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- All Subjects: Propulsion
- Creators: Chao, Shih-hui
Description
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.
ContributorsShi, Xu (Author) / Meldrum, Deirdre R. (Thesis advisor) / Zhang, Weiwen (Committee member) / Chao, Shih-hui (Committee member) / Westerhoff, Paul (Committee member) / Arizona State University (Publisher)
Created2013
Description
The ocean is vital to the health of our planet but remains virtually unexplored. Many researchers seek to understand a wide range of geological and biological phenomena by developing technologies which enable exploration of the deep-sea. The task of developing a technology which can withstand extreme pressure and temperature gradients in the deep ocean is not trivial. Of these technologies, underwater vehicles were developed to study the deep ocean, but remain large and expensive to manufacture. I am proposing the development of cost efficient miniaturized underwater vehicle (mUV) with propulsion systems to carry small measurement devices and enable deep-sea exploration. These mUV's overall size is optimized based on the vehicle parameters such as energy density, desired velocity, swimming time and propulsion performance. However, there are limitations associated with the size of the mUV which leads to certain challenges. For example, 2000 m below the sea level, the pressure is as high as 3000 psi. Therefore, certain underwater vehicle modules, such as the propulsion system, will require pressure housing to ensure the functionality of the thrust generation. In the case of a mUV swimming against the deep-sea current, a thrust magnitude is required to enable the vehicle to overcome the ocean current speed and move forward. Therefore, the size of the mUV is limited by the energy density and the propeller size. An equation is derived to miniaturize underwater vehicle while performing with a certain specifications. An inrunner three-phase permanent magnet brushless DC motor is designed and fabricated with a specific size to fit inside the mUV's core. The motor is composed of stator winding in a pressure housing and an open to water ring-propeller rotor magnet. Several ring-propellers are 3D printed and tested experimentally to determine their performances and efficiencies. A planer motion optimal trajectory for the mUV is determined to minimize the energy usage. Those studies enable the design of size optimized underwater vehicle with propulsion to carry small measurement sensors and enable underwater exploration. Developing mUV's will enable ocean exploration that can lead to significant scientific discoveries and breakthroughs that will solve current world health and environmental problems.
ContributorsMerza, Saeed A (Author) / Meldrum, Deirdre R (Thesis advisor) / Chao, Shih-hui (Committee member) / Shankar, Praveen (Committee member) / Saripalli, Srikanth (Committee member) / Berman, Spring Melody (Committee member) / Arizona State University (Publisher)
Created2014