Bioculture Journal
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Longshore Transport of Sediment in Freshwater Bay, West of Port Angeles
No full textUsing digital photographs, this study investigates sediment movement eastwards
by the dominant northwest swell in Freshwater Bay, WA. Twenty samples were taken at
five locations and analyzed with the Cobble cam analysis package. It was found that sand
and smaller pebbles were more prevalent on the western updrift shore than on the delta
face and that no silt and clay were found on the foreshore. Sand was not evident on the
most eastern site and mean sediment grain size increased eastward. Wave rays hit the
western face of the delta orthogonal to the shore and result in more pronounced cusps in
the eastern direction. The westerly portion experiences oblique waves and results in
longshore transport eastward in Freshwater Bay. Pacific Ocean swell from the west had
the most impact while local wind-generated waves from the northeast and northwest had
the least. Pebbles were selectively moved by the wave regime for each section of beach.
All the sediment along the western delta was removed and indicates that longshore
transport is sediment starved
Studies of Sample Compartmentalization By Microfluidic Methods
No full textThesis (Ph.D.)--University of Washington, 2012Miniaturization of reaction volumes into nanoliter sized droplets makes today's chemical analysis cheaper, faster, and more sensitive. These droplets can be generated by a variety of microfluidic methods that provide great control over size and composition, and can be performed at high speed. Other methods for droplet mixing and docking have been developed to allow droplet manipulation and subsequent analysis in continuous flow. These methods are designed to be modular systems, allowing the user to interchange or combine different methods in a "Lab on a Chip". The coupling of droplet generation, droplet manipulation, and analysis modules can be challenging if there is a mismatch between droplet generation frequency and time required to perform additional tasks in separate modules. As a result, droplet microfluidic methods can be very complex and can be less attractive for end-user applications, in particular in the biological sciences. During the past years, a new generation of microfluidic droplet platforms emerged which is called self-digitization and is novel for its simplicity. In this method an aqueous sample is compartmentalized into smaller droplets by an immiscible phase and stored on-site. Self-digitization does not require complex microfluidic design or complex pumping and valving technologies to generate droplets. The volume of these droplets is predefined by the geometry of microfluidic wells and this gives rise to loss-less filling of large arrays of nanoliter wells. The droplets can then be addressed and monitored over time as their positions are registered in an array of static droplets. This thesis summarizes the progress in the development of sample self-digitization in microfluidic arrays of side chambers and bottom wells, and provides a perspective view of the potential applications of this next generation droplet platform
The Public Work of Care: Emerging Art Curatorial Community Engagement Practices
No full textThesis (Master's)--University of Washington, 2012Public programming, community outreach, visitor studies and education departments have been central to discussions in the art museum field about strategies for community engagement. However, little documentation is available of the ways in which art curators today see their practice as actively participating in and even generating creative strategies to propel museums toward new levels of inclusion. The goal of this research has been to identify and describe emerging trends in practice among art curators who work to expand community access to art museums. Curators were selected for this study based on their employment at art institutions with commitment to 1) community engagement and/or 2) social justice as demonstrated through their online identity. At selected institutions, the BMW Guggenheim Lab, The Bronx Museum of Arts, The Yerba Buena Center for the Arts, and the Oakland Museum of California, curators were asked to participate in on-site semi-structured interviews. Key words and concepts were cross-referenced between all interviews to find similar themes in order to describe the range of emerging practices that can be found in a diverse set of exemplary art institutions. Findings indicate that curators interviewed for this study have not abandoned more traditional curatorial roles of organizing art exhibitions and interpreting collections through specialized skill and expertise, but instead added to them. Additional roles correspond with expanding the scope of exhibitions and programs in order to engage communities considered non-traditional art museum audiences. Curator participants respond to issues that shape communities and consider how art museum spaces can be programmed and changed in order to promote comfort, familiarity and elevate community expertise and creativity. All curators in this study are shifting the paradigm of curator/intellectual instructing public conversation to diverse communities guiding curatorial work. Art curator participant responses suggest that traditional curatorial roles can be perceived and practiced as complimentary to community engagement rather than contradictory. This research provides art curators with an introduction to exemplary and diverse cases of emerging curatorial community engagement and the ways in which these practices can be more sustainable in the field. It also recommends strategies with which art institutions can better support curators to be integrated into community engagement goals within their institutions and the field
Ultra-low Power Circuit and System Design for Deployable Body-worn Devices
No full textThesis (Ph.D.)--University of Washington, 2012Recent advances in ultra-low power chip design techniques, many originally targeting wireless sensor networks, will enable a new generation of body-worn devices for health monitoring. Off-the-shelf chips often consume too much power and are usally too bulky for body-worn applications. In this thesis, I have contributed in advancing the state-of-the-art ultra-low power circuit design techniques, including low-noise bioamplifiers for ExG (e.g. ECG, EMG, EEG, etc.) and neural applications, analog signal processors targeted for but not limited to ECoG applicaitons, transmitter and receiver for short-range wireless. In addition, I have also helped realizing the next-generation wireless sensing system ICs that aim at prolonging battery life, even eliminating the battery leveraging emerging energy-harvesting solutions. Lastly, a few works presented in the thesis (such as the "Bumblebee", "SoCWISP") have not only been published as literatures, but also deployed at various labs assisting scientists to perform experiments that are difficult if not impossible to be done otherwise
Dissecting the role of the major cleft gene, IRF6, in primary palatal epithelia
No full textThesis (Ph.D.)--University of Washington, 2012Mutations and common polymorphisms in Interferon Regulatory Factor 6 (IRF6) are associated with cleft lip/palate (CLP). IRF6 is expressed in the epithelium that mediates the outgrowth and contact of the embryonic tissue masses that fuse to form the upper lip and primary palate as well as in the epithelium that mediates fusion of the palatal shelves to form the secondary palate. Unfortunately, mice deficient in Irf6 display only secondary palatal clefts and abnormal intraoral adhesions but not classic CLP. To provide insights into the role of IRF6 in the pathogenesis of CLP, yeast two hybrid screens were performed to identify IRF6 protein interactors. Using this approach, NME2 was identified and confirmed as a bona fide IRF6 partner protein and this interaction is regulated by serine phosphorylation at the C-terminus of IRF6. In vivo studies revealed that NME2 co-localizes with IRF6 in the cytoplasm of primary palatal epithelial cells. Furthermore, NME1, the member of the NME family most closely related to NME2, heteromultimerizes with NME2 to form part of the same complex. Notably, NME proteins are NDP kinases that have been implicated in regulation of epithelial cell adhesion and E-cadherin endocytosis. The lack of a suitable IRF6 CLP model prompted the development of an in ovo electroporation protocol to facilitate use of the chick as an alternative model system. The application of a dominant negative form of IRF6 and shRNA constructs using this technique reproduced the phenotype seen in humans, demonstrating that IRF6 is required in epithelial cells to promote outgrowth and fusion of the facial prominences, with secondary effects on the differentiation of the underlying mesenchyme. It is proposed that localization and interactions of NME proteins with other factors may provide clues as to the cellular pathways in which IRF6 is involved, and therefore an explanation of the cellular etiology of the CLP. The data generated during this study have opened new directions not only for future studies on IRF6 itself, but in particular on the possible role of NME proteins in governing the behavior of facial epithelia during fusion of the primary palate and hence susceptibility to CLP
CARESCAPES: TRANSNATIONAL URBAN REDEVELOPMENT OF THE POST-COLONIAL HONG KONG
No full textThesis (Ph.D.)--University of Washington, 2012Drawing upon the massive redevelopment catalyzed by the government-led urban renewal in Hong Kong in the past two decades, this research pays attention to how biased normalization of care and dependency contributes to a neoliberal regime of urban redevelopment that dictates more than 200 urban renewal projects. It examines the ways in which the regime reconfigures the daily existence of urban citizens, and moreover, the intense competition among Pearl River Delta cities. Taking a transnational perspective from below, it reveals how the denial has affected a particular population on the move and more importantly, unsettled the civil society. By theorizing "carescapes" as a heuristic device, it trace the ways in which the transnational circulation of rent/capital travels across borders at the cost of care and needs. It illuminates the multiple displacements of care: the displacement of reproductive space and nested dependency relations; the displacement of urban residents to make room for the elite visitors; the displacement of citizens on a transnational scale, including both the underprivileged migrants and the elite expatriates who struggle to stay put in the liquid labor market
Engineering Gene Targeting Reagents Through Computational Design and Directed Evolution of Protein-DNA Interactions
No full textThesis (Ph.D.)--University of Washington, 2012Homing endonucleases have great potential as tools for targeted gene therapy and gene correction. These DNA cleavage enzymes are capable of inducing gene repair or disruption by stimulating DNA repair pathways at a specific location in a genome. However, identifying variants of these enzymes capable of cleaving specific DNA targets of interest is necessary before the widespread use of such technologies is possible. Enzyme engineering should be informed by detailed analyses of the wild-type system. In my early work redesigning the target site specificity of the homing endonuclease I-AniI, it was discovered that, despite the approximate two-fold symmetry of the enzyme-DNA complex, there is almost complete segregation of the interactions responsible for substrate binding and transition state stabilization. This separation of the roles of these domains was revealed by doing kinetic studies on target sites differing by a single base-pair from the wild-type substrate. Computationally redesigned variants of I-AniI that achieved new specificities on one side did so by modulating binding, while redesigns with altered specificities on the other side modulated catalysis. While some computational designs showed successfully altered specificity, many designs targeting other single base-pair substitutions were unsuccessful. The next step of my work involved developing better computational methods in order to improve recapitulation of the experimental data. I made improvements the ROSETTA program, giving an energy bonus to native-like interactions collected from the RCSB protein databank and developing protocols for sampling diverse design sequences. Despite advancements in both directed evolution and computational methods, protein engineering is challenging and exploring alternative methods for altering endonuclease specificity is necessary. New endonuclease ORFs can be identified due to substantial increases in available sequence data. I have additionally shown that enzyme hybrids can be built using homologue information, by transferring amino acids from homologues onto the I-AniI scaffold, improving activity and generating new specificities. This wealth of information from millions of years of endonuclease evolution will be used to guide and improve current rational engineering methods
Effects of Projected Twenty-First Century Sea Level Rise, Storm Surge, and River Flooding on Water Levels in Puget Sound Floodplains and Estuaries
No full textThesis (Master's)--University of Washington, 2012Near coastal environments have been identified as some of the most likely to be impacted by climate change. Observed changes in Puget Sound sea level and flood magnitudes are in line with those projected by previous climate change impacts studies. Current understanding of the combined effects of these changes is relatively low and has prompted us to explore the ways in which their co-occurrence will influence near coastal ecosystems and infrastructure. This project examines the effects of climate change on the lower reaches of Puget Sound rivers by investigating changes in storm surge, sea level rise, and riverine flooding. The project utilizes numerical models to quantify the shifts in hydraulic conditions expected in the Skagit and Nisqually river basins. Global climate model simulations from the ECHAM-5 climate model were used as the climate forcings and were 1) statistically downscaled using the hybrid delta method, and 2) dynamically downscaled using the WRF regional climate model. Naturalized flows produced using the Variable Infiltration Capacity hydrology model were used to drive reservoir models that simulate flood control operations. Storm surge was calculated using a regression approach that included anomalous atmospherics forcings simulated by the WRF model. A 2D hydrodynamic model was used to estimate water surface elevations in the Skagit and Nisqually River estuaries using resampled hourly hydrographs keyed to regulated daily flood flows produced by a daily time step reservoir simulation model and tide predictions adjusted for SLR and storm surge. Combining peak annual storm surge with expected sea level rise, the historic (1970-1999) 100-yr peak tidal anomaly is found to be exceeded every year by the 2020s. By the 2050s, the extrapolated 100-yr riverine flood events are found to increase by 30% and 25% in the Skagit and Nisqually Rivers, respectively. In the Skagit River, the combined effect of sea level rise and larger floods yields increased areal flood inundation up to 80% relative to the present "100-year" flood