Dissertations

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Development of a Novel Algorithm for Rapid HX-MS Data Analysis and Investigation of Antigen Induced Allosteric Effects on Monoclonal Antibodies by HX-MS
(University of Kansas, 2012-12-31) SHI, YUQI; Weis, David; Desaire, Heather; Weis, David; Desaire, Heather; Berrie, Cindy; De Guzman, Roberto; Boskovic, Zarko
Hydrogen exchange-mass spectrometry (HX-MS) has been widely adopted for probing higher order structure and dynamic of proteins in various fields ranging from academia research to biopharmaceuticals. HX-MS is considered as a medium resolution approach due to its ability to localize structural information of a protein at peptide level. As a consequence, HX-MS plays an important role in a variety of applications, such as assessing the comparability and stability of drug molecules, conducting equivalence analysis for biosimilars, performing epitope mapping, etc. Compared to rapid experimental and instrument development, informatics of HX-MS is still lagging behind. Conventional "feature extraction" approach impede wider adoption of this application. Described herein, are projects designed to, 1. develop a new algorithm for hydrogen exchange-mass spectrometry data analysis with less manual interpretation; 2. investigate allosteric Fc response in neutralizing antibodies upon antigen binding; 3. develop a strategy to evaluate the accuracy of peptide assignment for established peptide mapping data interpretation criteria.We developed a novel algorithm for rapid and simplified HX-MS data analysis. HX-MS raw data was compressed by inducing sparsity using LASSO regression algorithm. The algorithm was validated in terms of accuracy, precision and reproducibility using experimental data collect on maltose-binding protein. The algorithm accomplishes two goals: firstly, it is able to extract individual feature with less manual interpretation; secondly, it can generate structural fingerprint of proteins under different conditions for global comparability analysis. We established an in-solution bottom-up HX-MS experiment to investigate allosteric alterations on Fc region of the antibody upon antigen binding. Using one antigen to target three neutralizing antibodies, structural changes on the Fc region of three were investigated separately. Apart from changes in the CDR binding regions, statistical analysis of HX-MS results showed structural alternation in both Fab constant regions and Fc regions. Changes identified in three antibodies share similarities and differences. More interestingly, a portion of the structural changes overlapped with Fc receptor binding sites and glycosylation site. Our work demonstrates not only allosteric signaling to effector and Fc receptor binding but also that even within neutralizing antibodies recognizing different epitopes within the same antigen, that there are interesting differences in the allosteric response which must depend on how antigen engages with the paratope. Bottom-up HX-MS experiment interprets data at peptide level, therefore, it is important to establish a peptide mapping data interpretation criteria for peptide assignment. We developed a strategy that can determine the score cut-off for peptide assignment. By defining and matching hits with a library containing multiple decoys, false assignment rate was determined at different score cut-off. With NIST mAb as the study model, we demonstrated a benchmarking approach for peptide assignment criteria assessment.
Realizing Reformation: The Building of the American Correctional Association and the Carceral State
(University of Kansas, 2022-12-31) Wilhelm, Elizabeth; Kelley, Margaret; Perreira, Christopher; Esch, Elizabeth; Lamb, Jonathan; Frazier, Nishani
I examine federal and state prison policy development within the National Prison Association, now known as the American Correctional Association, between 1870 and 1925 to better understand how these early policies contribute to our ability as a society to confront mass incarceration today. The NPA/ACA is a professional organization formed in 1870 that has profoundly shaped carceral institutions in the United States at local, state, and federal levels. Ultimately, I interrogate how historical discourses shape current understandings of criminality and punishment and how the prison system and carceral institutions function to limit imagined solutions and possibilities for the future. To accomplish this task, I have topic modelled the annual conference proceedings of the NPA/ACA between 1870 and 1925. Topic modelling is a form of unsupervised text exploration that uses a computer algorithm to group chunks of text together based on latent patterns in the text. My model consists of 25 provided topics (textual patterns) with 10 top pages for each topic. Based on this topic model, conversations revolve around three main themes. The first theme is fulfilling the mission of the NPA/ACA through the advocation for and the successful adoption of supported policy aims. The second theme is the reformatory theories rooted in labor, education, religious ideology, and the use of various carceral institutions/policy mechanisms within and beyond prisons, which drive these policy aims. The last theme is how understandings of race, gender, age, class, mental status, and region shape their policy formation.
Climate, environment, neighborhood, & health: Pediatric asthma in Kansas City
(University of Kansas, 2022-12-31) Wesley, Elizabeth Jane; Brunsell, Nathaniel A; Rahn, David; Saint Onge, Jarron; Lyles, Ward; Lei, Ting
The purpose of this dissertation research is to investigate the spatial and temporal variability of public health as a manifestation of the complex interactions between climatic, social, and environmental systems. As a case study, we employ long-term acute pediatric asthma observations to explore the structure of environmental health the Kansas City Metro Area. By using simple models and emphasizing Bayesian methods we aim to generate knowledge that is interpretable, impactful, and actionable for public health policy makers. Specifically, to investigate the interactions between environmental and climatic variables and their effects on health and to diagnose racial disparities in asthma incidence we ask the following research questions: • How is the spatial variability of acute pediatric asthma related to PM2.5 concentrations and the amount of vegetated cover?• Is there evidence of socioeconomic disparities in acute asthma incidence? If so, how do environmental and climatic effects vary along these axes of difference? • Howisthetemporalvariabilityofacutepediatricasthmarelatedtometeorologicconditions? • Are racial disparities evident in the manifestation of these temporal effects? The spatial and temporal variation of acute pediatric asthma is explored in two studies. Chapter 2 explores the neighborhood-level spatial variability of asthma rates and investigates the effects of vegetation and air pollution exposure on asthma incidence. Additionally, Chapter 2 examines how these effects differ by socioeconomic characteristics of neighborhoods. Chapter 3 explores the temporal variability of asthma incidence and investigates the effects of meteorological conditions on daily asthma hospitalizations. Additionally, chapter 3 examines whether the temporal effects of environmental exposure on asthma exhibit racial disparities. An additional chapter discusses the translation gap between research and policy. Chapter 4 provides opinionated recommendations for environmental health research to ensure that knowledge produced is interpretable, impactful, and actionable. Lastly, Chapter 5 provides a summary of the dissertation. Each chapter is formatted as a journal article complete with introduction, methods, results, discussion, and conclusions.
Ultrafast photocarrier dynamics in hybrid van der Waals heterostructures
(University of Kansas, 2022-12-31) Valencia Acuna, Pavel Alejandro; Zhao, Hui H; Chan, Wai-Lun WL; Peelaers, Hartwin H; Cristopher, Fischer F; Cristopher, Elles E
Two-dimensional materials, as well as other non-2D materials in thin-film form, have been the topic of current extensive research. On top of that, due to their interaction, combining different materials to form heterostructures can result in other desirable properties from materials not found in nature. This work presents results for the study of photocarrier dynamics of hybrid van der Waals. The kind of heterostructures studied in this dissertation are type II, which results in electrons and holes being separated in different layered materials, due to the relative difference in energy minimas. The charge transfer mechanism is a fundamental process in these heterostructures, but a complete understanding is still lacking. To expand the possible charge transfer mechanisms and dynamics, we extend the systems typically used at these interfaces (heterobilayers), after detailing the techniques used to quantify charge transfer. We report a combined experimental and theoretical study of the effect of energy valleys on interlayer charge transfer in transition metal dichalcogenide heterostructures. By transient absorption measurements, we find that the electrons excited in the K valley of 4L WSe$_2$ can scatter to its $\Lambda_{min}$ valley, followed by their relatively slow transfer to the K valley of MoS$_2$ with a time constant of 14 ps. This transfer time is at least one order of magnitude slower than those of K-K charge transfer observed in all 1L/1L transition metal dichalcogenide heterostructures previously studied. These results provide experimental ingredients for understanding the interlayer charge transfer mechanisms, reveal the important role of the energy valley and momentum conservation in this process, demonstrate a method to control the charge transfer rate, and offer basic parameters for such heterostructures. Furthermore, we also construct a new kind of interface by using flourinated zinc phthalocyanine, F$_8$ZnPc with 1\textit{T'}-ReS$_2$. Two-dimensional (2D) ReS$_2$ monolayer flakes were exfoliated from bulk crystals, and an F$_8$ZnPc film with a thickness of 4 nm was thermally deposited on ReS$_2$. Density functional theory calculations done by our collaborator show that the two materials form a type-II band alignment. In transient absorption measurements, photocarriers are selectively excited in ReS$_2$ and monitored in F$_8$ZnPc. We found that holes in Re$_2$ can transfer to F$_8$ZnPc on a timescale shorter than 0.35 ps. The transferred holes have a long lifetime in F$_8$ZnPc on the order of 1 ns, confirming the lack of electron transfer. The efficient charge transfer from a 1\textit{T'} transition metal dichalcogenide monolayer to an organic semiconductor illustrates the feasibility of developing 2D/organic heterostructures with in-plane anisotropic electronic and optoelectronic properties. Lastly, a hybrid van der Walls multilayer heterostructure formed by monolayer graphene, few-layer transition metal dichalcogenides, and organic semiconductor of F$_8$ZnPc was fabricated. Transient absorption microscopy measurements are performed to study photocarrier dynamics. In heterostructures of F$_8$ZnPc/few- layer-MoS$_2$/graphene, electrons excited in F$_8$ZnPc can transfer to graphene and thus be separated from the holes that reside in F$_8$ZnPc. By increasing MoS$_2$ thickness, these electrons acquire long recombination lifetimes of over 100 ps and high mobility of 2800 cm$^{-2}$V$^{-1}$s$^{-1}$. Graphene doping with mobile holes is also demonstrated with WS$_8$ as the middle layers. These artificial heterostructures with novel photocarrier properties can improve the performance of graphene-based optoelectronic devices.
Analyzing Subcellular Liquid Biopsy Markers Using Microfluidic and Nanofluidic Devices
(University of Kansas, 2022-12-31) Thippala Gamage, Sachindra Shehani; Soper, Steven A; Dunn, Robert C; Lunte, Susan M; Kuczera, Krzysztof; Wilson, Sara E
Liquid biopsies are gaining significant attention as an attractive alternative to invasive tissue biopsy, specifically when tumor tissue is insufficient or when the patient’s tumor is in the vicinity of a sensitive organ that limits frequent tumor sampling. Microfluidics and nanofluidics are contributing substantially to the biomedical field with miniaturized systems that integrate different operational modules into a single motherboard to deliver effective diagnostic and screening tools for precision medicine. They are an attractive alternative to the standard benchtop assay kits because of unique operational characteristics such as closed architecture to reduce contamination, applicability for automation, and the ability to allow downstream process integration. To fulfill these efforts, we are designing and developing robust and innovative technology that is conducive to point-of-care testing (POCT) and high-scale production at a low-cost using thermoplastics. Among liquid biopsy markers such as circulating tumor cells and extracellular vesicles, cell-free DNA (cfDNA) are blood-based liquid biopsy markers that are fragments of DNA ~ 160 bp long or multiples of this size, circulating in the peripheral blood as a result of events such as secretion, apoptosis, and necrosis. They are attractive biomarkers to investigate since they contain a plethora of genetic information directly associated with the parent cells; these biomarkers can be gathered quickly from minimally invasive techniques such as blood draws. Accordingly, circulating tumor DNA (ctDNA), which is a subclass of cfDNA released by tumor cells, carries clinically actionable mutations that are characteristic of both the primary and metastatic tumor cells from which they were released. Hence, they provide comprehensive mutational profiling that would otherwise be undetectable due to tumor tissue heterogeneity. These mutations such as single nucleotide polymorphisms (SNPs) which can be the origin of certain cancers, can be identified by mutation detection methods such as next-generation sequencing for effective in vitro diagnostics. Therefore, the development of efficient technologies in isolating these biomarkers from body fluids such as blood is of great importance for the progression of targeted therapy tailored to an individual’s genetic makeup, and for screening and disease monitoring in clinical settings. However, these mutational profiling methods of rare biomarkers demand high-quality inputs with minimum contamination to reduce signal background and increase the sensitivity of the analysis. Yet, the availability of effective methods for the isolation of these rare biomarkers indicative of various diseases is limited. The existing commercial methods typically involve extensive sample handling that depends on skilled operators. Hence, due to these analytical and preanalytical factors, there is high interlaboratory variability seen which lowers the reproducibility of such assays targeting liquid biopsy biomarkers. Moreover, due to the low sample input, reported microfluidic assays suffer from the lack of enrichment of rare biomarkers that exist in the presence of high background. Thus, in this dissertation, we first present an efficient microfluidic assay (> 90% recovery in 100-700 bp and > 70 % recovery in 50 bp with 90% recovery in 100-700 bp and > 70 % recovery in 50 bp with 70 % recovery in 50 bp with < 0.01% gDNA contamination) for the extraction of cfDNA that can be coupled to downstream molecular analysis methods such as quantification by real-time PCR and mutation detection by Ligase detection reaction (LDR) and capillary electrophoresis to search for rare ctDNA fragments. We further developed this effort to negate the need for offline analysis by introducing nanofluidic devices that can perform solid phase LDR (spLDR) reactions and identify the different LDR products that are indicative of SNPs by their time-of-flight (TOF) measurements via resistive pulse sensing (RPS). Hence, in chapter three we introduce the nanosensor that is capable of performing the spLDR in its pixel arrays by providing solid support and subsequently separating unlabeled oligonucleotides of different lengths resulting from spLDR by TOF nanopore-based single molecule electrochemical sensing through dual in-plane nanopores. In the same chapter, we also introduce a novel method to tune the nanopore size to increase the S/N ratio for single-molecule sensing and demonstrate an increase in current amplitude by 3.5-fold via high throughput ? DNA translocation. In future directions, we also present a custom-built thermocycler that is capable of effectively transferring thermal energy into the microfluidic reactors to perform on-chip PCR and spLDR reactions. With the emergence of the SARS-CoV-2 pandemic, we addressed the drawbacks of the existing tests that hinder their large-scale global availability by expanding our technology to develop a surface functionalized microfluidic affinity isolation assay with DNA aptamers that effectively identify active SARS-CoV-2 particles in non-invasive and self-collectible saliva samples (100% clinical specificity and 95% clinical sensitivity). In chapter 4, we present the abovementioned reagent-less enrichment technology that can identify infectious COVID-19 patients and can also be rapidly adapted to test for other viruses, their variants, and extracellular vesicles by using alternative affinity agents. Furthermore, we introduce a high-sensitivity extended nano Coulter counter (XnCC) device in chapter 5 that is based on the principle of RPS for rapid label-less enumeration of the affinity-isolated virus particles (VPs) that are hydrodynamically and electrokinetically shuttled to the XnCC. The device consists of five parallel in-plane nanopores with a negative bias voltage applied across it to monitor the change in current using a miniaturized trans-impedance amplifier (TIA) circuit. To improve the throughput and the concentration limit of detection of the device, we also discuss modifying the fluidic network to have 25 nanopores in the future directions section. Moreover, we discuss the integration of the microfluidic affinity device and the XnCC presented in chapter 4 and chapter 5 into a portable instrument with miniaturized electronics, and a fluidic cartridge for rapid (<20 min) at-home or POC testing strategies.
Conservation through Parcellation: A Geographic Account of How Cabécar Communities Stopped an Arc of Deforestation in the Costa Rican Talamanca
(University of Kansas, 2022-12-31) Tappan, Taylor; Herlihy, Peter H; Egbert, Steve L; Kindscher, Kelly; Metz, Brent E; Chikanda, Abel; Dobson, Jerome E
Latin America’s indigenous territories contain nearly one-third of the region’s carbon stored in tropical forests. Yet these forests are under threat. In recent decades indigenous peoples have mobilized to demand formal land rights in response to the aggressive expansion of logging, mining, agricultural colonization, and cattle ranching onto their ancestral territories. Their coordinated activism has prompted governments, often supported by multilateral development agencies such as the World Bank, to title vast areas of land in Central America and the Amazon basin to indigenous communities. Geographers have begun to assess whether the titling of indigenous territories is an effective policy strategy for curbing tropical deforestation. However, few studies describe how land use and land tenure practices exist beneath the umbrella of titled indigenous territorial jurisdictions (ITJs) or how these practices correlate to forest cover outcomes. This dissertation combines archival research, a multitemporal land use/land cover (LULC) change study, and a subsistence parcel-scale land tenure survey conducted during 2018-2019 fieldwork in Chirripó Reserve—the largest indigenous territory in Costa Rica—to understand whether a home-spun system of parceling and privatizing lands along the reserve’s western boundary has effectively stabilized the colonization front since its establishment in 1976. The findings of my research illustrate how indigenous Cabécar communities have implemented their own cadastral-based property regime to allocate land inside Chirripó and, in turn, stopped an arc of deforestation along the agricultural colonization front.
“It’s an admission of guilt”: A critical case study of Indigenous fans’ identities and their perspectives of the Kansas City NFL franchise’s organizational policy changes and cultural misappropriation
(University of Kansas, 2022-12-31) Sperling, Julien Alexandre; Gist-Mackey, Angela N; Zhang, Yan Bing; Kunkel, Adrianne; Piercy, Cameron W; Gordan, Brian
Professional sports can serve a variety of secular functions for people. The passion of the fans, the commitment of the players and staff, and even the stadium plays a critical role in how fans identify with sports teams and brands. This critical case study employs Tribal Critical Race theory and Social Identity Theory to better understand the viewpoints of Indigenous Kansas City NFL fans. The purpose of this research is to understand how Indigenous fans’ make sense of and discursively construct their racial and fan identities in relation to the Kansas City NFL team. Second, this study explores how Indigenous Kansas City NFL fans interpret the Kansas City NFL team’s cultural misappropriation. Third, this study investigates how Indigenous Kansas City NFL fans understand the 2020 organizational policy changes that limit fans’ symbolic cultural misappropriation by restricting fans’ nonverbal communication. Most importantly, this study privileges the voices of Indigenous fans to better understand their perspectives on these concerns. This critical case study design uses semi-structured interview data and phronetic iterative qualitative data analysis. Also, during the interview process, participants brought artifacts that represented their affiliation to the Kansas City NFL team as fans. Findings resulted in three major themes. The first theme titled, “Navigating Internal Turmoil” revealed a typology of five different types of fans, which vary based on their identification with their Indigeneity and the team: supportive fans, balanced fans, reluctant fans, former fans, and anti-fans. The second theme titled, “Mocking a Race of Human Beings” revealed participants’ perspectives on specific Indigenous symbols (i.e., drums, war bonnet, and tomahawk chop) employed by the Kansas City NFL franchise. The third theme, titled, From “Small Baby Steps” to “Trying to Kill Ideas” revealed participants perceptions of the policy changes and amplified participant voices, which call for greater action from the franchise, such as more education and changing the name of the team. The thoughts and opinions of my participants tell a story filled with emotions on the matter of cultural misappropriation by the Kansas City NFL team. Theoretical and practical contributions are addressed in closing.
Quantifying the depth effects of environmental changes on soil structure and organic matter decay across scales in the Anthropocene
(University of Kansas, 2022-12-31) Faria Tavares de Souza, Ligia; Billings, Sharon; Foster, Bryan; Reuman, Daniel; Nagel, Joane; Kirk, Matthew; Sullivan, Pamela
Soils are the largest reservoir of terrestrial organic carbon (C). Changes in soil functioning to different environmental conditions imposed in the Anthropocene may result in CO2 feedbacks to the atmosphere and may further alter ecosystem functioning. Human-induced changes to climate and land use patterns are likely to modify soil features due to accelerated rates of biotic responses to these new environmental forcings. However, the degree to which the interplay between biota and soil processes reverberates with depth and across spatial scales is still poorly understood. In this dissertation, I investigate the imprints of the Anthropocene in soil functioning by connecting the responses of soil physical, biological, and chemical features across spatial and temporal scales. In Chapter 1, I developed a dataset characterizing the temperature sensitivity of a purified, extracellular enzyme across a pH gradient and combined it with published datasets of other two extracellular enzymes to similar simulated environmental conditions to explore the fundamental, biochemical limitations that may alter organic matter (OM) decay and dictate future ecosystem functioning under warming at the global scale. Because the soil’s ability to protect and store C is dependent on OM decomposition processes, in Chapter 2, I investigated the influence of land use change on soil organic C (SOC) depth distributions across a regional climatic gradient. I used two complementary scales to parse the degree to which some ecosystem features, such as rooting abundances and soil structure, modify the transport and, consequently, the persistence of C down-profile. In Chapter 3, I explored the potential pace at which soil structural changes can be observed in response to changes in ecosystem features under extreme moisture conditions. I found that warming has the potential to alter OM decay in ways dependent on soil pH, with potential consequences for ecosystem stoichiometry at the biosphere scale and ultimately affecting the protection of C in soils. I also found that decreases in water availability across a climatic gradient can lead to a decoupling of biogeochemical cycles across depths in native prairie soils, contrary to the more homogenous distributions of SOC in cultivated lands regardless of climate. Differential inputs of SOC throughout soil profiles also modified soil structure in ways important for the flow of solutes and water that drive biogeochemical coupling. In Chapter 3, I found that soil structural changes can be observed across relatively short timescales, such as over one growing season, especially at relatively deeper depths in the subsurface. Combined, these findings illuminate the extent of the combined effects of changes in ecosystem features and edaphic properties at different scales and how they can influence ecosystem functioning in the future. Understanding these responses is critical for investigating the ways in which the Anthropocene has altered soil functioning, and to develop well-informed policies that aim at mitigating the effects of climate change.
An artificial intelligence and remote sensing approach to iceberg distribution around the Greenland Ice Sheet
(University of Kansas, 2022-12-31) Shankar, Siddharth; Stearns, Leigh A; Walker, J. Douglas; van der Veen, Cornelis J.; McLean, Noah M.; Li, Xingong
The Greenland Ice Sheet has been losing mass at an accelerated rate, from 41±17 Gt/yrin the 1980s, to 286 ± 20 Gt/yr in the 2010s, to 532 ± 58 Gt/yr in 2019 [Mouginot et al., 2019, Velicogna et al., 2020, Mohajerani, 2020]. In addition to raising sea level by 13.7 ± 1.1 mm since 1972 [Mouginot et al., 2019], roughly half of this mass loss occurs due to iceberg calving and submarine melt at outlet glacier termini [Benn et al., 2017]. As a result, icebergs act as an important link between ice sheet and ocean processes. Changes in iceberg size and abundance can reflect changes in glacier dynamics (ice velocity, rheological damage) and geometry (buoyancy condition, ice thickness). In turn, the size and abundance of icebergs can impact their melt rates and thus influence fjord circulation [Moon et al., 2018]. Despite their importance, production of an ice-sheet wide, year-round, inventory of iceberg distribution around Greenland was not possible until recently. Greenland icebergs are relatively small (1000 m2 - 2 km2) and exist in complex environmental settings (pro-glacial m´elange, sea ice, waves). Using publicly-available imagery and a cloud-based computing platform, we can efficiently produce iceberg distributions around the Greenland Ice Sheet, every 2-weeks, year-round. Through this research, we improve our understanding of iceberg patterns and trajectories,which is essential for climate models, climate projections, and shipping logistics. Importantly, we can deduce where icebergs tend to travel, how quickly they move, and whether glacier, fjord or weather conditions are more likely to modulate their trajectories. High spatial and temporal resolution imagery that can provide continuous iceberg observations will also be useful for studies focused on freshwater flux, ocean circulation, calving laws, and iceberg trajectories.
Narrativas de tránsito: movilidades y colonialidad en novelas y filmes de los siglos XX y XXI en Colombia y Ecuador
(University of Kansas, 2022-12-31) Roman Alvarado, Juan Pablo; Garibotto, Veronica; Day, Stuart; Acosta, Rafael; Janzen, Marike; Perez, Jorge
Narrativas de tránsito explora la representación de movilidades en novelas y películas de Colombia y Ecuador desde el Segundo cuarto del siglo XX en adelante. La disertación propone que estas narrativas son el terreno de una interacción problemática entre dos tipos de movilidades. El primer tipo, practicado como “movilidad legítima”, está ligado a tópicos de progreso y modernización y es ejercido por sujetos privilegiados por razones de raza, clase y género. El segundo tipo, practicado como movilidad “ilegítima”, es actuado por personas sujetas a jerarquías raciales, de clase o de género. La disertación destaca cómo estas novelas y filmes representan un arreglo de prácticas alternativas de movilidad para resistir, entorpecer, y perturbar la movilidad colonial y para asegurar la supervivencia de comunidades marginalizadas. Los capítulos examinan tanto la representación de movimientos en este corpus de novelas y filmes, como la representación de comunidades marginadas por ellas mismas y por otros en estos movimientos. La disertación pone en diálogo dos campos teóricos: las teorías de la movilidad, un campo que propone una lectura crítica de los movimientos, pero no presta la suficiente atención a sus implicaciones coloniales, y las teorías latinoamericanas de la modernidad/colonialidad/ decolonialidad, que están muy interesadas en las prácticas coloniales y tratan con las movilidades de manera implícita, pero no abordan explícitamente la relación entre movilidad y colonialidad.
Poética caballeresca: libro y propaganda en la imagen literaria y editorial de Isabel I de Castilla (1489-1511)
(University of Kansas, 2022-12-31) Ranales Perez, Angel Maria; Rivera, Isidro I; Manning, Patricia P; Bayliss, Robert R; Corteguera, Luis L; Garibotto, Verónica V
“Poética caballeresca: libro y propaganda en la imagen literaria y editorial de Isabel I de Castilla (1489-1511)” expone la capacidad de la ficción caballeresca medieval en Iberia para demostrar el valor de las decisiones editoriales de artesanos del libro que deliberadamente cimentaron una imagen de legitimidad política de la reina Isabel de Castilla. Los libros de caballería bajo examinación central -Historia de la linda Melosina (Toulouse, Juan Parix y Estevan Clebat, 1489), La historia de los nobles caualleros Oliveros de Castilla y Artus d’Algarbe (Burgos, Fadrique de Basilea, 1499) y Los cinco libros del esforçado et inuencible cauallero Tirante el Blanco (Valladolid, Diego de Gumiel, 1511)- presentan elementos literarios, editoriales, materiales e ideológicos que intencionalmente salvaguardan el gobierno isabelino y que caracterizaron la mentalidad de lectura literaria en la península ibérica hacia finales del siglo 15 y comienzos del 16. A través de un acercamiento literario e historiográfico, planteo que la ficción caballeresca colaboró activa e intercambiablemente con otras manifestaciones materiales caballerescas para generar una poética expansiva y legítima en favor de doña Isabel. Los casos de estudio que se incorporan muestran que el mundo ibérico formó parte de una red europea de comunicación compartida en torno a la cultura libresca manuscrita e impresa que incitó la perspicacia e ingeniosidad de los talleres de impresión para estimular la creación de múltiples convenciones narrativas en constante diálogo entre sí. Mi articulación toma en cuenta selectas materialidades caballerescas como vehículos sociales de narración de historias que una vez integradas dentro del comercio literario definieron el desarrollo cultural bajomedieval ibérico. En total, la disertación despliega una postura innovadora en los estudios literarios medievales para examinar la relación del poder femenino isabelino con una serie de fenómenos caballerescos fundados en entender el libro como artefacto de transformación social y política.
Network Opinion Homophily and Account Status: How Does Perceived Riskiness Affect Facebook Political Expression?
(University of Kansas, 2022-12-31) Parviz, Elnaz; Banwart, Mary; Hall, Jeffrey; Muddiman, Ashley; Velasquez, Alcides; Watts, Amber
Guided by the assumptions of the risk-return framework (Weber, Blais, & Betz, 2002), this study used a 2 (network opinion homophily, account status) by 2 (similar/different, public/private) experimental design to investigate how risky individuals evaluate Facebook political expression to be, and how likely they are to engage in political expression on Facebook. Levels of network opinion homophily and account status were manipulated, and participants were randomly assigned to one of the four hypothetical scenarios. The analysis explored the main and interaction effects of the independent variable conditions and the indirect effects of the conditions on perceived riskiness of Facebook political expression and engagement in political expression on Facebook. Three sets of statistical analyses were conducted including a two-way MANCOVA, Hayes’s (2018) PROCESS model 2, and model 9. Political information efficacy and Facebook efficacy were included as moderators, and the effects of some individual differences including political interest and general risk propensity were controlled for in the moderation and moderated mediation models. Overall, network opinion homophily and account status did not have a significant effect on perceived riskiness and engagement in political expression on Facebook. Regardless of whether the models controlled for the effects of network opinion homophily or account status and all the other moderators and covariates, perceived riskiness remained a significant predictor of engagement in Facebook political expression. Theoretically, this study contributes to political communication studies by demonstrating that even though political expression on Facebook can be perceived as risky, this perception is not caused by network opinion homophily or having a public versus a private account. This study also contributes to the development of the perceived riskiness of political expression scale and expands this construct to digital political communication behavior.
Enhancement Of Magnetic Vortex Pinning by APCs with Coherent BZO 1D-APC/YBCO Interface
(University of Kansas, 2022-12-31) Ogunjimi, Victor; Wu, Judy Z; Wu, Judy Z; Baringer, Phillip S; Shi, Jack; Chan, Wai-Lun; Hui, Rongqing
Strong magnetic vortex pinning is crucial for in-field high critical current density (Jc) sustaining applications. This pinning force can be realized by inserting artificial pinning centers (APCs) in high temperature superconductors (HTS) such as YBa2Cu3O7-x (YBCO). Unfortunately, a degraded APC/YBCO interface can limit the pinning force making high field/high Jc applications unfeasible. The effect of APC/YBCO interface on pinning is best exemplified by the difference in pinning force generated by c-axis (direction of film growth) aligned one-dimensional (1D) APC fabricated with BaZrO3 (BZO) on one hand and BaHfO3 (BHO) on the other. A considerably higher pinning force density (Fp) was observed on the BHO 1D-APCs, which was attributed to a less defective BHO/YBCO interface than the BZO/YBCO case. This defect-ridden BZO 1D-APC/YBCO interface has been blamed for the reduced pinning efficiency of BZO 1D-APCs and is consistent with a microstructure analysis that revealed a defective, oxygen-deficient YBCO column around the BZO 1D-APCs due to the large lattice mismatch of ~7.7% between the BZO (3a=1.26 nm) and YBCO (c=1.17 nm). In this thesis, I report a dynamic lattice enlargement approach on the tensile strained YBCO lattice during the BZO 1D-APCs growth to induce c-axis elongation of the YBCO lattice up to 1.26 nm near the BZO 1D-APC/YBCO interface via Ca/Cu substitution on single Cu-O planes of YBCO, which prevents the interfacial defect formation by reducing the BZO/YBCO lattice mismatch to ~1.4%. Specifically, this is achieved by inserting thin Ca reservoir spacers in BZO/YBCO nanocomposite films. A defect-free, coherent BZO 1D-APC/YBCO interface is confirmed in transmission electron microscopy and elemental distribution analyses. This has led to a record high pinning force density Fp illustrating the critical importance of a coherent BZO 1D-APC/YBCO interface in the pinning efficiency. The question of how the APC/YBCO interface affects angular range of the pinning effectiveness for a given 1D APC is important for applications that require Jc to be maintained at all orientation in the presence of magnetic field. Although, as mentioned above, differences are present at the interfaces of BZO and BHO 1D APCs with YBCO, both materials have comparable diameters in the range of 5-6 nm. Therefore, they provide ideal systems for investigation of the angular range of pinning effectiveness by 1D APCs. By evaluating the nanocomposites’ maximum pinning force density (Fp, max) and its location Bmax, normalized to that of the reference YBCO film as functions of magnetic field (B) orientation at temperatures of 65–77 K, a quantitative correlation between the pinning efficiency of the BZO 1D-APCs and their effective angular range was obtained. Our results indicate that all 1D APCs can provide enhanced Bmax over certain angular ranges away from the c-axis. However, 1D APCs with higher pinning efficiency, such as BHO 1D APCs can have enhanced Fp, max over the entire angular range of B-orientations at temperatures of 65-77 K with respect to that for the reference YBCO sample. A microstructure analysis has revealed a defective, oxygen-deficient YBCO column around the BZO 1D-APCs due to the large lattice mismatch of ~7.7% between the BZO (3a=1.26 nm) and YBCO (c=1.17 nm), which has been blamed for the reduced pinning efficiency of BZO 1D-APCs. This thesis reports a dynamic lattice enlargement approach on the tensile strained YBCO lattice during the BZO 1D-APCs growth to induce c-axis elongation of the YBCO lattice up to 1.26 nm near the BZO 1D-APC/YBCO interface via Ca/Cu substitution on single Cu-O planes of YBCO, which prevents the interfacial defect formation by reducing the BZO/YBCO lattice mismatch to ~1.4%. Specifically, this is achieved by inserting thin Ca0.3Y0.7Ba2Cu3O7-x (CaY-123) spacers as the Ca reservoir in 2-6 vol.% BZO/YBCO nanocomposite multilayer (ML) films. A defect-free, coherent BZO 1D-APC/YBCO interface is confirmed in transmission electron microscopy and elemental distribution analyses. Excitingly, up to five-fold enhancement of Jc (B) at magnetic field B=9.0 T//c-axis and 65-77 K was obtained in the ML samples as compared to their BZO/YBCO single-layer (SL) counterpart’s. This has led to a record high pinning force density Fp together with significantly enhanced Bmax at which Fp reaches its maximum value Fp,max for BZO 1D-APCs at B//c-axis. At 65 K, the Fp,max ~158 GN/m3 and Bmax ~ 8.0 T for the 6% BZO/YBCO ML samples represent a significant enhancement over Fp,max ~36.1 GN/m3 and Bmax ~ 5.0 T for the 6% BZO/YBCO SL counterparts. This result not only illustrates the critical importance of a coherent BZO 1D-APC/YBCO interface in the pinning efficiency, but also provides a facile scheme to achieve such an interface to restore the pristine pinning efficiency of the BZO 1D-APCs. The hypothesis states that the highly strained YBCO columns around the BZO 1D-APCs due to the 7.7% larger lattice constant of BZO than YBCO’s in the c-axis provide channels to facilitate Ca diffusion, more preferably near the BZO/YBCO interface, that lead to an enlarged YBCO’s c-axis lattice constant as a consequence of the Ca/Cu substitution on the YBCO’s Cu-O planes. Confirmation of this hypothesis is hence important to understand the mechanism of Ca diffusion in BZO/YBCO ML films for further enhancement of pinning efficiency of the BZO 1D-APCs. A comparative study of two sets of BZO/YBCO ML films: singly-doped (SD-ML, BZO only) and the doubly-doped (DD-ML, BZO + Y2O3). The modulated strain field in the SD-ML films is in contrast to the non-modulated strain in the DD-ML samples as confirmed by transmission electron microscopy. Interestingly, improved pinning by four times of the reference SD single-layer (SD-SL) film’ was observed in the SD-ML samples even when the constituent BZO/YBCO layer thickness was varied between 50-100 nm, indicating that the Ca diffusion along the strained BZO/YBCO interface and the Ca/Cu substitution on YBCO’s Cu-O planes indeed correlate with the modulated strain field. In contrast, pinning degrades by twice in DD-ML samples with respect to their DD-SL counterpart’s. This result therefore suggests that strained BZO/YBCO interfaces serve as channels for Ca diffusion in SD-ML, which leads to the coherent BZO/YBCO interfaces and hence improved pinning of BZO 1D-APCs. This effect diminishes when such a modulated strain field is removed in the DD-ML samples.
Stratigraphy, Site Formation, and Geochronology at the San Esteban Rockshelter, Southwestern Texas
(University of Kansas, 2022-12-31) Niquette, Richard Mason; Mandel, Rolfe D; Sellet, Frederic; Raff, Jennifer; Adair, Mary; Schroeder, Bryon; Stinson, Philip
The San Esteban site (41PS20) is a stratified rockshelter in Presidio County, Texas with archaeological components dating from 6250 cal BP to the Modern period. Also, San Esteban contains a sedimentary record as old as 20,000 cal BP. Furthermore, 6250-year-old atlatl foreshafts represent the oldest in situ archaeological component in a rockshelter or cave in the Big Bend region of West Texas. Hence, San Esteban presents a rare opportunity to explore questions of past lifeways in the Big Bend, and is a potential source of paleoenvironmental data. That opportunity depends on a thorough understanding of site stratigraphy, formation processes, and geochronology. Geoarchaeological investigation at San Esteban co-occurred with archaeological excavation in the summers of 2019, 2020, and 2021. Stratigraphic analyses revealed a set of seven primary stratigraphic units, and a total of 13 sedimentary units across the site. Before 1800 cal BP, natural processes mostly drove site formation at San Esteban. After that time, however, anthropogenic activities became important site formation process, and over the past century, illicit collection became a significant process destroying some of the archaeological record. Despite the effects of looting, much of the archaeological record remains intact in areas that were difficult to access. Also, the configuration of the rockshelter prevented rainwater infiltration in the southern portions of the rockshelter, resulting in remarkable preservation of perishable materials. A total of 43 radiocarbon ages and one optically stimulated luminescence age were used in Bayesian modeling to understand the history of sedimentation and human occupation at San Esteban. The earliest sedimentary deposits recorded during the 2019-2021 excavations pre-date 17,000 years ago. Sedimentation was continuous throughout the terminal Pleistocene but appears to have paused during the Pleistocene-Holocene transition, perhaps because of bioclimatic change. Sedimentation was underway again by ca. 8800 cal BP, and while middle Holocene deposits have not been found at the site, they may occur in untested portions of the rockshelter. Occupation modeling indicates early use of San Esteban was likely brief, but by 2000 cal BP, human occupation intensified, resulting in longer and repeated use of the site.
Modeling Mechanical Processes of DNA-Interacting Protein Complexes Synthesizing Studies of the Binding and Catalytic Behavior of Constituent Subunits
(University of Kansas, 2022-12-31) Morgan, Aaron; Fischer, Christopher; Shi, Jack; Kong, KC; Wilson, Graham; Davido, David
I began my graduate research with a study of Chromatin remodelers, which are molecularmotors that play essential roles in the regulation of nucleosome positioning and chromatin accessibility. Here I present a quantitative analysis of nucleosome repositioning by the chromatin remodeler ISWI and demonstrate that nucleosome stability significantly impacts the observed activity. We show how DNA damage induced changes in the affinity of DNA wrapping within the nucleosome can affect ISWI repositioning activity and demonstrate how assaydependent limitations can bias studies of nucleosome repositioning. Together, these results suggest that some of the diversity seen in chromatin remodeler activity can be attributed to the variations in the thermodynamics of interactions between the remodeler, the histones, and the DNA, rather than reflect inherent properties of the remodeler itself. I moved from this seemingly inefficient system to a remarkably efficient system, the B. subtilis Φ29 bacteriophage. The gp16 ATPase is the constituent subunit of the pentameric dsDNA (Double-stranded Deoxyribonucleic Acid) translocation motor of the B. subtilis Φ29 bacteriophage. Although recent single-molecule studies have provided tantalizing clues about the activity of this motor, the mechanism by which the gp16 subunits couple the energy obtained from the binding and hydrolysis of ATP to the mechanical work of dsDNA translocation remains unknown. To address this need, we have characterized the binding of fluorophore labeled ATP and ADP to monomeric gp16 using a stopped-flow fluorescence assay. These experiments show that the binding of ATP/ADP occurs through a single-step mechanism with corresponding affinities of (523.8 ± 247.3) nM for ATP and a lower limit of 30μM for ADP. When analyzed through the lens of changes in free energy of the system, this difference in binding affinities is reasonable for a cyclical process of binding, hydrolysis, and product release. In addition to answering questions about the activity of monomeric gp16, these results are also a necessary step in constructing a model for intersubunit communication within the pentameric gp16 motor.
The Relationship Between Child Nighttime Blood Glucose Values and Parent Fear of Nighttime Hypoglycemia in Families of Youth with Type 1 Diabetes
(University of Kansas, 2022-12-31) Monzon, Alexandra D; Cushing, Christopher C; Patton, Susana R; Steele, Ric G; Roberts, Michael C; McDonough, Ryan; Akin, Becci
Objective: Youth with type 1 diabetes mellitus (T1D) are at risk for experiencing periods of nighttime hypoglycemia (i.e., nighttime low blood glucose levels). Due to this risk, many parents report significant nighttime fear and engage in maladaptive hypoglycemia avoidance behaviors at night (e.g., provide large snacks at bedtime, reduce insulin at night). To date, no study has used an objective measure of nighttime glucose to examine predictors of parent fear of nighttime hypoglycemia. Further, our current assessment tools to assess fear of hypoglycemia are lacking items that specifically assess fear of hypoglycemia specific to nighttime. The present study aimed to 1) add items to an existing measure to assess parent fear of nighttime hypoglycemia, 2) examine the psychometric properties of this modified measure, and 3) examine the relationship between parent fear of nighttime hypoglycemia and nighttime blood glucose levels as measured by continuous glucose monitors. Methods: In Phase I, the present study enrolled a sample of 10 pediatric diabetes healthcare providers (e.g., physicians, diabetes educators, pediatric psychologists) and 15 parents/caregivers of youth with T1D to generate items to add to an existing measure of fear of hypoglycemia. For Phase 2, the present study recruited an additional sample of 20 parents/caregivers of youth with T1D to pilot test the newly developed items. For Phase 3, the present study recruited a sample of 165 parents/caregivers of youth with T1D to examine the relationship between parents’ fear of nighttime hypoglycemia and child nighttime glucose values. The investigator evaluated structural validity via confirmatory factor analyses, reliability, and content validity of the modified measure to assess fear of nighttime hypoglycemia. Lastly, the investigator conducted a regression model with the child’s percent of nighttime glucose values in the hypoglycemic range as the independent variable and the parents’ modified fear of nighttime hypoglycemia total score as the dependent variable. Results: In Phase 1, The investigator generated 54 items from literature review and interviews. In Phase 2, seven items violated assumptions of distributional normality, 27 items demonstrated non-significant correlations, and two items were redundant. In Phase 3, the remaining 20 items demonstrated strong internal consistency (alpha=0.95). These items demonstrated strong to moderate relationships with criterion validity measures and strong to moderate relationships with content validity measures. Lastly, a four-factor model reflecting behaviors maintaining high glucose, helplessness, negative social consequences, and nighttime worries was the best fitting model χ2(519, n=136) = 815.33, p<0.001, RMSEA=0.065 90% CI [0.056-0.073], CFI=0.89, TLI=0.88. The results of the regression models revealed that youth’s percent of glucose values in the hypoglycemic range did not predict parents’ modified fear of nighttime hypoglycemia total score, however average youth nighttime glucose levels and nighttime glycemic variability were significant predictors of parents’ modified fear of nighttime hypoglycemia total score. Conclusions: The current study broadened the conceptualization of parent fear of hypoglycemia, and the results indicate that parents of youth with T1D may report higher fear of hypoglycemia if they observe increased fluctuations in their child’s nighttime glucose levels, regardless of how often their child’s glucose levels are in the hypoglycemic range. These findings are important to clinicians who may consider screening for parent fear of nighttime hypoglycemia and researchers interested in examining the relationship between parent fear of hypoglycemia and the use of T1D treatment devices.
Tipping the scales: alternative stable states and the role of soil microbes in ecosystem resilience
(University of Kansas, 2022-12-31) Michaels, Theo K; Bever, James D.; Sikes, Benjamin A.; Alexander, Helen M.; Billings, Sharon A.; Stock, Paul V.
Abrupt and persistent ecosystem state shifts often give rise to non-linear recovery behavior, which challenges ecosystem recovery and the societies that depend on them. The challenges of non-linear ecosystem behavior and our ability to address it, may be a mismatch of scale. Traditional approaches to the study of non-linear ecosystem behavior often assumes well-mixed systems where abrupt changes are driven by ecosystem-scale processes, and as such the role of local scale dynamics is not well understood. In this dissertation, I examine the role of local scale interactions mediated by soil microbes, and how these interactions drive changes between ecosystem states. In chapter 1, I highlight how transitions between alternative stable states are impeded by a mismatch of scale and developed a conceptual framework that draws from nucleation theory to incorporate spatial dynamics into the alternative stable states model. As part of this framework, I discussed the potential for autocatalytic nucleation dynamics within a variety of ecosystems, draw implications for ecosystem resilience and transitions between alternate states, and show how nucleation principles can be applied to ecosystem management. Applying this framework, in chapter 2 I test the conditions of, and potential for, nucleation leveraging tallgrass prairie and post-agricultural lands as a model system of alternative stable states. I found that introducing patches of late successional tallgrass prairie into post-agricultural lands, can generate the net local positive feedback dynamics necessary for patch expansion as predicted by autocatalytic nucleation. To understand the contribution of soil microbes in the maintenance or erosion of ecosystem resilience, in chapter 3, I examine the attributes of microbial fronts, with a specific focus on soil fungi, and their role in advancing or maintaining soil functional boundaries of adjacent ecosystems. Using experimentally created edges consisting of tallgrass prairie and post-agricultural fields, I found that land use history affected the pace, direction, and lag times of microbial front propagation. These findings point to ways of thinking about how we may want to encourage or prevent microbial front advancement to facilitate land management needs. While these three studies focus on local scale interactions from an ecological perspective, in chapter 4 I provide an account of a place-based social interaction based on my work at Anderson County Prairie Preserve. This account highlights the importance of building local scale relationships and asks how these interactions might scale to influence land management goals across private and institutional boundaries. Together these studies highlight how both social and ecological local scale interactions have the potential to manifest themselves in landscape scale change. By tipping the scales and considering the role of local scale interactions in ecosystem resilience, this dissertation fosters a deeper understanding of ecosystem state shifts, and offers up new perspectives to help guide restoration and land management techniques in order to meet the needs of the lands we steward in a time of unprecedented change.
Mind the Gap: Modeling Synaptic Development and Degeneration in Caenorhabditis elegans
(University of Kansas, 2022-12-31) Massengale, Molly Birrer; Ackley, Brian D; Lundquist, Erik; Macdonald, Stuart; Unckless, Robert; Gamblin, T. Chris; Subramanian, Jai
The nervous system is composed of a complex network of neural circuits, relying on synaptic connections throughout to ensure proper signal transmission. Disorders of the nervous system typically fall into two categories, developmental disorders, failure of the system to properly form circuits, or senile disorders, failure of the system to properly maintain their circuits. As such, the formation, modification, and maintenance of synaptic connections is crucial to nervous system function, and a failure in any stage may lead to disease. Here we will use C. elegans to look at both sides of the process, examining the molecules important in the development of synapses, as well as examining the consequences on synaptic maintenance found in tauopathies, a class of neurodegenerative disorders. Synaptic development is a multi-step dynamic process, relying on a precise balance between adhesion-mediated stability and calcium-driven expansion. In chapter III, we show that synaptic expansion relies on the presence of the C. elegans ortholog of the calcium and integrin binding protein, CALM-1. We show that mutations in a predictive phosphorylation site of CALM-1 result in over-elongated synapses, suggesting that phosphorylation of CALM-1 might be necessary for proper synaptic growth and maintenance. In chapter IV, we show that the C. elegans neuromuscular junction can be used to model tauopathies, a subset of neurodegenerative disorders defined by the presence of abnormally aggregated clusters of tau. We show that expression of wildtype human 2N4R tau protein in the GABAergic motor neurons is well-tolerated, with no effects on synapse size, shape, or number. In contrast, expression of two mutated variants of human tau, a known disease-causing variant, P301, and an aggressively assembling variant, 3PO, induced progressive synaptic loss associated with the animal aging, notably without causing other forms of neurodegeneration, such as cell death or axon degradation. We show that synaptic loss is not merely a loss of vesicle trafficking, as use of another marker for synaptic active zones also demonstrated progressive synaptic loss in tau variant animals. Finally, we show that synaptic loss is not limited to the GABAergic motor neurons, as expression of mutant tau in another subset of neurons, the cholinergic neurons, also induced progressive synaptic loss. In Chapter V we look to further expand our model, by examining the consequences of genetic and chemical modifiers on the synaptic loss phenotype shown in mutant tau variants. We show that our model of synaptic degeneration can be used to screen genetic risk factors for tauopathies, as loss of function of a proposed Alzheimer’s disease risk factor, ptp-3, strongly enhanced the synaptic loss seen in tau mutant animals. We also show that expression of a risk factor for a primary tauopathy, Progressive Supranuclear Palsy, induced axon defects that were significantly enhanced by the presence of P301 tau, indicating the utility of our model to look beyond just synaptic consequences of tauopathy risk factors. Additionally, we show that our model can be used to screen for chemical modifiers of tauopathies, as we show that treatment of animals with a proposed tau aggregation inhibitor, ANTC15, partially rescues the synaptic loss in 3PO and P301 animals. Finally, in Chapter VI we begin to examine potential mechanisms of tau-mediated synaptic degeneration. We show that synaptic loss is not due to interference with the endogenous C. elegans tau-like protein, ptl-1, and that disruption of the normal method of calcium driven synaptic expansion does not significantly alter the synaptic loss phenotype, suggesting that the loss of synapses is a result of a toxic gain of function consequence of the addition of the mutated tau variants. Finally, we show that any interference with microtubule stability, through the over stabilization or destabilization of tubulin, is sufficient to induce a progressive decrease in synapses, suggesting that the synaptic loss seen in tau mutant animals may be a result of the mutation interfering with tau’s ability to bind and stabilize microtubules. Overall, this report strengthens our understanding of synaptic development, homeostasis, and age-related declines. More importantly, it establishes the first C. elegans model where we can examine synapse degeneration as a function of aging as it relates to human disease.
NOVEL INSIGHTS INTO THE ROLE OF THE UNC-6/NETRIN RECEPTOR UNC-5 IN REGULATING GROWTH CONE POLARITY AND PROTRUSION
(University of Kansas, 2022-12-31) Mahadik, Snehal Sudhakar; Lundquist, Erik; Ackley, Brian; Macdonald, Stuart; Gamblin, T. Chris; Hileman, Lena
The central nervous system (CNS) is a complex network of connected neurons. In the developing nervous system, axons must reach their target for the formation of functional neuronal connections. During embryonic and postnatal development of a nervous system, neuronal precursor cells must migrate to their final destinations, and axons must navigate to the correct target to establish normal connectivity. Failure of axons to properly reach their target leads to incomplete development of a brain, resulting in several neurodevelopmental disorders such as mental retardation and autism, horizontal gaze palsy with progressive scoliosis (HGPPS) and schizophrenia (GUAN AND RAO 2003; NUGENT et al. 2012). Proper functioning of the nervous system depends on the development of proper neuronal connections, which in turn depends on the proper guidance of neurites from their neuronal cells of origin to their eventual synaptic targets. The outgrowth of developing axons is guided by growth cones, dynamic actin-based structures that sense and respond to extracellular guidance cues that drive the forward motion of the axon(TESSIER-LAVIGNE AND GOODMAN 1996). The growth are the dynamic structures which are present at the growing tip of an axon and made up of dynamic filopodial and lamellipodial protrusions, which are involved in axon outgrowth and guidance (GOLDBERG AND BURMEISTER 1986). The lamellipodium is an actin-based, membrane sheet-like structure at the leading edge of the growth cone consisting of a meshwork of actin filaments, which provide the forward motive force of the developing neurite(GALLO AND LETOURNEAU 2004). Filopodia, are the dominate structures of a growth cone that emanate from the growth cone lamellipodial body, consist of bundled filamentous actin (F-actin). Filopodia are thought to be involved in the sensation of directional cues and subsequent changes in directional locomotion as it contains receptors for various guidance cues. Netrins were the first family of guidance cues to be found in both invertebrate and vertebrate nervous systems. In C. elegans, a genetic screen for mutants that affects axon guidance identified UNC-6 which is involved in controlling both dorsally and ventrally guided projecting axons (MERZ AND CULOTTI 2000). UNC-6 is a laminin-related protein secreted by ventral cells in C. elegans and by floor-plate cells in vertebrates (HEDGECOCK et al. 1990; ISHII et al. 1992). UNC-6/Netrin is a bi-functional guidance cue which mediates its functions through two classes of single-pass transmembrane receptors, UNC-40 ad UNC-5. Much work has been done to identify role of UNC-6/ Netrins and its receptors in regulating end point axon guidance by studying the developed nervous system in vivo and by studying developing growth cones in vitro. However, very little is known about how UNC-6/ Netrin regulates in vivo growth cone morphology and dynamics to regulate proper navigation o axons to their targets. The work here attempts to do that by utilizing the free-living nematode Caenorhabditis elegans. C. elegans is a useful system to study axon pathfinding and growth cone development in vivo due to its simple, well-characterized nervous system, transparency and fully sequenced genome. In this work we focus on D-type GABAergic neurons 13 VD and 6 DD, which are motor neurons required for locomotion of C. elegans. VD/DD motor neurons resides in the ventral nerve cord their axons first migrate anteriorly before turning 90 degrees and forming commissures until reaching the dorsal nerve cord, at which point they spread both anteriorly and posteriorly and establish their synaptic targets. Previous work from lab using VD growth cone analysis display a polarity/protrusion model of growth cone repulsion from UNC-6/Netrin, UNC-6 first polarizes the growth cone of VD neuron via the UNC-5 receptor, and then regulates protrusion asymmetrically across the growth cone based on this polarity. Through the UNC-40/DCC receptor, UNC-6 stimulates protrusion dorsally, and through UNC-5 inhibits protrusion ventrally and laterally, resulting in net dorsal growth (GUJAR et al. 2018). The work presented here is focused on how UNC-6/Netrin utilizes the receptor UNC-5 with the help of other signaling molecules and mediate inhibition of growth cone protrusions. In chapter III, we identify the role of MAX-1 in inhibiting growth cone protrusion by possibly affecting the trafficking or stability UNC-5. We show that max-1 acts independently of other pathways that regulate growth cone protrusion, including unc-40/DCC, unc-6/Netrin, unc-33/CRMP, and unc-34/Enabled. Our findings involving MAX-1 in the growth cone are in the contrast with endpoint axon guidance analysis which display synergistic interactions between max-1, unc-5, unc-6, unc-40, suggesting that we are still missing a link that translates how morphological changes in the growth cone affects axon guidance. In chapter IV, we show how regulation of vesicle exocytosis is exclusively used by receptor UNC-5 to inhibit growth cone protrusions. We identify tom-1 genetically interacts downstream of receptor unc-5 to inhibit the lateral and ventral protrusions in dorsally migrating VD growth cone. We also uncover the isoform specific role of TOM-1 in inhibiting UNC-5 signaling, where the short isoforms perform the canonical function inhibition and long isoform is pro-protrusive in nature. Further extension of this work is explained in chapter V, where we have shown that the TOM-1mediates inhibition of growth cone protrusions by inhibition AEX-3, which has pro-protrusive role in vesicle exocytosis. In chapter VI, we show that the long and short isoform of UNC-5 differentially regulates VD growth cone morphology. The long isoform of UNC-5 displays a conserved canonical role of inhibition of protrusions, but the short isoform has a pro-protrusive role. Lastly in chapter VII, we identify role of SRC-1 tyrosine kinase in mediation UNC-5 signaling by possible activation of UNC-5 through phosphorylation. In summary, the results contained here provide novel insights into the mechanisms by which receptor UNC-5 of UNC-6/Netrin utilizes the novel genes in repulsion, growth cone inhibition and regulates several aspects of growth cone protrusion during the process of axon guidance. The studies performed here also emphasis on the benefits of analyzing growth cones during outgrowth in addition to post-developmental end point analysis of axon guidance.
Testing the transfer of the online /i/-/ɪ/ training effect in Korean L2 learners of English: From speech perception to spoken word recognition
(University of Kansas, 2022-12-31) Lee, Jinmyung; Tremblay, Annie; Jongman, Allard; Sereno, Joan; Zhang, Jie; Vitevitch, Michael
Second language (L2) learners often have difficulty perceiving L2 sound contrasts when the first-language (L1) and L2 sounds are acoustically similar and these similar L2 sounds correspond to an existing L1 sound (Flege, 1995). To improve L2 learners’ perception of sound contrasts, researchers have used high-variability phonetic training (HVPT) that helps L2 learners ignore irrelevant variability for perceiving the sound contrast, and as a result, focus only on the relevant acoustic and articulatory properties of the sounds (Barriuso & Hayes-Harb, 2018). The present study investigated whether training Korean L2 learners of English with HVPT on the /i/-/ɪ/ contrast in English would improve their use of spectral cues and duration cues not only in the identification of words that contain /i/ or /ɪ/ (outcome of spoken word recognition) but also in the activation of such words (processes of spoken word recognition). In addition, the present study examined whether Korean L2 learners of English could generalize their use of acoustic cues to talkers and words not heard in the training, and it investigated whether (and if so, how) cognitive abilities such as attention control and inhibition control, as well as English proficiency, are related to performance in the pre-test and/or training gains.During the online training, Korean listeners in the experimental group (who were trained on the /i/-/ɪ/ contrast) significantly increased their accuracy on the /i/-/ɪ/ contrast in the two-alternative forced-choice identification task, showing their progress from their first training session (session 1) to the last training session (session 8). Hence, the training was found to enhance Korean listeners’ identification of words (outcome of spoken word recognition). Korean listeners in the experimental group significantly enhanced their use of both spectral cues and duration cues in the two-alternative forced-choice identification task from the pre-test to the post-test while Korean listeners in the control group (who received the training on the /ɹ/-/l/ contrast) did not. Furthermore, in the post-test, Korean listeners in the experimental group were able to generalize their improved identification to new words but not to the new talker. However, there was no significant relationship between the experimental group’s cognitive abilities and their pre-test accuracy and/or training gains, and no significant relationship between the experimental group’s English proficiency and their pre-test accuracy and/or training gains. For Korean listeners’ spoken word recognition, the training was found to be less helpful. Korean listeners in either the experimental group or the control group did not show facilitative priming effects for semantically related primes and targets in either the pre-test or the post-test, and they did not significantly enhance their use of spectral cues and duration cues for either /i/-targets (targets semantically related to /i/-words) or /ɪ/-targets (targets semantically related to /ɪ/-words) in the cross-modal semantic priming task, although the use of duration cues for both targets became numerically stronger for Korean listeners in the experimental group (post-test). Korean listeners only showed a significantly smaller priming effect in the post-test compared to the pre-test for /ɪ/-targets across spectral cues, duration cues, and groups. Korean listeners in the experimental group were able to generalize their decreased priming effects in the spectral cue mismatch conditions to new words for /i/-targets and to new words and a new talker for /ɪ/-targets in the post-test, but these results can hardly be interpreted as generalization given the lack of improvement of the use of spectral or duration cues based on the priming results. There was no significant relationship between the experimental group’s cognitive abilities and their pre-test priming effect in the spectral cue mismatch conditions and/or training gains, and no significant relationship between the experimental group’s English proficiency and their pre-test priming effect in the spectral cue mismatch conditions and/or training gains. These results should be interpreted with caution, considering that native English listeners also did not show facilitative priming effects for semantically related primes and targets, and their significant reliance on spectral cues was only observed for /i/-targets in the cross-modal semantic priming task, although their reliance on spectral cues for /ɪ/-targets was numerically in the right direction. Taken together, this study provides supporting evidence for the effectiveness of online HVPT for L2 learners to improve and generalize their identification of words containing difficult sound contrasts in the L2. Further research should explore whether the effects of training on a single phonological context and a single sound contrast could be extended to new phonological contexts and new sound contrasts, respectively. Finally, online HVPT could be implemented outside of L2 classrooms to help L2 learners’ phonological learning at their own pace.

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