abstract: This thesis research focuses on developing a single-cell gene expression analysis method for marine diatom Thalassiosira pseudonana and constructing a chip level tool to realize the single cell RT-qPCR analysis. This chip will serve as a conceptual foundation for future deployable ocean monitoring systems. T. pseudonana, which is a common surface water microorganism, was detected in the deep ocean as confirmed by phylogenetic and microbial community functional studies. Six-fold copy number differences between 23S rRNA and 23S rDNA were observed by RT-qPCR, demonstrating the moderate functional activity of detected photosynthetic microbes in the deep ocean including T. pseudonana. Because of the ubiquity of T. pseudonana, it is a good candidate for an early warning system for ocean environmental perturbation monitoring. This early warning system will depend on identifying outlier gene expression at the single-cell level. An early warning system based on single-cell analysis is expected to detect environmental perturbations earlier than population level analysis which can only be observed after a whole community has reacted. Preliminary work using tube-based, two-step RT-qPCR revealed for the first time, gene expression heterogeneity of T. pseudonana under different nutrient conditions. Heterogeneity was revealed by different gene expression activity for individual cells under the same conditions. This single cell analysis showed a skewed, lognormal distribution and helped to find outlier cells. The results indicate that the geometric average becomes more important and representative of the whole population than the arithmetic average. This is in contrast with population level analysis which is limited to arithmetic averages only and highlights the value of single cell analysis. In order to develop a deployable sensor in the ocean, a chip level device was constructed. The chip contains surface-adhering droplets, defined by hydrophilic patterning, that serve as real-time PCR reaction chambers when they are immersed in oil. The chip had demonstrated sensitivities at the single cell level for both DNA and RNA. The successful rate of these chip-based reactions was around 85%. The sensitivity of the chip was equivalent to published microfluidic devices with complicated designs and protocols, but the production process of the chip was simple and the materials were all easily accessible in conventional environmental and/or biology laboratories. On-chip tests provided heterogeneity information about the whole population and were validated by comparing with conventional tube based methods and by p-values analysis. The power of chip-based single-cell analyses were mainly between 65-90% which were acceptable and can be further increased by higher throughput devices. With this chip and single-cell analysis approaches, a new paradigm for robust early warning systems of ocean environmental perturbation is possible. / Dissertation/Thesis / Ph.D. Civil and Environmental Engineering 2013

<p>This dissertation focused on the development of mass spectrometric methodologies, separation techniques, and engineered devices for the optimal analysis of complex mixtures relevant to the energy sector, such as alternative fuels, petroleum-based fuels, crude oils, and processed base oils. Mass spectrometry (MS) has been widely recognized as a powerful tool for the analysis of complex mixtures. In complex energy samples, such as petroleum-based fuels, alternative fuels, and oils, high-resolution MS alone may not be sufficient to elucidate chemical composition information. Separation before MS analysis is often necessary for such highly complex energy samples. For volatile samples, in-line two-dimensional gas chromatography (GC×GC) can be used to separate complex mixtures prior to ionization. This technique allows for a more accurate determination of the compounds in a mixture, by simplifying the mixture into its components prior to ionization, separation based on mass-to-charge ratio (<i>m/z</i>), and detection. A GC×GC coupled to a high-resolution time-of-flight MS was utilized in this research to determine the chemical composition of alternative aviation fuels, a petroleum-based aviation fuel, and alternative aviation fuel candidates and blending components as well as processed base oils.</p> Additionally, as the cutting edge of science and technology evolve, methods and equipment must be updated and adapted for new samples or new sector demands. One such case, explored in this dissertation, was the validation of an updated standardized method, ASTM D2425 2019. This updated standardized method was investigated for a new instrument and new sample type for a quadrupole MS to analyze a renewable aviation fuel. Lastly, the development and evaluation of a miniaturized coreflood device for analyzing candidate chemically enhanced oil recovery (cEOR) formulations of brine, surfactant(s), and polymer(s) was conducted. The miniaturized device was used in the evaluation of two different cEOR formulations to determine if the components of the recovered oil changed.