2020-

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https://hdl.handle.net/10217/182111

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Open Access
Towards interactive analytics over voluminous spatiotemporal data using a distributed, in-memory framework
(Colorado State University. Libraries, 2023) Mitra, Saptashwa, author; Pallickara, Sangmi Lee advisor; Pallickara, Shrideep, committee member; Ortega, Francisco, committee member; Li, Kaigang, committee member
The proliferation of heterogeneous data sources, driven by advancements in sensor networks, simulations, and observational devices, has reached unprecedented levels. This surge in data generation and the demand for proper storage has been met with extensive research and development in distributed storage systems, facilitating the scalable housing of these voluminous datasets while enabling analytical processes. Nonetheless, the extraction of meaningful insights from these datasets, especially in the context of low-latency/ interactive analytics, poses a formidable challenge. This arises from the persistent gap between the processing capacity of distributed systems and their ever-expanding storage capabilities. Moreover, the interactive querying of these datasets is hindered by disk I/O, redundant network communications, recurrent hotspots, transient surges of user interest over limited geospatial regions, particularly in systems that concurrently serve multiple users. In environments where interactive querying is paramount, such as visualization systems, addressing these challenges becomes imperative. This dissertation delves into the intricacies of enabling interactive analytics over large-scale spatiotemporal datasets. My research efforts are centered around the conceptualization and implementation of a scalable storage, indexing, and caching framework tailored specifically for spatiotemporal data access. The research aims to create frameworks to facilitate fast query analytics over diverse data-types ranging from point, vector, and raster datasets. The frameworks implemented are characterized by its lightweight nature, residence primarily in memory, and their capacity to support model-driven extraction of insights from raw data or dynamic reconstruction of compressed/ partial in-memory data fragments with an acceptable level of accuracy. This approach effectively helps reduce the memory footprint of cached data objects and also mitigates the need for frequent client-server communications. Furthermore, we investigate the potential of leveraging various transfer learning techniques to improve the turn-around times of our memory-resident deep learning models, given the voluminous nature of our datasets, while maintaining good overall accuracy over its entire spatiotemporal domain. Additionally, our research explores the extraction of insights from high-dimensional datasets, such as satellite imagery, within this framework. The dissertation is also accompanied by empirical evaluations of our frameworks as well as the future directions and anticipated contributions in the domain of interactive analytics over large-scale spatiotemporal datasets, acknowledging the evolving landscape of data analytics where analytics frameworks increasingly rely on compute-intensive machine learning models.
Open Access
Extreme ultraviolet laser ionization mass spectrometry: probing materials at the micro and nano scales
(Colorado State University. Libraries, 2023) Rush, Lydia Alexandra, author; Menoni, Carmen S., advisor; Duffin, Andrew M., advisor; Farmer, Delphine K., committee member; Marconi, Mario C., committee member; Rocca, Jorge J., committee member
The focus of this dissertation is the use of 50 to 10 nanometer wavelength extreme ultraviolet (EUV) laser light as a next generation probe for mass spectrometry analyses at the micro (>100 nanometers) and nano (≤100 nanometer) spatial scales. While the unique properties of EUV light have revolutionized the semiconductor industry through nanoscale lithography fabrication, the use of EUV lasers with analytical instruments, like mass spectrometers, for high spatial resolution chemical analyses is a relatively untapped area. This unexplored territory is owed partly to only recently bringing EUV lasers to an accessible "bench-top" scale. Herein I show how EUV laser ionization can be used with different types of mass spectrometers as a new route for interrogating nuclear and geologic materials with micro and nano scale lateral spatial resolution. I focus on the application of a compact capillary discharge EUV laser operating at a wavelength of 46.9 nanometers connected to a time-of-flight (TOF) mass spectrometer, called the EUV TOF. I also show for the first time how the 46.9 nm EUV laser ionization source can be connected to a commercial magnetic sector mass spectrometer, called the EUV magnetic sector. Specifically, I demonstrate that the EUV TOF instrument can measure the 235U/238U isotope ratio in 100 nm sized pixels in a heterogeneous uranium fuel pellet that was made by blending different feedstocks together. The results show that the EUV TOF maps similar micrometer sized areas of 235U/238U heterogeneity as nanoscale secondary ionization mass spectrometry (NanoSIMS), indicating that EUV laser ionization can be used to accurately probe complex nuclear materials within the scope of the study. I also show that the EUV TOF can be used to measure 206Pb/238U and 232Th/238U isotope ratios at the 8 µm scale in select geologic matrices of silicates, zircons, monazites, and iron manganese within error (±2σ) using a single non-matrix matched calibration standard. However, the precision on the ratio measurements was low for useful geologic applications, ranging between 1-10% at elemental concentrations exceeding hundreds of ppm because of the limitations of using a TOF for isotope ratio measurements. To this end, I show the current development of the new EUV magnetic sector instrument that uses the EUV laser ionization source with a commercial double-focusing sector-field multi-collector mass spectrometer with the aim of achieving more precise (<1%) and sensitive (≤ppm) isotope ratio measurements at high spatial scales (<10 µm down to the nanoscale). The EUV magnetic sector is being developed to probe more complex isotopic systems in nuclear and geologic materials that was not possible with the TOF mass spectrometer. The work here shows that the 46.9 nm wavelength EUV laser ionization source can be interfaced with Thermo Fisher's commercial sector-field multi-collector mass spectrometer called the Neptune by removing its inductively coupled plasma (ICP) region. The Neptune's ion optics, electric sector, and magnetic sector were modified for acceptance of the pulsed EUV-generated ions. These modifications resulted in ions from ≤2 µm diameter craters created by EUV laser ablation and ionization being successfully focused, separated by mass, and detected using the Neptune's electron multipliers. However, further system upgrades to the Neptune's detectors are needed for accurate isotope ratio measurements at high spatial scales because the 10 to 30 nanosecond wide EUV-generated ion pulses are on the order of the electron multipliers' dead time. With proper detectors, the EUV magnetic sector's accuracy, precision, sensitivity, efficiency, and spatial resolution can be measured in future experiments. The demonstration of the EUV magnetic sector instrument here represents the first time that an EUV laser ionization source has been used with a sector-field mass spectrometer, paving the way for future high spatial resolution isotope ratio analyses.
Open Access
Investigating the relationship between cover crop species diversity, composition and function of the soil microbiome
(Colorado State University. Libraries, 2023) Seitz, Valerie, author; Prenni, Jessica, advisor; Wrighton, Kelly, committee member; Schipanski, Meagan, committee member; Nishimura, Marc, committee member
Cropping diversification, such as cover cropping, can contribute to sustainable agriculture by enhancing soil health and promoting ecosystem services through interactions with the soil microbial community. One important mechanism through which cover crops impact soil health is via root exudation, the release of organic compounds from plant roots into the soil region surrounding the roots, the rhizosphere. Root exudation varies among cover crop species, growth stages, and edaphic and environmental conditions resulting in a myriad of effects on the rhizosphere. Plant-derived inputs, like root exudates, modulate the soil microbial community, influencing microbial biomass, community structure, and catalyzing biogeochemistry. As a result, cover crops are linked to microbial changes that impact soil nutrient cycling and organic matter decomposition leading to a legacy impact on primary crop yield and health. Understanding the intricate relationship between cover crop root exudation composition and the soil microbiome is crucial for optimizing cover crop selection, management practices, and harnessing cover crops for precision microbiome management in agroecosystems. My dissertation demonstrates that cover crop root exudation differs considerably across cover crop species, and cultivars within species, and reveals cover crop metabolic impacts on soil microbial composition and function, which play a large role in the generation and maintenance of healthy soils to support our agricultural needs.
Open Access
Functional organization of a cortical-medullary neural circuit mediating organismal adaptation to stress
(Colorado State University. Libraries, 2023) Pace, Sebastian A., author; Myers, Brent, advisor; Hentges, Shane, advisor; Tobet, Stuart, committee member; Foster, Michelle, committee member
Hindbrain regions responsible for epinephrine and norepinephrine production are critical for orchestrating stress responses, maintaining physiological equilibrium and integrating afferent information. The nuclei central to hindbrain epinephrine and norepinephrine production, create a neural network that interfaces with forebrain and spinal cord regions, facilitating the integration of neuroendocrine and autonomic functions. Despite significant strides in our comprehension of stress response systems, questions concerning the roles of sex, stress history, and circuit mechanisms endure. In this study, we unveil and characterize a prefrontal-medullary circuit crucial for the suppression of stress responses. First, anterograde and retrograde tract-tracing studies demonstrated a stress-reactive vmPFC-RVLM circuit. Activation of this vmPFC-RVLM circuit mitigates glucocorticoid stress reactivity in both males and females, by targeting non-catecholaminergic neurons. Therefore, vmPFC-RVLM circuit activation may utilize local inhibitory neurons to limit catecholaminergic activation. To better understand how chronic stress affects the medulla, we explored the impact of chronic stress on signaling machinery and revealed elevated tyrosine hydroxylase (TH) levels in both male and female rats following chronic variable stress (CVS). To understand how CVS interacts with the vmPFC-RVLM circuit, we used an intersectional TeLC (Tetanus toxin - light chain) approach to disrupt the circuit and evaluate multiple stress response systems. In males, circuit disruption and CVS largely left behavioral and cardiovascular stress reactivity unaltered, however, some neuroendocrine endpoints were affected. Conversely, females exposed to circuit disruption and chronic stress exhibited heightened stress reactivity in glycemic, corticosterone, and arterial pressure responses, coupled with avoidant-like behaviors. These findings underscore the sex-specific necessity of the vmPFC-RVLM circuit in countering chronic stress-related outcomes, emphasizing a greater protective role in females relative to males. To gain deeper insights into the role of vmPFC inputs to the RVLM in females, we once again utilized a circuit-based TeLC approach, employing in situ hybridization (ISH) coupled with immunohistochemistry (IHC) to assess TH and phenylethanolamine N-methyltransferase (PNMT) transcript density across various VLM subregions. Notably, the TeLC-induced elevation of PNMT expression in females suggests that disrupting this circuit could potentially enhance epinephrine production by RVLM neurons, potentially intensifying stress reactivity post-CVS. This comprehensive study demonstrated the critical role of the vmPFC-RVLM circuit in modulating stress responses and revealing female-specific effects in mitigating physiological, behavioral, and transcriptional outcomes after chronic stress. These findings emphasize the significance of the vmPFC-RVLM circuit in managing stress reactivity in the context of chronic stress and identify the circuit as a potential candidate for reducing stress responding.
Open Access
Exploiting noise, non-linearity, and feedback to differentially control multiple different cells using a single optogenetic input
(Colorado State University. Libraries, 2023) May, Michael P., author; Munsky, Brian, advisor; Stasevich, Tim, advisor; Krapf, Diego, committee member; Shipman, Patrick, committee member
Motivated by Maxwells-Demon, we propose and solve a cellular control problem in which the exploitation of stochastic noise can break symmetry between two cells and allow for specific control of multiple cells using a single input signal. We find that a new type of noise-exploiting controllers are effective and can remain effective despite coarse approximations to the model's scale or extrinsic noise in key model parameters, and that these controllers can retain performance under substantial observer-actuator time delays. We also demonstrate how SIMO controllers could drive two-cell systems to follow different trajectories with different phases and frequencies by using a noise-exploiting controller. Together, these findings suggest that noise-exploiting control should be possible even in the case where models are approximate, and where parameters are uncertain. Having demonstrated the potential of noise-enhanced feedback control through computational modeling, we have also begun the next steps toward automating microscopy to implement this potential in experimental practice. Specifically, we demonstrate a new integrated pipeline to automate the image collection including: (i) quickly search in two-dimensions to find fields of view with cells of desired phenotypes, (ii) targeted collection of three-dimensional image data for these chosen fields of view, and (iii) streamlined processing of the collected images for rapid segmentation, spot detection and tracking, and cell/spot phenotype quantification.
Embargo
Enhancing rootzone soil moisture estimation using remote sensing, regional characteristics, and machine learning
(Colorado State University. Libraries, 2023) Sahaar, Ahmad Shukran, author; Niemann, Jeffrey D., advisor; Chavez, Jose Luis, committee member; Green, Timothy R., committee member; Butters, Gregory, committee member
Accurate estimation of root-zone soil moisture (θ ̄) is essential for various agricultural applications, including crop yield estimation, precision irrigation, and groundwater management. This dissertation encompasses three interconnected studies that collectively investigate different approaches for improving soil moisture estimation. The first study delves into the utilization of remote sensing methods, particularly optical and thermal satellite imagery, to estimate fine-resolution (30 m) root-zone soil moisture across diverse regions. Traditionally, these methods relied on empirical relationships with evaporative fraction Λ_SEB or evaporative index Λ_PET. However, it has been shown that a single relationship does not universally apply to all regions. This study evaluates the influence of regional soil, vegetation, and climatic conditions on the shape and strength of these relationships using global sensitivity analysis. The results highlight that soil characteristics, such as clay and silt content, and vegetation properties, like leaf area index and rooting depth, play pivotal roles in determining these relationships. Moreover, the impact of annual precipitation in defining climatic regions is crucial. Consequently, region-specific relationships are proposed, adapting to local conditions and potentially enhancing soil moisture estimates. The second study extends this investigation by applying the regionally adapted relationships for the Λ_SEB " vs." θ ̄ and Λ_PET " vs." θ ̄ to estimate rootzone soil moisture (θ ̄) from remote sensing data across four study regions. The results consistently demonstrate the superior performance of the regionally adapted relationships over a single empirical relationship, with a substantial reduction in root mean squared error. These adapted relationships are particularly effective in arid and semiarid regions. The third study explores the application of machine learning models, including XGBoost, CatBoost, RF, LightGBM, and artificial neural networks, to predict soil moisture levels across various climates and depths in the contiguous United States. The findings emphasize the high accuracy and effectiveness of machine learning models, especially XGBoost, in predicting soil moisture across diverse climate regions. XGBoost outperforms other models, making it a potentially valuable tool for soil moisture prediction in environmental monitoring and management. The study also highlights the influence of climate and soil depth on prediction accuracy, with deeper layers having improved forecasts. Additionally, feature importance analysis identifies key predictors for predicting soil moisture, such as elevation, aridity index, soil composition, and depth. These findings contribute to the advancement of soil moisture monitoring and management, with practical applications in agriculture and environmental sciences.
Open Access
Leadership in crisis: the lived experiences of seven school leaders during COVID-19
(Colorado State University. Libraries, 2023) Asqueri, Emily, author; Cooner, Donna, advisor; Frederiksen, Heidi, committee member; Barnes, Wendy, committee member; O'Donnell-Allen, Cindy, committee member
This study, grounded in a constructivist view of phenomenology, explores the lived experiences of school leaders during the COVID-19 pandemic. The research identifies several implications for practice, including the need to re-evaluate teacher and administrator licensure programs, with a focus on providing opportunities for educators to gain practical experience in navigating crises. Additionally, professional development courses should be tailored to address educators' specific deficits and strengths, fostering better leadership. Addressing inequities in education, particularly regarding food security and the digital divide, remains critical. Furthermore, the study highlights the importance of allocating resources to mental health and self-care initiatives, not only for school leaders but also for staff, students, and the community, while actively working to destigmatize mental health. Finally, this research underscores the need to refocus on the primary purpose of education, which is to meet the needs of students, rather than becoming mired in divisive debates. Recommendations for future research include conducting interviews with a more diverse group of school leaders to capture a broader range of experiences. Additionally, long-term studies may be necessary to understand the lasting effects of leadership decisions during the pandemic. In conclusion, this research calls for collective action to address systemic inequities in education. It acknowledges the complexity of these challenges and urges stakeholders to support educators and students. In the interim, school leaders, licensure programs, and professional development courses must prioritize the development of leaders who can effectively navigate uncertainty and crises, thereby benefiting the entire educational community.
Embargo
Engineered mRNA therapeutic encoding beta-catenin increased bone formation in a murine tibial fracture model
(Colorado State University. Libraries, 2023) Nelson, Anna Laura, author; Ehrhart, Nicole, advisor; Bahney, Chelsea, advisor; Huard, Johnny, committee member; Popat, Ketul, committee member; Prawel, David, committee member
Fractures continue to be a global economic burden and impaired fracture healing cases, like delayed and non-union, occurring in about 14% of all tibial shaft fractures. Current treatments to aid in fracture healing involve surgical interventions and osteoanabolic, bone-morphogenetic protein-2 (BMP-2), yet is challenged supraphysiological doses and adverse side effects. Given the limited treatment options available, there remains a clinical need to develop injectable therapeutics to accelerate fracture healing in impaired fracture healing cases. Mechanistic data reveals β-catenin as a molecular driver in endochondral ossification. The central hypothesis for this dissertation is a stabilized, non-destructive β-catenin mRNA delivered locally in the fracture callus can accelerate fracture healing in a murine tibia fracture healing model. Using mRNA therapeutically continues to be challenged with stability and immunogenicity of the mRNA. To circumvent these limitations, delivery carriers have been employed to maximize gene stability, minimize off-target effects, and reduce immunogenicity. Recent advancements in liposomal technologies have led to the development of lipid nanoparticles (LNPs), leading to successful clinical translation of several novel and highly effective therapies, like SARS-CoV-2 vaccine. Alternative delivery carriers have emerged involving use of mineral coated microparticles (MCMs) as a biomimetic and biocompatible system to deliver liposomes at the site of a fracture in a controlled manner. Here, we explore mRNA delivery carriers for fracture healing applications, including manufactured cationic liposomes, MCMs, LNPs and a combination of these carriers. Manufactured liposome, Lipofectamine™, was found to be prolong transfection when tested in a murine fracture model in vivo as compared to TransIT Transfection Reagent. Using Lipofectamine™ to deliver mRNA, chemically-doped MCMs enhanced transfection and stimulated bone in vitro when delivered in chondrocytes. When testing these platforms in a murine tibia fracture model, chemically-doped MCM did not promote bone expression through testing RNA in the fracture callus for bone-related genes and through histomorphometry of the fracture callus 2 weeks post-fracture. The chemically doped MCM was found to prolong transfection of reporter gene, firefly luciferase mRNA, in vivo when compared to other treatment groups including the liposome and mRNA complex (lipoplex) alone. Ionizable-based LNPs are positively charged at a low pH and net neutral at physiological pH. Two FDA-approved ionizable phospholipids, MC3 and SM-102, were used to generate ionizable LNPs. First, MC3 LNP was tested for transfection capacity when combined with MCMs. While chemically-doped MCMs when combined with firefly luciferase mRNA encapsulated MC3 LNPs showed improved transfection in vitro, no improvements in transfection efficacy were found in vivo. Next, MC3 and SM-102 LNPs were then complexed with reporter gene, firefly luciferase mRNA to test transfection potential, immunogenicity, fracture interference and biodistribution in vitro and in a murine fracture healing model. SM-102 LNPs showed enhanced transfection efficacy in vitro, prolonged transfection in vivo, minimal fracture interference in vivo and showed no localized inflammatory response in the murine fracture callus. Ex-vivo IVIS images of main organs revealed no biodistributive effects when delivering SM-102 complexed with mRNA locally to the site of the fracture callus. Capitalizing on prior mechanistic data showing β-catenin's critical role in chondrocyte to osteoblast transdifferentiation, a non-destructive β-catenin, β-cateninGOF, mRNA transcript was generated using nucleoside modification, N1-methyl-pseudouridine, and cap analog, CleanCap. When testing the generated β-cateninGOF mRNA encapsulated in SM-102 LNPs in vitro for bioactivity, downstream canonical Wnt genes were significantly upregulated. When testing SM-102-β-cateninGOF mRNA therapeutic in murine tibia fracture model, more bone and less cartilage composition compared to PBS control was determined when analyzing histomorphometry at 25 and 45 μg concentrations at 2 weeks post-fracture. To further confirm SM-102-β-cateninGOF mRNA therapy's capabilities to promote bone in vivo, μCT was performed revealing significantly more bone volume over total volume with 45 μg dose as compared to PBS control. Taken together, we generated a novel mRNA based therapeutic encoding a non-destructive β-catenin mRNA and optimized ionizable LNP, SM-102, to maximize transfection efficacy with a localized delivery. This SM-102-β-cateninGOF mRNA therapeutic may accelerate fracture healing in a murine tibia fracture healing model.
Embargo
Advanced solutions for rainfall estimation over complex terrain in the San Francisco Bay area
(Colorado State University. Libraries, 2023) Biswas, Sounak Kumar, author; Chandrasekar, V., advisor; Cheney, Margaret, committee member; Gooch, Steven, committee member; James, Susan, committee member
Fresh water is an increasingly scarce resource in the western United States and effective management and prediction of flooding and drought have a direct economic impact on almost all aspects of society. Therefore it is critical to monitor and predict water inputs into the hydrological cycle of the Western United States (US). The complex topography of the western US poses a significant challenge in developing physically realistic and spatially accurate estimates of precipitation using remote sensing techniques. The intricate landscape presents a challenging observing environment for weather radar systems. This is further compounded by the complex microphysical processes during the cool season which are influenced by coastal air-sea interactions, as well as orographic effects along the coastal regions of the West. The placement and density of operational National Weather Service (NWS) radars (popularly known as NEXRAD or WSR-88D) pose a challenge in meeting the needs for water resource management in the western US due to the complex terrain of the region. Consequently, areas like the San Francisco Bay Area could use enhanced precipitation monitoring, in terms of amount and type, along watersheds and surrounding rivers and streams. Shorter wavelength radars such as X-Band radar systems are able to augment the WSR-88D network, to observe better the lower atmosphere with higher temporal and spatial resolution. This research investigates and documents the challenges of precipitation monitoring by radars over complex terrain and aims to provide effective and advanced solutions for accurate Quantitative Precipitation Estimation (QPE) using both WSR-88D and the gap-filling X-Band radar systems over the Bay Area on the US West Coast, with a focus on the cool season. Specifically, this study focuses on a precipitation microphysics perspective, aiming to create an algorithm capable of distinguishing orographically enhanced rainfall from cool-season stratiform rainfall using X-Band radar observations. A radar-based rainfall estimator is developed to increase the accuracy of rainfall quantification. Additionally, various other scientific and engineering challenges have been addressed including radar calibration, attenuation correction of the radar beam, radar beam blockage due to terrain, and correction of measurements of the vertical profiles of radar observables. The final QPE product is constructed by merging the X-Band based QPE product with the operational NEXRAD based QPE product, significantly enhancing the overall quality of rainfall mapping within the Bay Area. Case studies reveal that the new product is able to improve QPE accuracy by ~70% in terms of mean absolute error and root mean squared error compared to the operational products. This establishes the overall need for precipitation monitoring by gap-filling X-Band radar systems in the complex terrain of the San Francisco Bay Area.
Embargo
An investigation of synaptic vesicle docking and priming and a proposed method for quantitatively measuring both in Drosophila using electron tomography
(Colorado State University. Libraries, 2023) Twiggs, Jasmin A., author; Reist, Noreen, advisor; Hoerndli, Frederic, committee member; Hoke, Kim, committee member; Tamkun, Michael, committee member
The nervous system, as the body's command center, plays a crucial role in cellular communication within the brain and between the brain and other body systems. Neurons, the individual cellular units, transmit electrical information and communicate with other cells through neurotransmitter release in response to electrical stimuli. Chapter 1 introduces the foundational concepts of neuronal structure and function and delves into the mechanisms underlying neurotransmitter release. Special attention is given to the neuromuscular junction (NMJ), a well-studied chemical synapse crucial for muscle movement. The synaptic vesicle cycle is introduced, with particular emphasis on docking and priming. The significance of active zones, specialized sites for efficient signal transmission, and their associated structural components are underscored. Synaptotagmin, a pivotal protein in calcium-triggered vesicle fusion, is discussed with emphasis on its C2B polylysine motif. Throughout the chapter, the utility of Drosophila as a model system for studying synaptic processes, particularly at the NMJ, is emphasized. In sum, Chapter 1 provides the foundational knowledge essential for comprehending the intricate cellular and molecular facets of synaptic communication within the nervous system, serving as a precursor to subsequent chapters' investigations. Chapter 2 examines synaptotagmin's C2B polylysine motif and its role in synaptic vesicle docking at the Drosophila NMJ. It explores the polylysine motif's potential involvement in endocytosis, demonstrates an unaffected interaction with AP-2, and uses electron microscopy to find no significant changes in vesicle distribution. The findings suggest that the reduced neurotransmitter release in the polylysine mutant is likely due to an impairment in vesicle priming. Chapter 3 introduces a method for studying synaptic vesicle docking and priming in Drosophila, using electron tomography. I address the limitations of conventional electron microscopy and underscore the need for higher-resolution techniques to assess molecular structures that mediate physiological processes. Chapter 3 also emphasizes the significance of the contact area between docked vesicles and the presynaptic membrane as a correlate of vesicle priming. The protocol, expected results, and key considerations are discussed. The methods presented in Chapter 3 offer a promising approach for understanding synaptic processes. In Chapter 4, I discuss key considerations for when standard electron microscopy can be used for assessing vesicle docking. Then, I discuss how the electron tomography method presented in Chapter 3 could not only confirm the results found in Chapter 2, that the synaptotagmin C2B polylysine motif is not implicated in vesicle docking but could also be used to directly test the mutant's role in priming. Specific aims for future studies on the synaptotagmin polylysine mutation in Drosophila are presented, potential results and interpretations are discussed. Finally, I showcase interesting, unpublished findings from electron tomograms I have taken at the Drosophila NMJ and discuss their potential significance.
Embargo
A comprehensive study of Salmonella infections and microbial analysis of probiotics on beef cattle
(Colorado State University. Libraries, 2023) Thompson, Tyler Warren, author; Nair, Mahesh Narayanan, advisor; Geornaras, Ifigenia, committee member; Belk, Keith, committee member; Noyes, Noelle, committee member; Morley, Paul, committee member
Non-typhoidal Salmonella remains a significant concern for food safety in the United States, causing millions of infections, hospitalizations, and deaths yearly. The Healthy People 2030 initiative set forth by the U.S. Department of Health and Human Services aims to address this issue by establishing goals and objectives for national health promotion and disease prevention, including two objectives focused on Salmonella control in the food supply. The recent declaration of Salmonella as an adulterant in certain poultry products by the U.S. Department of Agriculture further highlights the urgency of this issue. To align with the Healthy People 2030 goals and achieve a 25% reduction in salmonellosis, the U.S. Department of Agriculture's Food Safety and Inspection Service (FSIS) implemented new performance standards for beef products. However, such policies must be supported by quantitative microbial risk assessments (QMRA) to determine their impact on Salmonella infections. Therefore, these analyses would benefit from a systematic review examining existing literature on Salmonella, considering factors such as illness rates, exposure, and bacterial loads. This review included 42 articles that provided data necessary for fitting a dose-response model to empirical data that describes how dose, virulence group, and food vector affect illness (attack) rates. Results from the mixed-effects logistic regression model showed significant impacts of log dose consumed, virulence group, and food vector on illness rates. Notably, Salmonella serogroups of "Higher" virulence were found to be associated with greater odds of illness than "Lower" virulence strains. The study highlights the need for improved data reporting and standardized outbreak investigations to enhance the fitting of models to outbreak data. By considering factors like serovar group and food vector in the modeling process, regulators can demonstrate what influences attack rate to frame more effective food safety policies. In conclusion, this systematic review provides valuable insights into Salmonella infection risk from food sources and emphasizes the importance of evidence-based policies to reduce the burden of Salmonella-related illnesses and improve food safety in the United States. Liver abscesses in beef cattle are a common problem associated with highly-fermentable carbohydrate diets during finishing, leading to decreased production efficiency and aggregate carcass value. Dietary antimicrobial supplementation, such as tylosin, helps to control liver abscesses but raises concerns about selection for antimicrobial resistance. This study examined the impact of a probiotic mixture of propionic and lactic acid bacteria on microbial communities and antimicrobial resistance genes (ARGs) in fecal and liver abscess samples from beef cattle alongside Salmonella populations of mesenteric lymphatic tissues. Treatment diets fed in this study included a probiotic mixture alone (DFM), inclusion of Tylosin (TYL), a combination of including both (DFM+TYL), and a control group diet that did not include any supplements (CON). Fecal samples were collected at the time that feeding started, and then 28 d before arriving at the abattoir, where liver abscesses and mesenteric lymph nodes were sampled. Fecal and liver abscess samples were subjected to 16S rRNA and targeted enriched shotgun metagenomics to evaluate microbial communities and resistance genes of bacteria present. A portion of the liver abscess and mesenteric lymph nodes were tested for presence of Salmonella using PCR with further analysis of enumeration and serotype classification for mesenteric lymph nodes. Results showed no differences (P > 0.05) between the fecal microbiomes of the different treatment groups, and the addition of tylosin or probiotic mixture did not impact the fecal resistome. Similarly, no differences (P > 0.05) were observed between the liver abscess microbiomes of the different (P > 0.05) treatment groups, with Fusobacteria and Bacteroidetes being the dominant phyla in liver abscesses. Results indicated that incorporating DFMs did not affect Salmonella prevalence in the cattle's mesenteric lymph nodes or liver abscesses. Presence of Salmonella was found at low levels in only 22% of samples (91 positive out of 503 samples), just below 1 log CFU/g, and was predominantly represented by the C1 serogroup in mesenteric lymph nodes. These findings suggest that while diet interventions may not have a substantial impact, Salmonella can colonize mesenteric lymphatic tissues in cattle at low frequencies and concentrations. Treatment groups tested had no impact (P > 0.05) on fecal and liver abscesses microbiomes and resistance gene presence, along with no impact on Salmonella prevalence in liver abscesses or mesenteric lymphatic tissues.
Embargo
Population ecology of black-footed ferrets (Mustela nigripes) in relation to sylvatic plague
(Colorado State University. Libraries, 2023) Livieri, Travis M., author; Angeloni, Lisa, advisor; Antolin, Michael, committee member; Biggins, Dean, committee member; Crooks, Kevin, committee member
Infectious diseases can have significant impacts, both direct and indirect, on the conservation of endangered species. A full understanding of these impacts is hindered by the difficulty of teasing apart disease effects from other factors that led to endangerment, the scarcity of population data from before and after disease detection, and the inherent challenge of studying rare species, which are often difficult to detect. Ideally, a disease and population monitoring strategy will detect outbreaks so effective management and mitigation strategies can be implemented. Disease mitigation strategies, such as vaccination or removal of infected individuals, can be effective but costly to implement and rigorous evaluations of such efforts are rare. Here we present a case study and evaluation of a multi-faceted effort to manage multiple impacts of sylvatic plague (plague hereafter), an invasive disease, in a reintroduced population of endangered black-footed ferrets (Mustela nigripes) and their prey, black-tailed prairie dogs (Cynomys ludovicianus), in Conata Basin/Badlands National Park, South Dakota. Since reintroduction in 1994-1999, this is the largest free-ranging ferret population. Chapter One provides a broad introduction to black-footed ferret natural history, ecology, and conservation efforts. We briefly described the life history of black-footed ferrets, their reliance upon prairie dogs (Cynomys spp.) as prey and habitat engineers, and the conflicts between prairie dogs and agricultural interests that motivated human efforts to eradicate prairie dogs and inadvertently drove ferrets towards extinction. Ensuing captive breeding and reintroduction efforts averted extinction of the species, but plague, caused by Yersinia pestis bacteria, led to high mortality in both black-footed ferrets and prairie dogs, was a second factor in ferret decline, and continues to threaten reintroduced populations. Plague management, through flea vector control and vaccination, is a high priority for the black-footed ferret recovery program, along with maintaining genetic diversity and securing habitat. We concluded that black-footed ferret recovery to date has been partially successful, but challenges remain, and plague represents the largest biological threat. In Chapter Two, we evaluated the efforts to manage plague for black-footed ferrets and prairie dogs at Conata Basin/Badlands National Park. We effectively monitored plague using carnivore serology, prairie dog testing, and visual surveys to detect the invasion of plague and inform our mitigation efforts. Both prairie dog colonies and black-footed ferret populations declined precipitously with the plague epizootic. We applied deltamethrin dust into prairie dog burrows to kill fleas and vaccinated black-footed ferrets against plague during annual monitoring efforts. Our results suggested that dusting was effective in maintaining prairie dog colonies compared to non-dusted colonies and significantly increasing survival of black-footed ferrets. Additionally, our vaccination of black-footed ferrets added incremental gains in ferret survival. These combined efforts of plague surveillance, dusting prairie dog burrows, and vaccinating black-footed ferrets likely prevented extirpation of this population. In Chapter Three, we used stable isotope analysis to understand the effects of plague on the proportion of prairie dogs in black-footed ferret diets. Previous studies on black-footed ferrets found up to one-third of ferret diet is comprised of non-prairie dog rodents. Plague causes high mortality in prairie dogs and other small mammals found on prairie dog colonies, potentially increasing variability in prey available for black-footed ferrets. We sampled black-footed ferrets and two prey items, prairie dogs and deer mice (Peromyscus sonoriensis), before and during a plague epizootic and used stable isotope analysis to estimate the diet proportions in relation to plague and dusting. We found that prior to plague black-footed ferret diets in Conata Basin/Badlands National Park were similar to previous studies, but during a plague epizootic ferrets shifted their diet almost completely to prairie dogs. Dusting prairie dog burrows prior to the invasion of plague had a similar effect in shifting black-footed ferret diets. We concluded that despite observed foraging plasticity, black-footed ferrets can be considered prairie dog colony specialists, and any diet effects following deltamethrin dust treatment are likely less severe than the impacts of plague on unprotected ferret populations.
Embargo
Crystallizing change in a tourism-based economy during COVID-19: an intermountain western gateway case study of Nederland, Colorado
(Colorado State University. Libraries, 2023) Branstrator, Julia, author; Cavaliere, Christina T., advisor; Bruyere, Brett, committee member; Cottrell, Stuart, committee member; Snodgrass, Jeffrey, committee member
The COVID-19 pandemic has reshaped mobility patterns within the tourism system uniquely stressing parks and protected areas (PPAs) and respective bordering gateway communities. Tourism research has explored changes related to PPAs since COVID-19 at the international (Spenceley et al., 2021), national (Lebrun, et al., 2021), and regional and local scales (Cavaliere & Branstrator 2023; Sohn et al., 2021). Recent scholarship in tourism has brought attention to the experiences and knowledge of residents living within communities bordering PPAs to understand the impacts of COVID-19 from local perspectives (Jones et al., 2021). However, tourism scholarship related to COVID-19 underrepresents the experiences of intermountain western gateway communities (IWGCs) - small communities within remote mountain regions bordering PPAs that often live with tourism-based economies (Stoker et al., 2021). Throughout COVID-19, IWGCs have lived through societal, political and health crises compounded by climate disasters such as wildfires and flooding. The remote geographic location and economic basis of tourism shapes the impacts, adaptations and needs of IWGCs, imperative to inform crisis and disaster management due to the presence and power of tourism-based economies. Residents from the Town of Nederland, Colorado hold lived, situated knowledge of changes experienced during COVID-19 which can further tourism scholarship of resiliency as related to the COVID-19 crisis. Therefore, this research aims to explore the relationships between changes experienced by Nederland residents hosting a tourism economy during COVID-19 through a narrowed scope of identity, affect, and technology use – each representing important components of crisis and disaster management needing further exploration. Three objectives are established to achieve the aim of this research. First, to further the critical and affective turns within tourism scholarship through an embodied research design exploring identities of Nederland residents. Second, to assess the role of technology in navigating spatial and social realities of the COVID-19 pandemic impacting identities. Third, cultural realignment is used as a tool of analysis to explore processes and agents of change revealing power dynamics within Nederland including community resilience and representation during the COVID-19 pandemic. Influential literature from social-ecological and psychological resiliency, embodiment and affect, biocultural knowledge, identities, and technology underpins this research. Through an embodied approach, the worldviews of myself as researcher and Nederland residents become new contributions to knowledge by considering the body as an intersecting point between affective, biocultural, and technocultural influences. A crystallization methodology is employed guided by a feminist new materialist epistemology to construct a robust representation of resident accounts through critical qualitative methods. Reflexive thematic analysis of semi-structured, in-depth interviews is complemented by field notes and secondary sources such as online featuring and representation of Nederland to conceptualize identities at the individual and community scale. This investigation of identities within crisis management and resiliency through the research context of Nederland, Colorado conducts holistic, empirical reflection upon resident agency and community resilience to changes during COVID-19. This methodological approach elicits rich knowledge to conceptualize identities of Nederland residents as complex, affective embodiments of multi-scalar changes mediated by tourism impacts during the COVID-19.
Open Access
Three essays in cultivating regional growth: brownfields and charter schools
(Colorado State University. Libraries, 2023) Trouw, Michael Frans, author; Weiler, Stephan, advisor; Pena, Anita Alves, committee member; Zahran, Sammy, committee member; Lopes, Tobin, committee member
This dissertation is comprised of three chapters focused on two important factors in cultivating regional growth. The first factor considered in chapter one is potential barriers to contaminated land reuse. As cities and towns grow, over time the stock of land within an area can be impacted by prior land use. A property which currently has a contamination issue from prior use which must be remedied before the land may be used in the future, whether for production or settlement, is called a brownfield. In this chapter we employ a survey of real estate professionals, and find developers require an additional risk premium on top of their normal rate of return on investment to incentivize them to invest in a brownfield. Importantly, this risk premium is found to be in excess of cleanup costs. Informed by the results of the survey analysis, a theoretical framework is used to explore the implications of this risk premium. We show this risk premium generated by information asymmetries potentially leads to inefficiency in the market for real estate and can perpetuate a cycle of underdevelopment due to a first mover problem. The redevelopment of this land is important, as these brownfield properties are typically located in the urban core of cities and towns and if not remediated can leave potentially productive swaths of land fenced off while expansion occurs in a sprawling manner on the fringes. The second factor in cultivating regional growth considered in chapters two and three of this dissertation is the role of educational alternatives. Specifically, I focus on the determinants of charter school formation and growth. Education quality and availability has been shown to be important in determining economic growth and migration patterns. Specifically, a strong education system can be viewed as an amenity to households and firms debating moving to a particular locale. Charter schools are publicly funded, privately run institutions crafted first as a pilot program for innovation, and more recently as a substitute or competitor for public schools. While the efficacy of charter schools has been heavily researched and remains controversial, little work has focused on the determinants of demand for the schools themselves. Chapter two builds on a small existing literature to provide light on what factors outside of direct measures of educational quality affect the creation rate of charter schools. Using a panel of core based statistical areas over the period 2006-2015, this analysis finds evidence that the composition of industry within a Core Based Statistical Area is related to the rate at which new charter schools are created, with more technical employment associated with a greater demand for alternative school options. The connection between industry and charter school creation is further explored by measuring the impact of intra-industry entrepreneurship on charter school proliferation, where findings suggest that higher levels of entrepreneurship within an CBSA is correlated with a higher charter school formation rate. Chapter three further explores the connection between charter schools and their interconnectivity with the broader economy. Posed as a method of returning education to the private market, charter schools are considered to be more exposed to market conditions, potentially more nimble to changing conditions and methodologies, but also potentially functioning in a more volatile market where school closings can occur more easily. This chapter uses the impact of the 2007 financial crisis to determine if charter schools were impacted differently than public schools. Using a nationally representative sample and aggregating to the Core Based Statistical Area, I find both traditional public and charter schools experienced small decreases in revenue but were largely sheltered from recessionary forces due to Federal intervention. Using a difference-in-differences approach I find that charter schools experienced both an increased rate of openings and an increase in the stock during the Great Recession. I attribute this effect to the decreased opportunity cost of charter school entrepreneurship. However, areas most affected by the Great Recession experienced a decrease in the stock of charter schools, as the challenges associated with opening a new school likely increased and lowered the viability relative to education entrepreneur's next best venture.
Open Access
Three essays on producer response to information disclosure
(Colorado State University. Libraries, 2023) Yu, Shuiqin, author; Costanigro, Marco, advisor; Burkhardt, Jesse, committee member; Hoag, Dana, committee member; Cutler, Harvey, committee member
This dissertation consists of three chapters studying how information and beliefs affect producers' behavior and decision making. The first chapter studies the effect of the Local Inspector Value Entry Specification (LIVES) program on restaurant hygiene in North Carolina. The LIVES Program, a collaboration between Yelp.com and municipalities, enables the display of restaurant inspection reports on Yelp's platform, simplifying access for consumers. Combining individual restaurant inspection data and restaurant level demographic data from Yelp.com, this study employs a difference-in-difference approach and geographic regression discontinuity design to analyze the LIVES program's impact on restaurant hygiene. The difference-in-difference analysis reveals a 1.143-point improvement in inspection scores for treated restaurants. The geographic regression discontinuity method, utilizing a neighboring county as a control group, corroborates the LIVES program's positive influence. The second chapter examines the effect of online consumer reviews on restaurant workers' wages. Online consumer reviews significantly influence the demand for experience goods, including movies, books, and restaurant meals. However, research on the impact of online reviews on restaurant workers' wages remains scarce. Utilizing decade-long panel data of quarterly consumer reviews and restaurant wages, this study demonstrates that an increase in average star ratings causes restaurant workers' wage growth. Notably, the effect varies across chain, major chain, and independent restaurants. The final chapter studies how Colorado farmers' and ranchers' subjective beliefs about the cost of adoption affect their intention to implement conservation practices. Promoting the adoption of conservation practices among farmers is challenging. Despite extensive research into farmers' reluctance to participate in conservation programs, few studies investigated how farmers' personal beliefs on the cost of adopting conservation practices affect their willingness to participate in those programs. This study adds to the literature by surveying over 150 Colorado farmers on their preferences for monetary and technical support regarding conservation tillage, soil testing, filter and buffer strips, and controlled-release fertilizers. Results from a choice experiment indicate that respondents' beliefs about costs can explain a large portion of the variation in farmers' willingness to adopt conservation practices.
Open Access
Hydraulic fracturing and the corporate colonization of the subsurface
(Colorado State University. Libraries, 2023) Fryer, M. Zoe, author; Macdonald, Bradley, advisor; Mumme, Stephen, committee member; McIvor, David W., committee member; Bubar, Roe, committee member
The United States presidential election of 2000 played a prominent role in determining the trajectory of the country for the next quarter of a century. The new millennium ushered in a new era with the George W. Bush administration chosen by the courts and the electoral college, the proliferation of hydraulic fracturing, Citizens United which flooded politics with money, restrictions in democracy, and persistent global climate crises. This dissertation will explore the role of the state in facilitating the corporate colonization of the subsurface. Drawing upon the ideas within Ralph Miliband's The State in Capitalist Society, this dissertation will critically analyze American pluralism and the state to reveal the many ways in which American democracy by the people has become democracy by the corporations. Analysis will be conducted using power structure research wherein key governmental positions held by the gas and oil elite will be identified, while using the overall framework of Miliband's state apparatus, including the five areas of the executive, the administrative, the coercive, the judicial, and the sub-state. The primary argument maintained throughout this dissertation is that the gas and oil industry elite have commandeered American democracy and policies to provide for their own benefit, at the expense of the American people and the health of the environment. The conclusion will include the work of Michael Lowy to argue for an eco-socialist leaning future wherein the gas and oil and subsurface are reclaimed as property of the state to be held in preservation.
Open Access
Spatiotemporal agent-based model explorations of white-tailed deer management in New England
(Colorado State University. Libraries, 2023) Kohler, Allison M., author; Boone, Randall B., advisor; Childers, Michael, committee member; Van Deelen, Timothy, committee member; Lynn, Stacy, committee member
This dissertation research addresses the intricate challenge of managing white-tailed deer (Odocoileus virginianus, henceforth "WTD") populations in the New England region while considering evolving ecological dynamics, changing interests of various stakeholders, and the role of management coordination among municipalities across scales. With a mixed-methods approach, I integrate qualitative and quantitative techniques such as agent-based modeling and case study analysis, helping to contribute multifaceted insights into the realm of WTD management in the region. In Chapter 2, I focus on investigating the role of hunter recruitment and land access in shaping local WTD populations across 11 focal towns in New England. The purpose of this chapter is to explore how these factors influence WTD populations, specifically by identifying the thresholds at which they become significant drivers in controlling these populations. To achieve this, I employ a mixed-methods approach that combines ecological modeling and the analysis of empirical data. The study's results emphasize the specific thresholds of hunting land access required to trigger a decline in WTD populations for different hunter density scenarios. I estimate that in most towns, the existing combination of hunter density and land access is effective in managing local WTD populations. However, under conditions of declining hunter recruitment, towns may require higher amounts of hunting access to achieve similar levels of population control. These findings underscore the significance of addressing issues related to declining hunter numbers and enhancing opportunities for hunting to sustain effective deer population management the region. This chapter's implications stress the importance of adaptive strategies and community engagement in the realm of WTD management in New England. In Chapter 3, I assess the role of sharpshooting as a potential urban WTD management strategy across various contexts in New England. The chapter's primary purpose is to examine the feasibility of sharpshooting when factors like declining hunter numbers and limited hunting land access impact the efficacy of current deer management approaches. I conduct this investigation using a mixed-methods approach, combining ecological modeling with social science surveys and assessments. The results from this chapter offer insights into the role of sharpshooting as a strategy if the effectiveness of hunting diminishes. The findings suggest that most of the towns studied can effectively manage WTD populations without the need for sharpshooting. However, as hunter recruitment declines and hunting access becomes more limited, sharpshooting may become a reasonable solution when it aligns with community preferences. This chapter concludes that sharpshooting can serve as a management tool in certain scenarios, emphasizing the significance of prioritizing stakeholder education, engagement, and acceptance. The implications drawn from this research underscore the need for community involvement in shaping management decisions, particularly in relation to adopting sharpshooting for local WTD population control. In Chapter 4, I focus on the broader theme of WTD management coordination in New England, examining its implications in controlling WTD populations across spatial scales. The main purpose of this chapter is to assess the impacts of stakeholder cooperation and coordination among municipalities on the effectiveness of WTD population management. My methodology involves the development and application of theoretical agent-based models to simulate different coordination scenarios. The chapter's results consistently demonstrate the significant role of coordination in shaping management outcomes, both within individual towns and across multiple municipalities. Based on model outcomes, effective cooperation between neighboring towns consistently leads to lower WTD densities both in towns with and without active management, exemplifying the role of collaborative efforts at larger scales. Additionally, the findings highlight the need for flexible strategies that consider the unique circumstances of each municipality. When aligned with community interests, the results demonstrate the potential for significant reductions in WTD densities with coordinated lethal management efforts, offering a path for more successful WTD population management in New England and similar regions. The implications of this chapter emphasize the role of regional cooperation and the importance of tailoring management strategies to specific contexts and community dynamics. This research not only contributes insights into the complexity of WTD management in New England, but it also serves as a broader blueprint for wildlife management worldwide. I encourage other researchers to build agent-based models to inform management of other situations and species across geographical locations and contexts. In this research, I reveal that the challenge of managing WTD populations largely arises from the spatially heterogeneous distribution of WTD and resulting conflicts, in addition to the complexity of achieving stakeholder consensus across spatial scales. This demonstrates the tradeoff between accommodating diverse stakeholders and achieving regional WTD population control. With adaptive, science-based, and community-based approaches, I explore the roles of adaptability, collaboration, and innovation in contributing to sustainable WTD management efforts. In the end, I hope this research contributes to informing management practices, promoting a balanced and harmonious coexistence between humans and resident wildlife in a changing world.
Open Access
Edible mealworms: can fermentation improve consumer acceptability and nutritional value?
(Colorado State University. Libraries, 2023) Wilson, John W., author; Weir, Tiffany, advisor; Bunning, Marisa, committee member; Stull, Valerie, committee member; Nair, Mahesh, committee member
As the global population increases, the demand for animal-based protein is also on the rise. To meet this demand, it is important to identify sustainable sources of animal protein that have a smaller environmental impact than conventional animal protein production. One potential solution to this challenge is the development of consumer-acceptable insect-based protein products utilizing the larva and pupae of Tenebrio molitor, a type of darkling beetle whose larval and pupal states are edible. These beetles can be reared in small spaces, do not require direct sources of fresh water, and convert feed into protein more efficiently than conventional meat production. In addition, their waste (frass) is dry, making it easier to contain than waste from conventional animal rearing operations, reducing the risk of contaminating the surrounding environment. In addition, the larvae and pupae can be eaten in their entirety, eliminating potential waste streams of byproducts associated with conventional meat processing. With less space, less water usage, more efficient feed conversion ratios, and nearly zero waste, the development of an edible mealworm industry in the global West would help relieve some of the pressures on the current animal protein systems and improve global food security. To accomplish this, it is necessary to generate a consistent demand in the global West for insect protein. Currently, in the United States, edible insects are largely relegated to ground powders designed to "hide" the insects or are placed in novelty products like chocolates and lollipops to confront people's notion of disgust. To introduce mealworm protein into the mainstream, it must be in a form that is accessible to the average American consumer, be safe to eat, and have comparable nutritional attributes as other protein-based products on the market. Tempeh fermentation techniques may be an appropriate approach to accomplish these goals. Tempeh fermentation uses Rhizopus oligosporus mycelium to knit together legumes into a solid cohesive substrate. The product can then be utilized in a variety of ways that are familiar to American consumers including stir frys, burgers, nuggets, and crumbles. This project seeks to utilize tempeh fermentation techniques to develop an insect-based product that is both consumer-friendly but also capitalizes on the known and emerging nutritional and environmental benefits of edible insects. In Chapter 1, I examine the safety of tempeh produced with various life stages of the Tenebrio molitor beetle. Samples were assessed for water activity (aw), and pH to determine the shelf stability of the products. Pathogenic risk was assessed through testing for coliforms, Salmonella and Listeria, and samples were analyzed for heavy meatal content via utilized Inductively Coupled Plasma and Mass Spectrometry (ICP-MS). This exploration allows us to determine best storing and cooking methods and helps identify critical control points in production to help minimize the risk to the consumer. In this chapter, I was able to demonstrate that tempeh made with Tenebrio molitor was just as safe as conventional soy-based tempeh and requires similar storage and cooking precautions to minimize the risks of consumption. In Chapter 2 we conducted a nutritional analysis of the insect-based tempeh products in comparison to traditional soy-based tempeh. We utilized ICP-MS to quantify the presence of micronutrients within each example. Samples were also analyzed for vitamins, macronutrients, and amino acid profile. We then calculated the protein digestibility using the Protein Digestibility-Corrected Amino Acid Score (PDCAAS). Comparison of results with traditional soy-tempeh products helps us to determine if the products provide comparable nutrition to products already on the market. It also helps to determine if the novel products will fill the nutritional space of more conventional sources of protein. This chapter found that the tempeh products made with the Tenebrio molitor had nutritional attributes comparable to conventional soy tempeh. Chapter 3 examines the bioavailability of iron within the sample set and compare the results to conventional bee samples, current on-the-market plant-based meat alternatives, and traditional soy-based tempeh. ICP-MS was utilized to quantify the amounts of iron present in each chemically digested sample. Then, digestates were added to Caco-2 human colonic cells to allow absorption of available iron. Iron absorption rates were then determined by using a human ferritin Eliza kit. This assessment helps us determine if the presence of insect protein improves the bioavailability of iron in a traditionally plant-based food and allows us to compare the availability of the iron in the novel products to conventional beef and current plant-based meat products. The bioavailability of iron in the novel products exceeded that of the conventional beef and the plant-based meat alternative. In Chapter 4, we conducted a consumer acceptability study to analyze the potential for consumer acceptance of a tempeh product made with 50% mealworms and 50% soybeans when compared to a commercial soy-based tempeh. An online survey was conducted to assess the public's attitudes to entomophagy, their current level of exposure to the practice, and the willingness to consume insects. Next, the mealworm soybean tempeh was evaluated by a trained sensory panel to develop a lexicon that describes the organoleptic attributes of the product. Finally, a blind in-person sensory evaluation was conducted to assess the overall acceptability of the product. During the in-person evaluation, participants were provided with different prompts to determine if details around the environmental impact of insect eating versus conventional meat production would affect the favorability of the product. Participants in this study rated the flavor equal to that of the commercial soy tempeh and majority of participants indicated they were equally or more likely to consume insect-based products again. The final chapter explores the need for research around branding and availability on insect-based food products to increase acceptance of entomophagy in Western society. This dissertation aims to determine the safety of utilizing edible insects in tempeh fermentation, examine the nutritional attributes of tempeh products made with various life stages of the Tenebrio molitor beetle, determine how effective these products are in filling their intended nutritional niches, and assess the potential for consumer acceptance of insect-based tempeh products. This dissertation provides a strong foundation for the understanding of the safety, nutrition, and acceptability of utilizing T. molitor-based tempeh as an alternative source of protein.
Embargo
Characterization and insights into the molecular mechanism of cytokinin-induced priming of plant defenses
(Colorado State University. Libraries, 2023) McIntyre, Kathryn, author; Argueso, Cristiana, advisor; Bush, Daniel, committee member; Leach, Jan, committee member; Stewart, Jane, committee member; Reddy, Anireddy, committee member
Plants have developed several mechanisms to cope with pathogenic challenges. One of these mechanisms, known as defense priming can be effective at reducing susceptibility to pathogens. Compared to unprimed plants, the immune response from primed plants, upon pathogen attack, is much stronger. This mechanism of induced disease resistance can be initiated by biological and chemical agents. The major benefit of priming is the induction of a high level of protection with considerably low fitness costs making it an attractive disease management strategy to preserve agricultural output. Recent research has demonstrated that the plant hormone cytokinin (CK) has a priming effect against biotrophic pathogens, a phenomenon referred to here as cytokinin-induced priming (CIP). This dissertation aims to gain further understanding of CIP against the hemibiotrophic bacterial pathogens Pseudomonas syringae pv. tomato (Pst) and Pseudomonas syringae pv. maculicola (Psm) in Arabidopsis thaliana (Arabidopsis) and Brassica napus, respectively as well as the necrotrophic fungal pathogen Botrytis cinerea in Arabidopsis. Chapter 2 focuses on characterizing CIP as a true priming agent by investigating the timeframe in which CIP is most effective at reducing susceptibility to Pst and Psm in both Arabidopsis and its closely related relative, B. napus and the impacts on plant growth due to CIP in these pathosystems. Moreover, we discovered that other known priming agents depend on endogenous CK signaling suggesting CK-mediated processes are involved in the priming of defense responses. The role of CK in primed defenses against B. cinerea is explored in chapter 3 where CIP is demonstrated to reduce necrotic lesion size caused by B. cinerea in a manner dependent on the JA-mediated defenses and partially on SA-mediated defenses. Transcriptome analysis revealed that during the priming stage, CK prepares the plants for pathogenic challenge through the accumulation of cellular components needed for translation and metabolites utilized for energy production and defense. Following B. cinerea inoculation, CIP suppresses defense while increasing photosynthetic-related processes. In the final chapter, molecular mechanisms are explored during CIP against Pst. Through transcriptome changes, priming by CK potentiates gene expression associated with systemic induction of defense, also known as systemic acquired resistance (SAR), following Pst challenge. Using this information, it is demonstrated that CK treatment can also induce SAR and that the known SAR inducer, L-pipecolic acid, is dependent on endogenous CK signaling. Due to the previously identified relationship between CK and source-sink relationships, amino acid transport was demonstrated to have a role in both CIP and CK-induced SAR. New agricultural practices that mitigate crop loss due to plant diseases are beneficial in terms of sustainability and economic costs. The use of CK as a priming agent offers an avenue for a new disease management strategy in that CIP protects plants against a broad range of pathogens with minimal effects on plant growth. The molecular mechanisms underlying CIP discovered here offers new insights into the relationship between plant metabolism and defense, where its exploitation could be used to create disease protection strategies.
Embargo
Recent and future Colorado water: snow drought, streamflow, and winter recreation
(Colorado State University. Libraries, 2023) Pfohl, Anna K. D., author; Fassnacht, Steven R., advisor; Barnard, David M., committee member; Kampf, Stephanie K., committee member; Rasmussen, Kristen L. , committee member
Water in the western United States is a crucial resource for ecosystems, the abiotic environment, and people (for industrial, agricultural, and residential purposes). A majority of this water originates in the seasonal snowpack in the mountains. The snowpack is responsible for maintaining the water supply, and changes to this system have broad and severe implications. Various metrics have been used to quantify these patterns when snow is less than normal, often referred to as a snow drought or a low snow year. In recent decades, the number of years with low snow have increased, and this will continue and intensify into the future. With observed decreases in long-term snow and modeled decreases for the future, high snow years become more critical to support the water supply. Beyond supplying water for downstream use, the seasonal snowpack also sustains the winter recreation industry, which is a large component of many local and state economies. The Weather Research and Forecasting Model (WRF) is a 4-km mesoscale model that can capture orography and convective processes over complex terrain. WRF includes two time periods: the control (CTL) based on historic conditions and the future under pseudo-global warming (PGW) conditions. This dataset was used to drive SnowModel (WRF-SM) to produce 100-m, daily snow water equivalent (SWE), total precipitation, solid precipitation, snowmelt, runoff, and air temperature. Using these datasets, this research examines past and future snow and streamflow in Colorado. We evaluated 1) common metrics and trends for snow drought; 2) used WRF data to drive the Ages hydrologic model to examine changes (snow, streamflow, and flow partitioning) in two high snow years; and 3) ski opportunities at nine different resorts. To evaluate methods of defining snow drought, we used SWE and winter precipitation data from Snow Telemetry stations and the WRF-SM dataset described above. Classifying drought with the ratio of SWE to winter precipitation resulted in drought occurrence for more than 50% of station-years from 1981 to 2020. Using percentiles of long-term peak SWE indicated that occurrence of low or very low years increased from 2001 to 2020 compared with the previous 20 years. Under PGW conditions, elevations between 1800 and 2400 m shifted drought classification towards low or very low, with higher elevations (3200 m and above) remaining relatively unchanged. To examine changes in snow, streamflow, and flow partitioning under a PGW scenario for two high snow years (2008 and 2011), we used Ages, a spatially distributed watershed model, in the Upper Blue River watershed in central Colorado. Changes in snow (snowmelt and solid precipitation) were greatest in magnitude at high elevations. Timing of peak streamflow shifted to nearly two months earlier under a PGW scenario. To examine ski opportunities, we developed metrics to quantify ski conditions. The number of opportunities for snowmaking in the future will decrease throughout the season, but especially in October and November. Ski days (snow depth greater than 50 cm) will decrease in early and late season and increase at lower elevations from January through March. Powder days (fresh depth greater than 15 cm and fresh density greater than 125 kg/m3) follow a similar pattern. Ski resorts at low elevations will generally be more susceptible to changes under a PGW scenario. Additionally, using a fine-resolution dataset allowed investigation of smaller study areas to understand the changes that are not captured with coarser resolutions.