Novel Reagents and Approaches for Portable Sample Preparation and Detection of Foodborne Pathogens

Significant advances have been made in recent years to develop portable endpoint detection methods for foodborne virus detection, particularly in the form of isothermal nucleic acid amplification methods. However, these methods have significant drawbacks; namely, they can only analyze a very small sample volume, and are vulnerable to matrix-associated amplification inhibitors. If these isothermal amplification methods are to be effective in in-field settings, there is a need for equally portable sample preparation methods. The first step in any diagnostic assay is disinfection. Both intact microbes and residual nucleic acid from previous samples can contaminate nucleic acid-based detection assays, leading to false positive results. However, few surface disinfectants have been validated against free nucleic acid. For this reason, we tested the capacity of several commercial surface disinfectants to degrade three types of nucleic acid (viral ssRNA, eukaryotic DNA, PCR product). Only hypochlorite-based disinfectants were effective (dilute chlorine bleach and a commercial hypochlorite-based disinfectant). However, the bleach must be diluted fresh in distilled water before each use for best results, while the commercial disinfectant gave consistent results over several months without the need for extra preparation steps. Therefore, the commercial hypochlorite-based disinfectant would work better as part of a portable microbial detection kit. The next step is sample preparation, specifically target separation and concentration from the sample matrix. For this purpose, we evaluated a class of capture reagents known as magnetic ionic liquids (MILs) which would be ideal for in-field applications as their use requires minimal electrical equipment and no cold-chain storage. The MIL formulations used had already been evaluated for capture of bacterial pathogens from liquid food matrices, but had not yet been tested with non-enveloped viruses. Therefore, we tested a number of parameters impacting MIL-based capture and recovery of both an intact human norovirus surrogate (bacteriophage MS2) and purified viral ssRNA from aqueous suspension. All MIL formulations were effective for both targets, though they varied some in capture and recovery efficiency, and none appeared to significantly damage the virus capsid. We also determined that maximizing MIL dispersion is critical for ensuring optimal performance, and is determined by both the complexity of the input suspension and the relative volume of MIL used. We also showed that MILs have some capacity to concentrate the target. Most interestingly, they were able to effectively capture and recover free RNA while also appearing to give some protection from degradation in suspension. This raised the possibility that they could play a role in nucleic acid extraction. The last sample preparation step needed for nucleic acid-based detection is genomic extraction. However, though many established methods exist for viral nucleic acid extraction, few are designed with a focus toward in-field applications. Therefore, we explored the use of MILs as a binding substrate similar to the magnetic silica beads in commercial kits, which would enable target separation, concentration, and genomic extraction to occur in a single tube with minimal target loss. We found that some MIL formulations were able to recover target RNA at levels comparable to magnetic silica beads when used with commercial RNA extraction reagents. We also developed our own lysis, wash, and elution buffers that showed comparable performance to the commercial reagents when used with both MILs and magnetic silica beads. Though there is still much to explore, this work constitutes a meaningful step toward development of a complete and portable sample preparation method for foodborne virus detection. When combined with a portable endpoint detection method, this could significantly reduce barriers to in-field pathogen detection, facilitating faster outbreak tracking and more routine testing for foodborne viruses.Work for chapter 3 and 4 was partially funded through the Chemical Measurement and Imaging Program at the National Science Foundation (Grant number CHE-2203891). Other funding sources for collaborators include the Alice Hudson Professorship at Iowa State University and the Iowa Agriculture and Home Economics Experiment Station Project No. IOW04202, sponsored by the Hatch Act and State of Iowa Funds. This work was also supported by the USDA National Institute of Food and Agriculture, Agricultural and Food Research Initiative Competitive Program, grant numbers: 2023-67011-40392 FELLOWSHIP and 2022-67021-36408.Doctor of Philosophy (Ph.D.

Naves inventoras de regiones. Colonial Spanish American Epic Poetry and the Invention of America

In La invención de América (1958), Edmundo O’Gorman highlighted the need to understand the discovery of the New World as an ontological process through which the Americas came to be conceived as an emerging geopolitical entity. This process was carried out through a series of historical accounts and pictorial productions that traced the contours of the New World and the meanings attributed to its history in accordance with European representational practices. I posit that poets of the Spanish colonies in the Americas produced a distinctive trend of epic poetry by transposing the semiotic and epistemological tools developed in the historical accounts of the early modern period. This specific trend, which I deem historiographical, allowed poets in the Americas to advance interpretations of a recent history of conquest and colonization built upon the poetization of early modern debates around historical truth, memory, and eyewitness testimony. By analyzing how the epic poems of the Americas contributed to the polemics of “the invention of America,” I trace a genealogy of works that converse simultaneously with the literary and historiographical tradition and thus allow us to further interrogate Latin America’s colonial history.Doctor of Philosophy (Ph.D.

Module 3

This module contains materials on vector data analysis concepts and practice, and a brief exercise reviewing Module 2 concepts

Handheld Device for Burn Depth Analysis Through Skin Hydration: A Proof of Concept

About 500,000 Americans seek treatment for burns annually, but burn depth, used to create treatment plans and determine whether surgery is needed for treatment, is only correctly found about 50-80% of the time in the US. In the UK and other countries, clinicians have used laser doppler imaging (LDI) with clinical evaluation to increase diagnostic accuracy, however US based physicians tend to just use clinical evaluation, citing cost and difficulty of use as reasons for not using this technology. The purpose of this thesis is to present an innovative, cheap, and easy to use device that can be used to evaluate burn depth in a non-contact modality. When researching the pathophysiology of burn injuries, I found Jackson’s thermal wound theory, postulating that besides the degradation of proteins in the immediate environment, poor fluid flow is the next biggest challenge, without fixing more tissue will die. LDI uses this idea to look for fluid movement, while I planned to use this by finding water. The macro scale seemed to support this as well, burn victims with a significant amount of skin area burned lose so much fluid that they require IV fluid resuscitation for recovery. Based on this detection method, I created a device with a pair of LEDs that emit light at 910 and 970 nm, where 970 nm is a water absorption peak. To ensure that the device meets standards, a mathematical model was created and tested.Master of Science in Biomedical Engineering (MSBME

CBT-based Lifestyle Modification Education to Improve Hypertension Management for Spanish Speaking Patients at One Community Health Center

Hypertension affects Hispanic populations in the U.S., requiring culturally tailored interventions. This quality improvement (QI) project evaluated the effect of Cognitive Behavioral Therapy (CBT)-based lifestyle modification education and individualized hemodynamic monitoring program for Spanish-speaking patients at a community health center. The four-week intervention incorporated CBT principles, including SMART goal-setting to improve diet, physical activity, smoking cessation, and sleep hygiene. Seven participants enrolled, with five completing the program. Self-care outcomes were measured using the Self-Care of Hypertension Inventory (SCHI) and Self-Care Self-Efficacy (SCSE) surveys. Hemodynamic parameters were assessed using the NICaS Hemodynamic Navigator, a non-invasive bioimpedance device. Results showed a mean reduction in systolic blood pressure from 172 mmHg to 133 mmHg and total body water percentage from 64.8% to 51.1%, indicating improved cardiovascular function. The SCHI exhibited strong adherence to recommended self-care management behaviors across three domains: self-care maintenance (M = 80.00, SD = 9.50), self-care monitoring (M = 78.57, SD = 22.45), and self-care management (M = 75.00, SD = 13.18). The SCSE score (mean=86.00, SD = 13.76) suggested high confidence in managing hypertension. Participants feedback demonstrated they valued Spanish-language instruction and culturally relevant education, reporting reduced sodium intake, increased physical activity, and attempts at smoking cessation. While sleep improvement remained a challenge, CBT-based strategies supported behavioral change. Findings suggest integrating CBT-based education with SMART goal-setting and hemodynamic monitoring can enhance hypertension management. Future research should explore long-term adherence and clinical outcomes to validate this approach.Doctor of Nursing Practice, Psychiatric Mental Health Nurse Practitioner (PMHNP

A Subject of Interest: Silence, Memory and the Dramaturgical Journey of Writing

This thesis traces the creation of A Subject of Interest, an original play exploring the complex relationship between Brazil and the United States during the Brazilian military dictatorship (1964–1985). Blending dramaturgy, journalism, and creative writing, the project investigates how historical silences—personal and collective—shape memory and identity. Inspired by personal family history, extensive historical research, and interviews, the thesis reflects on the creative challenges of adapting factual research into a dramatic narrative. It examines the tension between historical accuracy and emotional truth, the responsibility of storytelling in confronting silence, and the process of shaping real-world trauma into theatrical form. Throughout, the work highlights dramaturgy’s potential to bridge journalism, politics, and fiction, and argues for storytelling as a tool of resistance against historical erasure.MFA Thesis Research GrantMaster of Fine Arts (M.F.A.

Compassion and Contempt: Dante's Moral Corrections of Shades in the Inferno

In Dante’s Commedia, he uses his contrapasso as an enforcing justice of punishment as the mirrored consequence of sinner’s Earthly sin. The contrapasso is used as a tool of moral correction for how Dante responds to the shades’ choices committed in sin. Dante’s responses range from pity, contempt, and more rarely, violence. These instances of violence raise ethical questions to the reader that challenge preconceived notions about sin’s severity of punishment. These instances also include disassembling the dichotomy that is Dante auctor and Dante agens, by raising questions of historical narrative into his treatment of certain shades. This question of justice is prompted by the poet for the reader and for himself as the pilgrim. His responses are often guided or scolded by Virgil, who serves as his personification of reason, offering Dante the opportunity to extend this influence of reason to those in Hell who betrayed it in life

Module 11

This module contains materials on GIS modeling concepts and practice

How Household Separation and Dispersion Affect the Well-being of Left-behind Parents in Rural China?

Evidence has shown that departure of adult children from households has profound, yet contradictory consequences for left-behind parents’ well-being. This study argues that dispersion, i.e. close or distant separation of households, is the key to understanding the divergent evidence for both positive and negative influence from separation. Drawing on longitudinal data from the China Health and Retirement Longitudinal Study (2011-2018), this study reveals that household separation improves parents’ financial conditions through increased monetary transfers but deteriorates mental health challenges, while physical health remains unaffected. Critically, the spatial dispersion of children shapes these outcomes. Parents with children residing in the same village experience stronger financial and physical health benefits compared to those with children farther away, while this loss of health benefit can be mitigated by regular contacts. The findings highlight families’ adaptive strategies to sustain intergenerational solidarity through spatially dispersed yet mutually supportive ties.Master of Arts (M.A.)2026-09-0

TROPICAL CYCLONES AND SEDIMENT DYNAMICS IN MOUNTAINOUS ISLANDS: EROSION, TRANSPORT, AND COASTAL DELIVERY IN PUERTO RICO

Small, tropical and sub-tropical mountainous islands exposed to episodic tropical cyclones export a disproportionate sediment mass to the world’s coasts. Yet, the multiple mechanisms of sediment erosion via landslides in mountainous landscapes, fluvial transport, and export to the coast that occur during tropical cyclones are difficult to measure, thus limiting our understanding of the role of tropical cyclones in watershed-scale sediment dynamics and their importance in coastal sediment delivery. Sediment supply to coastal landforms in tropical coasts serve as building blocks to sustain beaches and mangrove forests wetlands. These landscapes provide high ecologic and economic value, and often serve as natural infrastructure and barriers to protect human activities along the coast. Despite their value, these ecosystems are threatened by a combination of coastal erosion and sea level rise, hence making sediment supply potentially critical for these systems to adapt. However, we do not know how important episodic tropical cyclone sediment delivery to mangrove forests is. Here I aim to study the role of tropical cyclones in three components of the basin-scale sediment budget dynamics in tropical islands: (1) sediment erosion via landslides, (2) fluvial transport, and (3) sediment export captured in reservoirs stratigraphy. I use Hurricane María (2017) and Fiona (2022) in Puerto Rico (PR) as an example of extreme events. And finally, I aim to quantify the relative role of tropical cyclones in delivering sediments to riverine and tidal fringe mangrove forests and how important minerogenic sediments are in soil carbon stocks and sequestration potential. In Chapter 2, I aim to characterize the sedimentary and stratigraphic signature of María (2017) and Fiona (2022) relative to background sediments and compare how well internal stratigraphic structures reflect temporal patters in extreme flooding and sediment delivery associated with tropical cyclones. Here I collected repeated sediment cores at Caonillas reservoir to measure down-core geochemical and physical sediment properties: X-ray fluorescence (XRF), grain size, and loss-on-ignition (LOI). I found that María in 2017 generated three deposits characterized by relatively inorganic, medium-sized sand that is enriched in Sr and Ca elements relative to background mud. Additional cores collected after Fiona in 2022 revealed an additional event deposit attributed to the event, enriched in Be-7, which suggests recent deposition. Event deposits are linked to multiple flash floods generated during Maria and linked to individual rain bands evident in radar imagery collected during the event. Several rainbands of intense precipitation created the ideal conditions to erode sediments via landslide triggering and generate high transport capacity in the fluvial network to export sediments from upland watershed. In Chapter 3, I aim to quantify the sediment budget from landslide erosion and fluvial transport during extreme events like María, and contextualize the role of tropical cyclones in sediment yields in the Caonillas reservoir, using María as an example of an extreme geomorphic event. Here I used repeated bathymetric surveys from 1990, 1995, 2000, 2012, and 2020 to assess sediment accumulation after María and contrast it with background rates of sediment accumulation. I found that 69% (± 2.9%) of the sediment deposited between 1995-2020 were related to four tropical cyclones, where María represents 23% (3.0 ± 0.1 x 106 Mg) of the total sediment accumulation. To assess sediment delivery, I built two rating curves for the period of 1995-2022 from an upstream hydrograph to assess suspended sediment delivery during María, Fiona, and three other earlier tropical cyclones. I found that 72.5% (± 3.3%) of the suspended sediment delivery were related to these tropical cyclones between 1995-2022, where María delivered 25% (5.3 ± 0.2 x 106 Mg) of the total suspended sediment transported over the entire study period. Sediment deposition and suspended sediment delivery estimates correspond to the equivalent of 20-22 and 23-24 years of long-term, background sediment yields, respectively. In addition, sediment erosion from landslides was calculated using lidar-derived DEMs collected before María in 2015, and after the event in 2018. I found that María mobilized 1.2 ± 0.2 x 106 Mg of sediments via landslides, which represent 8-11 years worth of annual sediment yields and 40% of the total María deposits, assuming all eroded sediment gets exported. Although this 1995-2022 period was particularly active in tropical cyclone impacts relative to the 20th century, our observations show that tropical cyclone-related sediment erosion and transport are the main drivers of sediment mobilization and transport in the 1995-2022 period, more than doubling long-term sediment delivery before 1990. In Chapter 4, I aimed to determine the relative importance of minerogenic sediment supply on soil organic carbon stocks and sequestration rates in semi-arid mangrove systems. I sampled three mangrove forests whose soils represent different levels of sediment supply. Tidal fringe mangrove forests of Los Machos and Jobos Bay represent sites with minimal minerogenic sediment supply evident by their high organogenic, peaty substrate soils, while Rio Yauco Delta represents high sediment supply with minerogenic substrate and low organic-rich peat development. Despite these differences, carbon stocks for both tidal fringe and riverine mangrove soils contained similar soil organic carbon stocks with median values of 362 Mg C ha-1 and 352 Mg C ha-1, respectively. Organogenic mangrove sites in tidal fringe geomorphic setting showed lower accretion rates (1.04 mm yr-1 for MAC and 0.78 mm yr-1 for JOB) than the riverine site (4.5 mm yr-1 for RYD). Tidal fringe mangroves have also been historically prone to extensive die-off events with up to 45% in mangrove cover reduction These fringe systems are also more constrained in space than riverine mangroves, which showed mangrove expansion prior to a reductions in sediment supply likely caused by upstream damming in 1952. Our findings further inform soil carbon stocks accounting in underrepresented semi-arid mangroves environments and documents diverse anthropogenic impacts and their effects on carbon sequestration services by these systems. The findings presented in this dissertation improves our understanding of upland sediment mobilization, transport, and export during large tropical cyclones in sub-tropical mountainous islands as well as their relative role in providing valuable sediments to coastal mangrove forests ecosystems. I found that intense rainfall derived from tropical cyclones, when occurring frequently enough, can be main drivers of sediment export in steep, landslide-prone basins. Landslides are a significant source (40%) of sediments in Caonillas sediment budget during hurricane María (2017), yet other geomorphic sources (e.g. gullies and channels) are important as well. Although outside of the scope of this study, it is acknowledge that gully and channel erosion are two additional sources that have yet to be constrained. Event derived sediment yields from steep upland basins can be 23-25 years of annual background sediment export, yet no significant event sediment deposition from María is observed in the two organogenic, tidal fringe mangrove forests sites. Contrastingly, small mangrove expansion was observed at the river mouth in the minerogenic substrate, riverine mangrove forests. Despite smaller area cover and reduced sediment supply due to upstream dam construction in 1952, high minerogenic sediment accretion rates at this riverine site makes it more effective in sequestering soil organic carbon as sea level increases. This illustrates the trade-offs between securing water and clean hydroelectric energy sources via dams and reservoirs, while the reduced sediment supply to the coast diminishes the carbon sequestration potential of downstream mangrove forests.The work presented in this dissertation was supported by NSF NRT ELEVATE (Elevating Equity Values in the Transition of the Energy System) (Award Number: 2021693), UMass Spaulding Smith Fellowship, Leo M. Hall Memorial Fund, Gloria Radke Memorial Fund, and NSF/GSA Graduate Research Fellowship, and John A. Black award.Doctor of Philosophy (Ph.D.)2026-02-0