Bioculture Journal
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Structural Analysis of CavAb, a Prokaryotic Voltage-Gated Calcium Channel
No full textThesis (Ph.D.)--University of Washington, 2016-12Voltage-‐gated calcium channels are large membrane proteins that coordinate the movement of calcium into and out of the cell in response to changes in membrane potential, mediating signaling processes such as muscle contraction and synaptic transmission. We used CavAb, a bacterial calcium channel, as a structural model for three Cav channel characteristics; ion selectivity, drug binding, and disease mutations. First, CavAb reveals three binding sites for hydrated calcium within the selectivity filter of the channel, confirming the theory of a “knock-‐off” mechanism of calcium selectivity. Second, CavAb mimics mammalian Cav antagonist binding properties, providing visualization of bound drug molecules and potential direction for structure based drug design. Finally, the addition of Timothy Syndrome disease mutations into CavAb shows small conformational changes, highlighting the potential importance of channel regulation by lipids. Even though CavAb is a distant ancestor to the mammalian calcium channels, it has proven to be a valuable tool for answering classic calcium channel questions
ANTI-RACIST EDUCATION REFORM IN BRAZIL
No full textCreated as part of the 2016 Jackson School for International Studies SIS 495: Task Force.This report is the product of the collaboration between sixteen students in the Henry M. Jackson School of International Studies at the University of Washington under the guidance of Professor Jonathan Warren, and in consultation with Professor Rodrigo Peixoto. Having extensively researched and analyzed academic sources as well as teaching resources and media relating to Brazilian race relations and racism, we recommend the following: 1. Formally acknowledge the problem of racism within Brazilian society and take steps to correct it through education. 2. Further and broaden the implementation of laws 10.639/03 and 11.645/08 by moving beyond the simple teaching of history and expanding curriculum reform to other areas of the education sector. 3. Require the training of teachers in areas of multicultural and antiracist education. 4. Use the following teacher guide as a model by which to reform current education systems. 5. Begin small by implementing in the city of Belém with the eventual goal of implementing the project nation-wide . The purpose of this report is to provide a discussion of racial politics and a tool with which teachers can bring this discussion into their classrooms. Our goals are: to train educators how to deal with racism, to instruct both teachers and students in anti-racist practices and teach people how to valorize their own identities as well as those of the people around them
Progression: Preventing Recidivism through Post-Secondary Education
No full textMaster of Arts in Interdisciplinary Studies (MAIS)In the United States of America there are more people incarcerated than in any other developed country. The majority of people released from incarceration become recidivists. Many people who are incarcerated serve their time and return to the same circumstances that led to their incarceration. First time offenders are often released to much worse circumstances because they now have their options in regards to life essentials such as housing and employment limited by a criminal conviction. Despite these unfortunate realities, the potential within many people affected by this vicious cycle can still be reached. Many researchers have concluded that post-secondary education can have a positive impact on preventing recidivism. Through pursuing an education, formerly incarcerated college students embark on a transformative journey that leads to a reduced risk of becoming a recidivist. In addition to new opportunities for employment, transitioning from prison to college can play a role in reshaping character, identity, and values for the formerly incarcerated. There are many studies on prison-based college programs but there is very little research in regards to the experiences of students in college post incarceration (Halkovic & Greene, 2015; Strayhorn et al., 2012). In order to address this gap, the method of inquiry chosen for this project was autoethnography. The result of this project is a workshop and workbook designed to help people transition from prison to college. Workshop participants will be introduced to many key topics regarding the transition from prison to college. Participants will be walked through the process of applying for admission as well as financial aid. They will also be introduced to campus and community resources that can assist them in their transition. There are ten workshop sessions and 10 related workbook units. The goals and objectives of the workshop and workbook are directly related to the lived experiences uncovered through the research process. The topics include The Transformative Nature of Post-Secondary Education, Leaving the Criminal Lifestyle Behind, Community Resources, Academic and Career Options, Financial Aid, College Life, Being a Felon on Campus, Facing Adversity, Doing School Work, and Bringing it all Together. Within the major topics, each areas of focus is addressed through secondary content that helps reach the workshop objectives
Extending Harvest-Scheduling Using Spatial Optimization: Road Access and Edge Effects.
No full textThesis (Ph.D.)--University of Washington, 2016-12The scheduling of management actions across forest stands is a fundamental task in the world of forestry. However, the spatial and temporal layout of management actions can lead to a combinatorial explosion of potential options to consider. Additionally, these management alternatives must often meet various constraints and limitations. The sheer quantity of options quickly pushes these problems out of the realm of “eyeballing” a good, or even feasible, solution. Because of this, managers have turned to optimization models to help determine the best harvest schedule that meets all requirements. Due to the computational complexity of these models, managers are forced to make simplifying assumptions, and to limit the scope of the models to only the most fundamental aspects. Now, with continued progress in both computational power and solution techniques, it is becoming both practical and feasible to extend these harvest scheduling models to consider broader aspects of the process. In this dissertation I consider two major extensions to harvest scheduling models: road access and edge effects. In chapter 1, I worked with the Washington State Department of Natural Resources to extend their harvest schedule modeling to consider the endogenous cost of rebuilding and maintaining the road network used to access a forest. I propose the Endogenous Fixed Charge Model (EFCM) to incorporate road costs that that vary endogenously with the system’s harvest decisions. In a case study in the Pacific Northwest, the EFCM was integrated into DNR’s standard workflows through the use of custom software called “Builder” that amended the EFCM constraints and variables to DNR’s exiting harvest schedule optimization. Results from the case study show the EFCM was able to increase net present value over a million dollars and to reduce the overall road network by some 14%. In chapter 2, I explore how edge effects between managed forest units can be controlled and mitigated. Newly created edges caused my management actions to alter the landscape and can affect many environmental factors. These altered environmental factors have a variety of impacts on forest growth and structure and can alter harvest yields and habitat for wildlife. After discussing how edge effects can arise from a variety of management actions, I propose a general optimization modeling framework to detect and flag newly created edges while determining an optimal management schedule. I use the real world context of clear-cut harvesting to illustrate multiple possible management objectives tied to the creation and delineation of newly formed edges. In a case study in the Pacific Northwest, I demonstrate how the modeling framework can be used to mitigate damage associated with increased wind exposure caused my neighboring harvests. Results from the case study show the modeling framework functions as intended and that a significant reduction in wind damage can be achieved by considering the spatial and temporal sequencing of harvest actions. In chapter 3, I return to the road access problem to examine how an alternative representation of the road network affects the solution behavior of a joint harvest-scheduling and road-access model using route-finding. Route-finding removes the assumption of predefined routes and allows the optimization model to choose the best hauling route while considering all other harvests that need routing. The number of constraints and variables used for route-finding depend on the size and configuration of the road network. Therefore it is important to consider how alternative representations of the road network effect the solution behavior of these difficult-to-solve models. To test network representations, I propose a Mixed Integer Program (MIP) to include road-access using route-finding within a harvest-scheduling optimization. I apply this model to two different representations of the road network: the Traditional Spatial Representation (TSR) where roads are modeled as arcs connecting nodes, and the Line Graph Representation where roads are modeled as nodes, and arcs represent shared intersections. This transformation retains the same information as the original network, but can alter the number of nodes and arcs in the system. I illustrate the mechanics of the model in a case study in the Pacific Northwest and show that the LGR was able to outperform the TSR in many of the tested scenarios
Zero-rating in emerging mobile markets: Free Basics and Wikipedia Zero in Ghana
No full textDespite widespread controversy surrounding zero-rating—that is, the practice of subsidizing mobile data—the field suffers from a lack of inquiry into user understanding of and experience with zero-rated services. This paper explores how Ghanaian mobile users interact with zero-rated mobile applications Free Basics and Wikipedia Zero. Based on semi-structured interviews with users and non-users of the applications, I discuss how mobile phone users perceive Free Basics and Wikipedia Zero, what motivates them to use or not use the applications, and how the availability of the applications influences their data-buying strategies. Findings suggest that respondents, including those who did not actively use the applications, understood and experienced Free Basics and Wikipedia Zero in ways divergent from the providers’ aim of expanding access to online content and services
Floating Wetlands in the Puget Lowlands: Design, Construction, and Viability
No full textThesis (Master's)--University of Washington, 2016-06Floating wetlands are rafts that host wetland plants, supporting wildlife habitat and contributing to improved water quality. Floating wetlands have been developed and deployed worldwide to restore wetland structure and function to degraded urban aquatic environments. Informed by river and wetland structure and function, as well as by "naturally occurring" floating wetlands, this research involved developing, building, monitoring and assessing one dozen new floating wetland designs intended to improve plant and animal biodiversity in degraded urban aquatic environments of the United States Pacific Northwest. From 2013 to 2016, field research was conducted on plant species’ overwintering, volunteerism, and position relative to water surface within these rafts. The most successful planted species was Juncus ensifolius (dagger-leaf rush), showing a 100% survival rate and volunteering in 20% of rafts. The most prolific volunteer was Epilobium palustre (marsh willowherb), present in 65% of rafts. This thesis provides a preliminary understanding of how the various raft designs and plants fared, and offers insights for improving upon the designs. Knowledge gained from the research will inform plant selection as well as future studies evaluating usage of floating wetlands by fish and wildlife in the region
33D1+ Dendritic Cells in Tolerance and Immunity
No full textThesis (Ph.D.)--University of Washington, 2016-11CD4+ Foxp3+ regulatory T cells (Tr cells) are potent anti-inflammatory cells which naturally suppress autoimmune disease by tempering immune responses to self- and foreign-antigens. Given their integral role in the maintenance of self-tolerance, the manipulation of Tr cell abundance and/or function has tremendous implications for the treatment of a spectrum of diseases including autoimmunity, graft rejection, and cancer. Although once thought to represent a uniform group of immuoregulatory cells, work from our lab and others over the past several years has demonstrated considerable phenotypic and functional heterogeneity exist amongst Tr cells. Broadly, Tr cells can be subsetted based on their localization within secondary-lymphoid (SLO) and non-lymphoid tissues where they exhibit a unique dependence on IL-2 signaling and TCR/co-stimulatory receptor activation for their homeostatic maintenance and function, respectively. Loss of either of these distinct Tr cell subsets is sufficient to invoke lethal autoimmunity. However, Tr cells are incapable of IL-2 production due to transcriptional repression at the IL-2 locus by Foxp3 and are therefore dependent on paracrine sources of IL-2 downstream of cellular and molecular interactions which are largely Tr cell-extrinsic. The results presented in this dissertation comprehensively identify the components of the circuit sustaining IL-2-dependent Tr cells in the spleen. Here we demonstrate the presentation of MHCII-restricted auto-antigens by CD80/86-bearing 33D1+ CD11bint DCs to self-reactive CD4+ T cells within T cell zones of the spfleen synchronizes the frequency and function of IL-2-dependent Tr cells, preventing spontaneous autoimmunity. Furthermore, the amount of homeostatic IL-2 generated through this circuit is limiting for Tr cells and subtle perturbations in its availability can enhance immune activation directly through its impact on IL-2-dependent Tr cells. Therefore, altering the IL-2 reservoir, either directly or through the manipulation of 33D1+ CD11bint DCs or additional molecules which stimulate its production, could be therapeutically beneficial in augmenting immune responses naturally constrained by Tr cells. Our findings also help reconcile the apparent paradox of lethal autoimmunity which develops in mice constitutively lacking DCs, which we posit results from the selective loss of IL-2-dependent Tr cells no longer supported by IL-2 release downstream of 33D1+ CD11bint DCs. Moreover we report DC-intrinsic CD4 expression, historically used to delineate DCs in the spleen but functionally undefined, is dynamically regulated on 33D1+ DCs in a cell intrinsic manner and augments the function of 33D1+ DCs in part through its ability to influence IL-2 production from CD4+ T cells in response to complex antigens. Thus, 33D1+ DCs are integral for sustaining self-tolerance through their indirect maintenance of Tr cells, and modulate CD4 expression to potentially regulate the magnitude and/or duration of an immune response
Don't Forget to Play: Examining what Play looks like in Museums for Adult Visitors
No full textThesis (Master's)--University of Washington, 2016-06While play in museums for children is not a new concept, there is little research on what play looks like for the adult visitor. This study investigates adult play in museum exhibits designed for family learning, using Stuart Brown’s (2010) typology of play. Thirty visitors were observed between five exhibits at the City Museum, St. Louis MO and Science World, Vancouver B.C. Results showed that adults do play in these exhibits, and that they engage in various types of play, typically favoring body/movement play. These findings can be used by museums to understand how to create active opportunities to fully engage adult visitors
UW Symphonic Band UW Concert Band UW Wind Ensemble May 26, 2016
No full textConcert ProgramUW Symphonic Band UW Concert Band UW Wind Ensemble May 26, 201