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Inducible CRISPR-Targeted ‘Knockdown’ of Human Gut Bacteroides in Mice Reveals Glycan Utilization Strategies
Get PDFLearning how members of the human gut microbiota compete and cooperate for dietary nutrients, such as fiber-associated glycans, should help facilitate development of more precise nutritional recommendations for improving health. To model how bacteria prioritize the utilization of different fiber glycans in the mammalian gut, germ-free mice were colonized with a 13-member consortium of cultured, genome-sequenced human bacterial strains, including seven Bacteroides species. Animals were fed a Western diet supplemented with pea fiber. Once the consortium had time to assemble, an inducible CRISPR-based system was used to deplete the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to 60-fold. Each type of knockdown resulted in specific, reproducible increases in the absolute abundances of other Bacteroides, with accompanying changes in their glycan prioritization, most notably involving changes in the expression of their polysaccharide utilization loci (PULs). The emergence of these ‘alternate consumers’ was associated with preservation of the community’s capacity to metabolize fiber glycans, as judged by measurements of degradation of polysaccharides covalently attached to orally administered artificial food particles, and of monosaccharides and glycosidic linkages remaining in cecal contents. Finally, using a Cas9-PmCDA1 base editing system, we disrupted translation of transporters critical for utilizing abundant dietary polysaccharides in Bacteroides vulgatus, a B. cellulosilyticus knockdown-responsive taxon, to further characterize mechanisms associated with its increased fitness following knockdown. Using this approach to define how nutrient resource utilization is prioritized among community members could help delineate the origins of robustness and resiliency in the microbiota, as well as aid in the design of microbiota-directed therapeutics
Three Essays on Education Policy, Intergroup Relations, and Human Capital Accumulation
Get PDFThe impact of education on fostering the development of human capital and molding sociopolitical attitudes from an early age is a well-explored topic in the field of social sciences. This dissertation takes a broader approach by delving into the consequences of two critical components of the education system: (1) the language used for instruction, and (2) citizenship education. To accomplish this, I employ a combination of observational and experimental research methods to disentangle the causal effects of these educational factors within the contexts of Malaysia and Singapore. Chapter 2 delves into the ramifications of adopting a non-native language of instruction on students’ educational outcomes, specifically examining the consequences of a language reform in Malaysia. In Chapter 3, I investigate the impact of the same language reform in Malaysia and how bilingual instruction might alleviate ethnic discrimination against outgroups by encouraging perspective-taking. The final chapter explores the influence of citizenship education on promoting ethnic tolerance through a cross-national analysis and a case study of a citizenship education reform in Singapore
Investigation of Volatility, Composition, and Gas-Particle Phase Partitioning of Atmospheric Organic Compounds through Novel Instrumentation and Techniques
Get PDFAtmospheric aerosols are ubiquitous indoors and outdoors and their impact on human life on Earth is extensive. Aerosol particles scatter and absorb solar radiation, are key in the formation of clouds and precipitation, and can affect the abundance and distribution of greenhouse and atmospheric trace gases by physicochemical multiphase processes, thus they play an important role in regulating regional and global climate. On the other hand, poor indoor and outdoor air quality associated with high particulate matter (PM) levels is among the leading health risks worldwide, affecting life quality and expectancy by increasing the risk of cancer, cardiovascular and respiratory diseases. Organic aerosols (OA) have been recognized to account for a significant portion of atmospheric PM covering a wide range of volatilities that encompass thousands of individual compounds. Therefore, the extent of aerosols impact on human life strongly depends on the volatility and chemical composition of the species that comprise the OA population. The work presented in this dissertation focuses on the improvement of OA characterization through the development of novel instrumentation and methods, and the application of these techniques to investigate the process influencing aerosols’ volatility and chemical composition variability. Chapter 2 discusses the challenges in recovering volatility information through thermal evaporation measurements alone and presents improvements in OA volatility characterization when combining thermal evaporation with thermal desorption gas chromatography-mass spectrometry. Chapter 3 focuses on the full development of a modified Semi-Volatile Thermal Desorption Aerosol Gas Chromatograph (SV-TAG) with an automatic calibration system. This version of the SV-TAG features a newly developed cell designed to improve the collection of intermediate volatility and semi-volatile gases and particles, extending the analytical capability of the instrument in the quantification of higher-volatility chemical species. This new instrument was deployed during the Alaskan Layered Pollution and Chemical Analysis (ALPACA) field campaign to help understand the dynamics of speciated gas-particle partitioning under extreme cold and dark conditions with results discussed in Chapter 4. The time-dependent chemical information provided by the SV-TAG also aided in the investigation of the major sources contributing to poor air quality during wintertime in this Arctic region, which is detailed in Chapter 5
Optimization and Applications of Whispering Gallery Mode Microbubble Resonator
No full textOptical biosensors are frontrunners for rapid and real-time detection of analytes, particularly for low concentrations. Among them, whispering gallery mode (WGM) resonators have recently attracted a growing focus due to their robust optomechanical and optofluidic features and high sensitivity, measuring down to single binding events in small volumes. With their unique advantages and their compatibility with different sensing modalities, these sensors have the potential to become major game changers for biomedical and environmental monitoring, among many other relevant target applications. In this dissertation we focus on one geometry of whispering gallery mode resonators, the microbubble resonator. This platform is unique, among others, because of its superior ability to integrate fluidic handling and optical sensing. This geometry has inline silica capillaries which are perfectly suited to deliver analytes, in liquid of gas phase, to the sensing area. This dissertation can be broken into two main parts; optimization and applications of the whispering gallery mode microbubble resonator. We begin by optimizing the fabrication procedure by a standardization of the fabrication parameters, leading to higher fabrication success rates and lower cost. Next, we show work into polymer packaging of the resonator platform to protect the device from contamination and outside perturbations – showing applications in displacement sensing as well. The last part of our optimization work gets around the use of expensive tunable diode laser sources typically used in whispering gallery mode resonators and replaces it with a single wavelength source without sacrificing the platforms sensing capabilities. The second part of this dissertation will show two novel applications of the whispering gallery mode microbubble platform. First, we imbue the microbubble resonator with sensitivity to changes in pH, a parameter the device is not inherently sensitive to, through the use of “smart” hydrogels. To isolate the whispering gallery mode from sensing refractive index instead of pH, we employ a “thick-walled” microbubble resonator to protect and insulate the mode from outside influences. Lastly, we show the microbubble resonator coupled to machine learning algorithms can be used to not only detect, but also classify nanoparticles and cells based on their photoacoustic spectroscopy signals
Tree Recovery by Dynamic Programming
Get PDFTree-like structures are common, naturally occurring objects that are of interest to many fields of study, such as plant science and biomedicine. Analysis of these structures is typically based on skeletons extracted from captured data, which often contain spurious segments or cycles that need to be removed. We propose a dynamic programming algorithm which seeks to recover directed trees from these noisy skeletons. Our method recovers trees by removing edges and duplicating nodes while adhering to edge-label constraints. Our algorithm proceeds by iteratively merging graph nodes, such that the solution on the original graph can be obtained from those on the contracted graphs. Furthermore, we show that our method can recover trees in many settings, such as from rice root images, retinal fundus images, 3D corn root images, and 3D grapevine images
Toward full-cycle organizational research on group relational accounting: Multimethod investigation of the impact on business, labor, and social movements
No full textNumerous instances of individuals organizing and participating in collective actions in response to their in-group’s perceived inequities in intergroup exchange abound. Despite this, there is currently a lack of psychological accounts explaining this phenomenon, resulting in a limited understanding of the psychological process that motivates individuals to engage in collective action. This dissertation redresses this oversight in current research by conducting a multi-method investigation into this phenomenon. It provides a comprehensive theoretical framework for understanding the psychological process behind collective actions aimed at rectifying one’s in-group’s perceived inequities. To build this theory, I conducted an inductive study examining six cases of intergroup exchanges, each comprising interrelated intergroup exchange events. Subsequently, two experiments were designed and conducted to test hypotheses derived from the inductively-driven theory. Qualitative data reveal that individuals engage in a process that I term ‘group relational accounting.’ In this process, they keep track of, recall, and update the interactions between their in-group and another group over time. As a result of this process, they engage in intergroup behaviors, including organizing and participating in collective action, to address their in-group’s perceived inequities in their exchange with an out-group. Emotions play a mediating role in the relationship between perceived inequities in one’s group relational account and their intergroup behaviors. Results from both Experiment 1 and 2 provide empirical support for this theoretical framework. Both the theoretical and practical implications of this theoretical framework are discussed
Digital Cartography
No full textDigital Cartography covers foundational cartographic principles that are needed to make effective maps. lt explores such concepts as data, lettering, along with multivariate and uncertainty visualization. By the end of this book, a reader will be able to: (1) Describe how cartographic concepts such generalization, scale and projection will affect mapping products; (2) Identify the medium, purpose, and spatial data requirements to create a map that is appropriate to a specific audience; (3) Evaluate maps produced by peers and various organizations; and (4) Construct maps that effectively use color, font, and other design elements using ArcGIS Pro.
Digital Cartography was adapted from Penn State University’s GEOG 486 – Cartography and Visualization Open Educational Resource.https://openscholarship.wustl.edu/books/1065/thumbnail.jp
Segregation by Design [5.0]: A Historical Analysis of the Impact of Planning and Policy in St. Louis, Student Version (2024)
No full textCatalina Freixas, Associate Professor in Architecture, Washington University in St. Louis, Instructor and Editor, Segregation by Design, PI, The KingsVille Collaborative
Research for Segregation by Design was initiated by Assoc. Prof. Freixas and her research team in the Spring of 2022, and continued through the summer. Systematic observations and archival data was collected at that point. The work was supported by the SFS, research assistant funding and gave the foundation to the recommendations laid by the students during the semester.
The course Segregation by Design was supported by CityStudioSTL, Sam Fox School of Design & Visual Arts, Washington University in St. Louis. The collected work was presented at Hickey Elementary School on December 16th, 2022. The Provost COVID Grant, allowed Freixas to continue the research after the winter break and complete this document.
“Segregation by Design” (SBD) was first offered during the Fall 2016 semester and has been offered each fall since then at both SFS and at HSSU, enrolling students from both universities. As with the three previous offerings, SBD 2018 offered SFS and HSSU students a cross-university, cross-disciplinary environment to respond to the importance of this issue. Taking advantage of the academic resources in the region, inter-university student teams developed mitigation plans for the community of Kingsville in the St. Louis metropolitan region. These two communities were selected because they both represent a unique challenge of attempting to undo decades of racial segregation without displacing long-time, low-income, African American residents.
As in previous semesters, the course was structured into two parts. The first part entailed a series of lectures and panels by scholars from universities in the region and professionals from the metropolitan area examining current literature and issues in segregation as well as data analysis and textual analysis of community-based publications and scholarly literature review by the students. The second part consisted of field-work in communities in metropolitan St. Louis involving extensive systematic observations, stakeholder interviews, focus groups, and visioning sessions (charettes) and the production of a report for the given community. For this, the teams were assisted by volunteer professional mentors from diverse fields and residents from the selected communities. Residents helped collect data through neighborhood surveys, organized neighborhood meetings, and helped devise mitigation strategies. A three-part project looking at: i. causation, ii. consequences, and iii. mitigation strategies led to the final report that analyzed segregation in each community and proposed potential design and policy remedies. This document serves as the compilation of the work of the students in detailing the history of the communities, causes and consequences of segregation, as well as, potential policy and design strategies. In addition, the work produced during the semester was added to the in a traveling exhibition.
Neighborhood Mentors: Mark Abbott. Ph.D., Professor Emeritus of History, Harris-Stowe State University, Former Director of Center for Neighborhood Affairs; Jasmine Aber. Ph.D. candidate, MA, Director CEL Center for Architecture and Design St. Louis; Judith Arnold. MA, Urban Planner, SLACO
Hickey Elementary Community Partners: Cote Brilliante Presbyterian Church, Dream Center, EyeSeeMe African American Book Store, Family Engagement Policy, Girl Scouts & Boy Scouts, Gateway Greening, Harris-Stowe State University, Healthy Schools Healthy Communities, Julia Davis Public Library, KingsVille Neighborhood Association, National Jewish Women’s Council, Operation Food Search, Missouri Forest ReLeaf, R. Whittington Foundation, St. Louis Association of Community Organizations (SLACO), St. Louis Chess Club, The M.A.D. Mentor Program, Urban League of Metropolitan St. Louis, Washington University in St. Louishttps://openscholarship.wustl.edu/books/1064/thumbnail.jp
Biology Department Publications: 2016
Get PDFThis document is a noncomprehensive list of publications made by graduate students, post-doctoral researchers, and faculty members in the Biology Department in 2016. It indexes those publications available through major databases, and serves as an archival record of the Department’s robust scholarly contributions