chemical properties that potentiate it as an excellent host for the aforementioned ions, envisaging its use in different areas, including in lighting and optical sensors applications, such as pressure sensors and biosensors. Following the demand for outstanding luminescent materials, there is also a request for fast, economic and an easy scale-up process for their production. Regarding these demands, laser floating zone, solution combustion synthesis and pulsed laser ablation in liquid techniques are explored in this thesis for the production of single crystals, nanopowders and nanoparticles of lanthanides doped zirconia based hosts. Simultaneously, a detailed study of the morphological, structural and optical properties of the produced materials is made. The luminescent characteristics of zirconia and yttria stabilized zirconia (YSZ) doped with different lanthanide ions (Ce3+ (4f1), Pr3+ (4f2), Sm3+ (4f5), Eu3+ (4f6), Tb3+ (4f8), Dy3+ (4f9), Er3+ (4f11), Tm3+ (4f12), Yb3+ (4f13)) and co-doped with Er3+,Yb3+ and Tm3+,Yb3+ are analysed. Besides the Stokes luminescence, the anti- Stokes emission upon infrared excitation (upconversion and black body radiation) is also analysed and discussed. The comparison of the luminescence characteristics in materials with different dimensions allowed to analyse the effect of size in the luminescent properties of the dopant lanthanide ions. The potentialities of application of the produced luminescent materials in solid state light, biosensors and pressure sensors are explored taking into account their studied characteristics.

Development and Application of Predictive Models for Survival, Growth, and Death of Enteric Pathogens in Leafy Greens Supply Chain

Leafy greens are essential part of a healthy diet. Because of their health benefits, production and consumption of leafy greens has increased considerably in the U.S. in the last few decades. However, leafy greens are also associated with a large number of foodborne disease outbreaks in the last few years. The overall goal of this dissertation was to use the current knowledge of predictive models and available data to understand the growth, survival, and death of enteric pathogens in leafy greens at pre- and post-harvest levels. Temperature plays a major role in the growth and death of bacteria in foods. A growth-death model was developed for Salmonella and Listeria monocytogenes in leafy greens for varying temperature conditions typically encountered during supply chain. The developed growth-death models were validated using experimental dynamic time-temperature profiles available in the literature. Furthermore, these growth-death models for Salmonella and Listeria monocytogenes and a similar model for E. coli O157:H7 were used to predict the growth of these pathogens in leafy greens during transportation without temperature control. Refrigeration of leafy greens meets the purposes of increasing their shelf-life and mitigating the bacterial growth, but at the same time, storage of foods at lower temperature increases the storage cost. Nonlinear programming was used to optimize the storage temperature of leafy greens during supply chain while minimizing the storage cost and maintaining the desired levels of sensory quality and microbial safety. Most of the outbreaks associated with consumption of leafy greens contaminated with E. coli O157:H7 have occurred during July-November in the U.S. A dynamic system model consisting of subsystems and inputs (soil, irrigation, cattle, wildlife, and rainfall) simulating a farm in a major leafy greens producing area in California was developed. The model was simulated incorporating the events of planting, irrigation, harvesting, ground preparation for the new crop, contamination of soil and plants, and survival of E. coli O157:H7. The predictions of this system model are in agreement with the seasonality of outbreaks. This dissertation utilized the growth, survival, and death models of enteric pathogens in leafy greens during production and supply chain.

Development of computer application for determination of chemical diffusion properties in biological tissues

The main objective of this work was to develop an application capable of determining the diffusion times and diffusion coefficients of optical clearing agents and water inside a known type of muscle. Different types of chemical agents can also be used with the method implemented, such as medications or metabolic products. Since the diffusion times can be calculated, it is possible to describe the dehydration mechanism that occurs in the muscle. The calculation of the diffusion time of an optical clearing agent allows to characterize the refractive index matching mechanism of optical clearing. By using both the diffusion times and diffusion of water and clearing agents not only the optical clearing mechanisms are characterized, but also information about optical clearing effect duration and magnitude is obtained. Such information is crucial to plan a clinical intervention in cooperation with optical clearing. The experimental method and equations implemented in the developed application are described in throughout this document, demonstrating its effectiveness. The application was developed in MATLAB code, but the method was personalized so it better fits the application needs. This process significantly improved the processing efficiency, reduced the time to obtain he results, multiple validations prevents common errors and some extra functionalities were added such as saving application progress or export information in different formats. Tests were made using glucose measurements in muscle. Some of the data, for testing purposes, was also intentionally changed in order to obtain different simulations and results from the application. The entire project was validated by comparing the calculated results with the ones found in literature, which are also described in this document.

Development of paper-based color test-strip for drug detection in aquatic environment: Application to oxytetracycline

The wide use of antibiotics in aquaculture has led to the emergence of resistant microbial species. It should be avoided/minimized by controlling the amount of drug employed in fish farming. For this purpose, the present work proposes test-strip papers aiming at the detection/semi-quantitative determination of organic drugs by visual comparison of color changes, in a similar analytical procedure to that of pH monitoring by universal pH paper. This is done by establishing suitable chemical changes upon cellulose, attributing the paper the ability to react with the organic drug and to produce a color change. Quantitative data is also enabled by taking a picture and applying a suitable mathematical treatment to the color coordinates given by the HSL system used by windows. As proof of concept, this approach was applied to oxytetracycline (OXY), one of the antibiotics frequently used in aquaculture. A bottom-up modification of paper was established, starting by the reaction of the glucose moieties on the paper with 3-triethoxysilylpropylamine (APTES). The so-formed amine layer allowed binding to a metal ion by coordination chemistry, while the metal ion reacted after with the drug to produce a colored compound. The most suitable metals to carry out such modification were selected by bulk studies, and the several stages of the paper modification were optimized to produce an intense color change against the concentration of the drug. The paper strips were applied to the analysis of spiked environmental water, allowing a quantitative determination for OXY concentrations as low as 30 ng/mL. In general, this work provided a simple, method to screen and discriminate tetracycline drugs, in aquaculture, being a promising tool for local, quick and cheap monitoring of drugs.

Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification

Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.

Biomachining of oxygen-free copper: development of a continuous process for industrial application

245 p.

Specification of a smart meter/actuator description mechanism & development of a mobile application

Home Automation holds the potential of realizing cost savings for end users while reducing the carbon footprint of domestic energy consumption. Yet, adoption is still very low. High cost of vendor-supplied home automation systems is a major prohibiting factor. Open source systems such as FHEM, Domoticz, OpenHAB etc. are a cheaper alternative and can drive the adoption of home automation. Moreover, they have the advantage of not being limited to a single vendor or communication technology which gives end users flexibility in the choice of devices to include in their installation. However, interaction with devices having diverse communication technologies can be inconvenient for users thus limiting the utility they derive from it. For application developers, creating applications which interact with the several technologies in the home automation systems is not a consistent process. Hence, there is the need for a common description mechanism that makes interaction smooth for end users and which enables application developers to make home automation applications in a consistent and uniform way. This thesis proposes such a description mechanism within the context of an open source home automation system – FHEM, together with a system concept for its application. A mobile application was developed as a proof of concept of the proposed description mechanism and the results of the implementation are reflected upon.

Development of new analytical procedures of isotope geochemistry by mass spectrometry. Application to the study of high-pressure metamorphic rocks from the Iberian Massif

319 p.

Development of hydroxyapatite-based nanomaterials to enhance biological response of osteoblast cells for clinical application

Purpose: To develop a novel chitosan/gelatin-hydroxyapatite (CGHaP) microspheres for evaluating the biological response of pre-osteoblast cells. Methods: The microsphere was prepared by water-in-oil emulsion method. Cell proliferation was studied using AlamarBlue colorimetric assay and DAPI staining while alkaline phosphatase assay was carried out by colorimetric assay method. Chitosan microspheres as well as chitosan-hydroxyapatite microspheres was prepared and tested for biological response from MC3T3-E1 cell line. Results: The results showed that CGHaP promotes MC3T3-E1 cell proliferation and spread on the surface of microspheres. The cells were clustered with more actin filaments and well-linked with neighbouring cells or adjacent cells when cultured in CGHaP microspheres whereas fewer cells were spread on chitosan (CH) microspheres. CGHaP microspheres significantly (p < 0.05) promoted cell attachment, proliferation and extracellular matrix mineralization. CGHaP microspheres presented significantly (p < 0.02) higher calcium deposition (0.5 ng) than CH microspheres (0.28 ng). Specifically, CGHaP microspheres exhibited high ALP activity (8 units; 2-fold) compared to CH with 3 units, after 7 days of incubation. The results suggest that CGHaP possesses a great ability to facilitate bone ingrowth formation and possibility of good osteointegration in vivo. Conclusion: The nanomaterial enhances the proliferation of pre-osteoblast cells in tissue engineering microspheres. The outcome of this study may have a major impact on the development of novel nanomaterials for bone tissue engineering.

DEVELOPMENT OF ION EXCHANGE MODELS FOR WATER TREATMENT AND APPLICATION TO THE INTERNATIONAL SPACE STATION WATER PROCESSOR

The International Space Station (ISS) requires a substantial amount of potable water for use by the crew. The economic and logistic limitations of transporting the vast amount of water required onboard the ISS necessitate onboard recovery and reuse of the aqueous waste streams. Various treatment technologies are employed within the ISS water processor to render the waste water potable, including filtration, ion exchange, adsorption, and catalytic wet oxidation. The ion exchange resins and adsorption media are combined in multifiltration beds for removal of ionic and organic compounds. A mathematical model (MFBMODEL™) designed to predict the performance of a multifiltration (MF) bed was developed. MFBMODEL consists of ion exchange models for describing the behavior of the different resin types in a MF bed (e.g., mixed bed, strong acid cation, strong base anion, and weak base anion exchange resins) and an adsorption model capable of predicting the performance of the adsorbents in a MF bed. Multicomponent ion exchange ii equilibrium models that incorporate the water formation reaction, electroneutrality condition, and degree of ionization of weak acids and bases for mixed bed, strong acid cation, strong base anion, and weak base anion exchange resins were developed and verified. The equilibrium models developed use a tanks-inseries approach that allows for consideration of variable influent concentrations. The adsorption modeling approach was developed in related studies and application within the MFBMODEL framework was demonstrated in the Appendix to this study. MFBMODEL consists of a graphical user interface programmed in Visual Basic and Fortran computational routines. This dissertation shows MF bed modeling results in which the model is verified for a surrogate of the ISS waste shower and handwash stream. In addition, a multicomponent ion exchange model that incorporates mass transfer effects was developed, which is capable of describing the performance of strong acid cation (SAC) and strong base anion (SBA) exchange resins, but not including reaction effects. This dissertation presents results showing the mass transfer model's capability to predict the performance of binary and multicomponent column data for SAC and SBA exchange resins. The ion exchange equilibrium and mass transfer models developed in this study are also applicable to terrestrial water treatment systems. They could be applied for removal of cations and anions from groundwater (e.g., hardness, nitrate, perchlorate) and from industrial process waters (e.g. boiler water, ultrapure water in the semiconductor industry).