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A multi-omics approach to assessing growth, stress, and disturbance in soil microbial communities
Get PDFMicrobes in soil are well-known drivers of several ecosystem processes, yet our ability to study their genetic controls on a community level is relatively recent. The total DNA and RNA of a microbial community—referred to as the metagenome and metatranscriptome and collectively part of the field of study known as “omics”—can yield valuable insight into microbial physiology and function, community structure, and the evolutionary processes of microorganisms. This dissertation leverages metagenomics and metatranscriptomics to assess soil microbial communities with a particular focus on understanding how this approach can be used to better understand dimensions of growth, stress, and disturbance. The first chapter introduces this topic and reviews the current state of the literature and crucial knowledge gaps, as well as a brief description of the subsequent chapters. Chapter 2 describes an experiment where we observed the transcriptional controls of soil microbial communities in response to labile carbon inputs and found that inputs of glucose rapidly stimulated the transcription of nitrogen cycling genes. Chapter 3 is a broad-scale data analysis of genomic traits in bacterial communities from soil, marine, host-associated, and hot-spring microbial communities. We found that soil communities have relationships between genomic traits which are distinct from those in other ecosystems—indicating a unique set of selection pressures in soils. In Chapter 4 we follow-up on these results and examine the distribution of genomic traits in soils along multiple environmental parameters. This analysis showed that bacterial traits in soils are likely driven by carbon limitation and soil pH. In Chapter 5 we reexamine the transcriptional response described in Chapter 2, this time focusing on how genomic traits such as nucleotide and codon selection impact the short-term response of soil microbes during growth and stress. Together, these results highlight the numerous ways in which we can derive insights from multi-omics data and how these findings can enhance our understanding of microbial life in soils
The effects of nitric oxide on metastatic breast cancer cells: linking NOS2 expression and immune modulation to the anti-tumor response
Get PDFNitric oxide (NO) has dual roles which include pro- and anti-tumorigenic properties that are fundamental to metastatic breast cancer, Triple Negative Breast Cancer (TNBC). Recently, NO has surfaced as a key protein that drives TNBC. Under a normal physiological state, the production of NO is synthesized by the nitric oxide synthase (NOS); which forms three isoforms. Although, there are three isoforms of nitric oxide, NOS2 the inducible form generates higher amounts of NO and is overexpressed in TNBC. In TNBC, inappropriate NOS2 expression enhances tumor growth, metastasis, and production of tumor-derived cytokines and chemo-attractants. However, the effects of NO in TNBC, linking NOS2 expression to the anti-tumor response have been inconclusive. Further, the relationship between NO with immune cells in the tumor microenvironment is not well studied. The studies detailed in the thesis investigate the correlation involved in immune modulation of NOS2 in metastatic breast cancer to the antitumor response. Moreover, we used 4T1 murine metastatic breast cancer cells and CRISP/CAS9 mediated NOS2 knockouts (KO) E3 and A40 cell lines to further study the role of NOS2 in the tumor microenvironment. We were able to induce NOS2 expression in the 4T1 wild-type (parental) cells with inflammatory cytokines in serum deprivation as well as confirm that the NOS2 knockouts E3 and A40 lack the NOS2 gene. Additionally, we show that NOS2 expression does not depend on cytokine concentration in the 4T1 wild-type cells. Several surface receptors that may be overexpressed in the TNBC cells such as PD-L1, MHC-I, FAS, and CD47 were studied in the 4T1 cells. Interestingly, we saw upregulation of PD-L1 and MHC-I, and FAS during cytokine stimuli in nutrient starvation in the NOS2 knockout cell lines when compared to the parental cell line. Further, we used DETA/Nononate, a slow-releasing NO donor in the 4T1 wild-type and NOS2 KO cell lines. We observed, that in high concentrations the NOS2 knockout cell lines decreased when compared to the untreated cytokine serum-free media cells
Short interval wildfires and post-fire resilience in interior Alaska
No full textNearly one third of global forest carbon stocks are stored in boreal forests, and as the climate warms and dries, wildfire frequency and severity in the circumpolar region are increasing. These changing fire regimes and their effects on boreal forest structure may significantly impact carbon pools and fluxes, and therefore climate feedbacks. Within this framework, identifying the conditions where ecological resilience may be lost is vital. The conifer dominated boreal forests of western North America have historically had high resilience to wildfire, but as the frequency of fires increases, this resilience is threatened. Recent studies have found evidence of shifts in species dominance from conifer to deciduous and a loss of compositional resilience as a result of increased fire severity or shortened fire return intervals. This study aimed to determine how changing fire return intervals affect post-fire stand dynamics, specifically seedling recruitment, across a gradient of fire severity and soil moisture conditions within Interior Alaskan boreal forests.
We found that changing fire regimes, namely shortened fire return intervals, alter post-fire seedling recruitment patterns, leading to a shift in species composition towards deciduous dominance post-fire in many previously conifer dominated stands. The differences observed in conifer and deciduous regeneration between short and long interval plots confirm the idea that shortened fire return intervals in boreal forests will result in a shift in dominance from conifer dominated to deciduous dominated forests if these post-fire densities remain steady as the stands mature. Our study also provides evidence that seed availability and, to a lesser extent, seedbed quality, can affect patterns of seedling recruitment in stands that burn at shorter fire return intervals. Interactions with environmental factors such as soil moisture may amplify the effects of shortened fire return intervals on species dominance.
This research contributes to mounting evidence that the increase in the frequency of disturbance events can fundamentally alter boreal forest stand dynamics, leading to the loss of compositional resilience. The rate of short interval wildfires is increasing in northwestern boreal forests, so it is imperative that we continue to study the effects of changing fire regimes on boreal forest resilience to understand the broader impacts on climate feedbacks
"Having the job coach work with employers, it's a good thing": A qualitative examination of vocational supports for autistic adults
No full textExtant literature suggests that employment outcomes for autistic adults are poor and have significant implications for their future health and wellbeing, such as inability to achieve independence and a decline in their mental health. Sources of support from service providers, employers, and coworkers may facilitate individual workplace success and improved outcomes such as greater independence, gains in self-perceptions of ability, and improved mental health and wellbeing. However, prior work on successful employment of autistic individuals is quantitative in nature and much of it is conducted outside of the United States. The few qualitative studies that have been completed in the United States have focused on autistic adults and other stakeholders (e.g., their parents, service providers, and employers) living on the East Coast. Examining the perspectives of these individuals in other regions of the United States is important for understanding their lived experiences and contributions to the vocational success of autistic adults. The aim of the current study was to expand the literature by examining the views of stakeholders in a large metropolitan city in the Southwestern United States regarding supports for successful employment of autistic adults. An analysis of semi-structured interviews of five service providers and five employers of autistic individuals was conducted using a thematic analysis research approach. Thematic analysis revealed that service providers were an integral support member in preparing an autistic individual for employment, however employers and coworkers became the primary sources of support once the autistic individual was employed. Furthermore, employers cite service providers as giving them invaluable information and guidance on how to support their autistic employees. This study contributes to the literature by informing other stakeholders of the supports they may offer their autistic clients or employees and emphasizes the importance of involving both a service provider and an employer in working together to facilitate the vocational success of autistic individuals. Future directions for research are discussed in the context of the study’s strengths and limitations
A collection of essays and short stories
Get PDFThis thesis aimed to synthesize my evolution as a storyteller. My aim coming into the MFA program was to sharpen my writing skills, but I conclude my studies with a wider skillset. The biggest motive that fueled my work was a rekindled appreciation for history as a study discipline. The first essay titled “The four elements” is a creative rendition of a historiography of the Masculinity of Basotho men. My exploration of scholarly literature around the concept of Masculinity within the Sesotho culture spilled over into the other creative works included in this body of work. It was the primary lens with which I read and understood historical work that informed my fiction writing in particular. I was struck by the delivery of the content of the works I interacted with in my research. It was plain, harsh and in some instances, quite economical with the truth. I initially approached my writing with the notion that it is time “the lion told its story” so the hunter doesn’t glorify himself all the time. This notion evolved as I familiarized myself with the politics of reading and writing history.
Historical research is paramount to the fiction I write as I work primarily in historical fiction. I realized the emphasis placed on accounting for what happened is one-dimensional, almost clinical. I wondered what the subjects in these historical accounts felt. Also, having noticed that the interpretation of certain cultural phenomena was misconstrued, I wondered what that break-down robbed contemporary readers of, in terms of detail and preservation of the dignity of the subjects discussed. I wanted to re-imagine the events written about with the intention of bringing in my personal knowledge of the cultural and traditional knowledge of Basotho that was passed down to me. As a result, I used close third person point of view often to expose the feelings and struggles of the characters. In historical texts, this is not considered. I also wanted to pin an emotional epic against a rich political background that centers traditional chiefs and demystifies supernatural occurrences.
The last story titled “Seqha” was written in the traditional style of Sesotho folklore, litšomo, as an attempt at writing in a non-Western format. I tried to incorporate storytelling formats in my work that reflect the many identities and the many worlds I represent. The essay “Reflections” captured my experience as a writer coming from another cultural context and the dynamic of conforming to the standards stipulated by dominant workshop models and the process of challenging these. The podcast sample was my way of capturing oral tradition, which plays a significant role in storytelling the Sesotho way. These two works are in direct conversation with the video that accompanies this thesis, which probes at the standards of judgement used to understand history in the Sesotho context. It challenges the application of Western ideologies and thought into the philosophy and way of life of ancient Basotho.
This work has allowed me to sharpen the tools I use to research and write characters and worlds from past eras that I can only imagine. I now approach imaginative writing with critical thinking and a careful consideration of context – cultural and otherwise
High school students’ perception of school climate following a district-wide equity and inclusion program implementation
No full textThe purpose of this study was to analyze the effects of an equity and inclusion program on students’ perception of their school culture and examine if differences in their perceptions depend on school attended and their ethnicity. The intent of this analysis is to identify if an equity and inclusion program can positively influence students’ perception of their school culture. This ex-post facto study utilized data collected during the 2018-2019 school year in a large school district in the southwestern region of the U.S. Participants of this study included 10-12 grade students at two study high schools within the district and totaled 1031. The schools selected for this study were chosen because of their differences in student populations. One school serves a majority white student population while the other a majority of students of color. Student perception data were gathered utilizing a 20-question school climate survey administered at the beginning and end of the first year of the district’s implementation of the district-wide equity and inclusion program. The survey consisted of Likert-scaled questions about school climate and students answered indicating their level of agreement with corresponding statements. The design of this study was a quantitative analysis of students’ mean pre- and post-survey scores to determine if there was a significant difference in scores reported after the students were exposed to the program.
Research Question 1 aimed to identify if there was a difference in students’ perceptions of their school climate following completion of the equity and inclusion program. The study revealed that there was a significant difference in the mean survey scores with an overall decrease in students’ perception of their school environment.
Research Question 2 addressed any differences in students’ perceptions of their school climate following the completion of the equity and inclusion program by study school. The data at both study schools showed a significant difference in the mean survey scores identifying a decrease in students’ perceptions of their school environment.
Research Question 3 again focused on the differences in students’ perceptions of their school climate following the completion of the equity and inclusion program by ethnicity. Although Asian students did not see a significant difference in their survey scores, Black, Hispanic, Multiple Race, and White students all experienced a significant decrease in their post-survey scores. Additional analysis was performed and illustrated that only White students who attended the predominately white school saw a significant decrease in their survey scores, while Black, Hispanic, and White students at the school with a predominate population of students of color saw their scores significantly decrease.
When evaluating the findings, students in general had a less positive perception of their school climate after the implementation of the district-wide equity and inclusion program
The language in digital games: register variation in virtual and real-world contexts
No full textThis dissertation provides an in-depth linguistic description and analysis of the discourse in a target domain of digital games, a domain referred to as single player offline role-playing games. Gaming discourse from this domain is represented by a 4.8-million-word corpus of spoken and written language extracted from the digital files of four popular and commercially successful titles: Fallout 4, The Elder Scrolls V: Skyrim, Divinity: Original Sin II, and The Witcher 3: Wild Hunt. Within these four games, six registers were identified, and a multidimensional analysis reveals four dimensions of gaming discourse. Each dimension identifies sets of co-occurring linguistic features. The game registers’ use of each dimension’s features shows the characteristics that make each register linguistically unique which are functionally interpreted through their situational characteristics. These game registers are also compared to real-world situations of language use. Findings show strong evidence that games represent language exposure that compares quite similarly to several real-world language use situations. These findings give strong support that 1) register variation in games should not be ignored in L2 gaming contexts, 2) register variation in games represents a wide range of real-world registers, and 3) more research is needed that targets specific game designs and mechanics so that their unique discourse can be better understood and leveraged for L2 learning purposes and the development of L2 educational technology.The motivation for this research stems from the praise that applied linguistics researchers and practitioners have given to digital games for their meaningful and engaging second language (L2) input. Despite this praise, little research has thoroughly investigated and documented this language input in targeted domains of digital games. This dissertation aims to fill that gap by applying the register analysis framework detailed by Biber and Conrad (2019)
A spatially explicit greenhouse gas footprint of beef production supply chains in the United States
Get PDFAcross all food products, beef has consistently been reported as having one of the largest greenhouse gas (GHG) footprints. In order to reduce the amount of GHGs emitted as a result of beef production, a better understanding of the GHG emissions linked to the complexities of the beef supply chain is critical. Here we estimate the GHG footprint attributed to domestic beef consumption in major U.S. metropolitan areas and non-metro regions using a spatially and temporally explicit model of the U.S. beef production supply chain network which tracks the flow of feed, cattle, and beef from origin to destination. The beef production network was created for the year 2012 using commodity flow data from the Commodity Flow Survey and Freight Analysis Framework, commodity production data, and leverage network principles. A life-cycle assessment based on the resulting beef production network is conducted using GHG emission factors and energy consumption data obtained through a comprehensive literature review and established GHG accounting protocols. We estimate a U.S. average GHG footprint of 8.7 ± 3 kg CO2e/lb retail beef. Cattle production contributes the vast majority (75%) of GHG emissions related to beef production with enteric-fermentation alone contributing 66%. Across all domestic beef destinations (except Alaska and Hawaii), the proportional contribution of GHG emissions from each step of the supply chain to the total supply chain GHG footprint was relatively consistent. Though transport as a emissions source showed the greatest range in emissions relative to other sources in individual beef supply chains, at the national level transportation only accounts for 4% of beef supply chain emissions. This underscores the importance of addressing feed and cattle production practices, particularly enteric fermentation as the largest emissions source, as opposed to focusing only on reducing vehicle miles traveled within the supply chain. Unlike previous work that focuses on calculating GHG emissions for either one individual region or generalized across the U.S., this study developed a hybrid life cycle assessment - urban metabolism approach combined with regional-level commodity flow data to track GHG emissions for individual beef supply chains in a manner that is inclusive of and comparable across each metro- and non-metropolitan area
Evaluating spatial variations in upper plate deformation at the northeast Japan and Nankai subduction zones using submarine tectonic geomorphology and seismic reflection data
No full textThe outer forearc, frontal prism, and the shallow plate boundary interface (décollement) of subduction zones are deformational domains that accommodate plate boundary strain and have the potential to host shallow, tsunamigenic earthquakes. Asperities on the incoming plate, such as outer-rise normal faults, can modulate décollement mechanics and upper plate deformational processes as they are subducted, which can influence the potential to promote or inhibit shallow plate boundary slip. Therefore, it is important to quantify spatial variations in upper plate deformation that can elucidate décollement heterogeneity, mechanics, and frontal prism evolution. Furthermore, evaluating spatial variations in the magnitudes and rates of upper plate deformation has important implications for strain accommodation, partitioning, and the potential for seismogenic and tsunamigenic hazards.Upper plate deformation and the physical properties of the décollement are typically constrained using subsurface geophysical and geological data, such as direct sampling of sub-seafloor drill cores, borehole geophysical measurements, and seismic surveys. However, even in the most densely instrumented and imaged subduction zones, spatial gaps between seismic data, cored geologic data, and the varied resolution of geophysical imaging can limit our understanding of the lateral continuity of décollement and upper plate deformational processes. High-resolution seafloor digital elevation models (DEMs) are spatially continuous, and therefore provide the opportunity to interpret the bathymetric expression of faulting and deformation in the submarine setting. In this dissertation, I develop bathymetric criteria for mapping the tectono-geomorphic signatures of faulting, folding, and slumping, and methods for evaluating spatial variations in magnitudes and rates of forearc and frontal prism deformation. This dissertation research demonstrates the utility of using bathymetric DEMs and DEM derivatives for determining spatial variations in subduction zone deformation in settings that may have limited or lack subsurface geological and geophysical data.
I apply tectono-geomorphic, bathymetric methods to evaluate forearc deformational processes and décollement mechanics at the Nankai and NE Japan subduction zones. In Nankai, high-resolution, tectono-geomorphic mapping shows a possible out-of-sequence thrust fault and an active, margin parallel, strike-slip fault that may partition active plate boundary strain and accommodate active, shallow, seismogenic slip. At the Japan trench, mapping of seismic reflection data shows the importance of incoming plate properties, namely sediment thickness and outer-rise fault throw, for controlling styles of frontal prism deformation, lateral variations in the relative occurrence of sediment accretion, sediment subduction, and frontal tectonic erosion, and shallow décollement heterogeneity. Additionally, tectono-geomorphic analyses at the Japan trench show that the upper plate has direct topographic responses to the subduction of horsts and grabens that are modulated by styles of frontal prism deformation and sediment flux along-strike of the margin. Results from this dissertation research in both margins in Japan demonstrate how bathymetric signatures of the upper plate deformation revealed from tectono-geomorphic methods can elucidate the mechanics and evolution of the décollement at depth
Trading presidential rhetoric: the relationship between shifting rhetoric and policy in trade from Obama to Trump
No full textThe rhetoric of President Donald J. Trump was aggressive, racist and often inaccurate and represented a significant shift in how the President of the United States communicates with the American public and the broader world. He spoke to the historic levels of polarization and discontent in the nation, fundamentally ignoring the historical role of communication from the office of the President. His predecessor, President Barack H. Obama, in contrast, spoke with clarity, knowledge and eloquence and used communication to unify a nation through economic and global struggles. This rhetorical difference between the two presidents was no clearer than in communication with the global trading community. Despite the differences in rhetoric, many of the trade policies between the Obama and Trump administrations remained consistent with decades of trade precedent. This dissertation evaluates the shift in rhetoric, through the lens of the Rhetorical Presidency established by Jeffery Tulis, from Obama to Trump, while also identifying whether policy shifts accompanied the changing rhetoric. Despite the changes in content between the two presidents, they both, together, used new practices within the rhetorical presidency, including an increased social media presence, which signaled a change in how modern presidents communicate with the American Public moving forward. Regardless, the adjustments in communication within the Trump administration with trade partners and prospective trade partners, globally, also elicited a significant response from international leaders, United States leadership and the larger bureaucratic corps. The reaction from United States officials and global leaders highlights the reality that the change in rhetoric under the Trump administration mattered and created concrete shifts in diplomatic and global trade partnerships. Not only did Trump change the communication practices of the United States presidency as an institution during his administration, he threatened the power and economic standing of the United States. The effects of the Trump presidency on trade rhetoric and policy have continued after his administration and President Joseph R. Biden has had to navigate a new global landscape when negotiating trade and foreign relations