Physical Sciences and Mathematics Commons^™

Better Understanding Genomic Architecture With The Use Of Applied Statistics And Explainable Artificial Intelligence, Jonathon C. Romero

Doctoral Dissertations

With the continuous improvements in biological data collection, new techniques are needed to better understand the complex relationships in genomic and other biological data sets. Explainable Artificial Intelligence (X-AI) techniques like Iterative Random Forest (iRF) excel at finding interactions within data, such as genomic epistasis. Here, the introduction of new methods to mine for these complex interactions is shown in a variety of scenarios. The application of iRF as a method for Genomic Wide Epistasis Studies shows that the method is robust in finding interacting sets of features in synthetic data, without requiring the exponentially increasing computation time of many …

Hiding In Plain Sight: Accounting For Rate Heterogeneity In Trait Evolution Models, James Boyko

Graduate Theses and Dissertations

Within the last four decades, phylogenetic comparative methods have become the defacto method of analysis for comparative biologists. The availability of high-quality comparative datasets has been matched by an explosion of possible phylogenetic models. In large part, the efforts to increase the realism of phylogenetic comparative methods has been successful as evidenced by their widespread use. To this extensive literature, my contributions are modest. I have focused my dissertation work on two main themes. First, most phenotypic evolution is not independent of other phenotypes. Changes in a particular character may influence changes in another and modeling these characters in isolation …

Assessing Consumer Demand, Producer Profitability, And The Environmental Impacts Of Conservation Agriculture Adoption In Sub-Saharan Africa, Willy Byamungu Mulimbi

Graduate Theses and Dissertations

This dissertation explores three aspects of conservation agriculture (CA) in the Sub-Saharan African region (SSA). The first article examines the demand side of CA and explores whether urban maize (Zea mays L.) consumers in the Democratic Republic of the Congo (DRC) would be willing to pay a premium for CA-produced maize flour. The second article estimates the effects CA provides to adopters and their farms in smallholder farming systems in the DRC, focusing on changes in soil properties and cowpea (Vigna unguiculata) yields. The final article uses a Life Cycle Assessment (LCA) approach to monetize the environmental impacts of adopting …

Optimization Techniques For Soil Organic Carbon Prediction Using Mid-Infrared Spectroscopy, Minerva J. Dorantes

Graduate Theses and Dissertations

Resource-efficient techniques for accurate soil carbon estimation are necessary to satisfy the increasing demand for spatiotemporal data. In the last thirty years, mid-infrared (MIR) soil spectroscopy has developed as an accurate, rapid, cost-effective, and non-destructive technique for soil organic carbon (SOC) analysis. In soil spectroscopy, a calibration model relates spectral data to a corresponding measured soil property and is subsequently used to predict this value from new spectral data. Various optimization techniques have been used to improve the statistical performance of calibrations; however, there is little consensus on the conditions that make these techniques effective. The objectives of this research …

The Effect Of Water Management And Ratoon Rice Cropping On Methane Emissions And Harvest Yield In Arkansas, Marguerita Leavitt

Graduate Theses and Dissertations

Sustainable intensification of rice farming is crucial to meeting human food needs while reducing environmental impacts. Rice produces 8% of all anthropogenic CH4, which is a potent greenhouse gas. CH4 emissions can potentially be reduced by cultivation practices that minimize the number of days the fields are saturated, such as dry-seeding instead of water-seeding and irrigation using the alternate wetting and drying (AWD) technique instead of delayed, continuous flooding (DF). Ratoon cropping, wherein a second crop of rice is grown from the harvested stubble of the first crop, can be used to produce additional yield with minimal labor, but may …

Evaluation Of Factors That Contribute To Injury To Quizalofop-Resistant Rice From Quizalofop Applied Postemergence, Navdeep Godara

Graduate Theses and Dissertations

Quizalofop-resistant rice technology allows for over-the-top applications of quizalofop, an acetyl-coenzyme A carboxylase-inhibiting herbicide. However, quizalofop caused significant injury to quizalofop-resistant rice in some Arkansas fields during the first year of commercialization. Experiments evaluated the effect of early-season soil moisture and nitrogen availability; pre-exposure to low rates of glyphosate and imazethapyr; planting date; and environmental conditions including, soil moisture content, air temperature, and light intensity on quizalofop-resistant rice tolerance to quizalofop applications. All experiments assessed sequential quizalofop applications made to 2-leaf followed by 5-leaf stage of rice. Sequential quizalofop applications alone and with surface irrigation or nitrogen application at the …

Tree Ring Reconstructions Of Streamflow For The Lower Rio Grande Valley Of Texas, Adedolapo Mutiyat Adeyanju

Theses and Dissertations

The Rio Grande River is a major water source for people living within the USA-Mexico border. The Rio Grande River has its headwaters in the San Juan Mountains in Colorado and the Sierra Madre Occidental in Mexico before flowing into Texas through El-Paso. The water supply issues facing the Lower Rio Grande Basin (LRGB) are extremely complex from international restrictions to severe climate change. The river shares its flow between the U.S.A and Mexico based on the provisions of the 1944 treaty between the U.S.A and Mexico. The LRGB flow is regulated by releases from Falcon and Amistad Reservoirs managed …

Water Sourcing Strategies Of Desert Vegetation In Varying Soil Textures With Vegetation Competition: A Stable Isotope Analysis, Martha Elizabeth Gardea

Open Access Theses & Dissertations

Recent studies have suggested an ecohydrological separation of water exists in the northern Chihuahuan Desert, where vegetation types, rainfall regimes, and location in the terrain seem to determine the type of water (e.g. isotopically depleted or enriched in 18O and 2H) plants are able to source and use throughout their growing cycle. That work found evidence of creosote (Larrea tridentata) and mesquite (Prosopis glandulosa) using tightly bound soil water at both a site on an ephemeral channel and a site in higher elevated flat area because the isotopic signature of plant water at the beginning of the study did not …

Chromosome Number Evolution, Phylogeography, And The Effects Of Climate Change On Species Distributions In Polyploid Plant Systems, Courtney H. Babin

University of New Orleans Theses and Dissertations

Polyploidy, a term used to describe organisms with cells having more than two paired sets of chromosomes, is a significant driver of diversification among land plants. Over a century of research has advanced our understanding of polyploidization in some taxa, but polyploid organisms remain understudied. In this dissertation, I investigate chromosome number evolution, phylogeographic structure, genetic differentiation, and the effects of climate change on ploidy level distribution using polyploid plant systems. In the first chapter, I inferred a molecular phylogeny of Allium, an economically important genus that includes cultivated crops and ornamentals, to investigate evolutionary transitions in chromosome number …

Orthotrichum Lyellii As An Active Moss Biomonitor: Examining The Interplay Between Ambient Pm10, Bulk Deposition And Heavy Metals In An Urban Environment, Scott Bradley Kiel

Dissertations and Theses

The importance of monitoring and preventing pollution in the environment is a globally recognized issue. Of the criteria pollutants outlined by the United States Environmental Protection Agency, particulate matter is among these least understood in relation to toxicity and most wide-spread. Many governments have employed continuous air quality monitoring networks to track ambient levels of particulate matter, but are often too widespread to capture the heterogeneity of the urban environment, especially for heavy metal deposition. In Portland, OR, the epiphytic moss Orthotrichum lyellii was successfully used as a low-cost passive biomonitor to increase the spatial resolution of pollution around the …

Developing A Miniature Smart Boat For Marine Research, Michael Isaac Eirinberg

Computer Engineering

This project examines the development of a smart boat which could serve as a possible marine research apparatus. The smart boat consists of a miniature vessel containing a low-cost microcontroller to live stream a camera feed, GPS telemetry, and compass data through its own WiFi access point. The smart boat also has the potential for autonomous navigation. My project captivated the interest of several members of California Polytechnic State University, San Luis Obispo’s (Cal Poly SLO) Marine Science Department faculty, who proposed a variety of fascinating and valuable smart boat applications.

Cover Crops And Irrigation Impacts On Corn And Soybean Production In The Mid-Southern Usa, Dillon Aaron Russell

Theses and Dissertations

Reducing groundwater withdrawals from the Mississippi River Valley Alluvial Aquifer is imperative to sustain future irrigated cropping systems in the mid-southern USA. This research was conducted to determine the impacts of cover crops and irrigation sensor thresholds on corn (Zea mays L.) and soybean (Glycine max L.) production, water productivity, irrigation water use efficiency, and soil physical properties in the Mississippi Delta. The cover crop treatments included cereal rye (Secale cereale L.), hairy vetch (Vicia villosa R.), wheat (Triticum aestivum L.)-radish (Raphanus sativus L.)-turnip (Brassica rapa L.) mix, and no cover crop. The irrigation thresholds included -40 kPa, -90 kPa, …

Root Phenotyping Of Peptide-Treated Glycine Max, Salem Jackson

Biological Sciences Undergraduate Honors Theses

Plant elicitor peptides (Peps) – endogenous chains of amino acids involved in natural plant defense – have been shown to decrease damage from herbivores and pathogens by inducing an immune response, increasing the emission of volatile organic compounds (VOCS), transcripts, and metabolites. Exogenous treatment of soybean seeds with plant elicitor peptide GmPep3 has been shown to induce these broad-spectrum defenses and offers a new method for increasing crop yield. However, the effects of GmPep3 on indicators of soybean health – root characteristics, growth stages, etc. – have not been fully realized.

Using the root-phenotyping platform RhizoVision Explorer, several root traits …

Investigation Of The Binding Domain Interfaces Of The C-Terminus Of The Albino3 Insertase And The 43kda Chloroplast Signal Recognition Particle Subunit Via Single Molecule Förster Resonance Energy Transfer, Amanda Tomanek

Chemistry & Biochemistry Undergraduate Honors Theses

Fluorescent labeling is a technique used for visualizing functional groups contained in biomolecules by fluorescence imaging. This technique was used in this project to analyze post-translational targeting of light-harvesting chlorophyll-binding proteins (LHCP), which are the core complexes that harvest sunlight to drive photosynthetic electron transfer. This protein is synthesized in the cytosol and post-translationally targeted to the stroma of chloroplasts. CpSRP43 is a signal recognition particle (SRP) subunit unique to chloroplasts, which has been shown to interact with the stroma-soluble C-terminus of the thylakoid-bound Albino3 insertase (Alb3-Cterm). In the chloroplast stroma, targeting to thylakoids is performed via the cpSRP pathway …

Using Thermal Units To Predict Biomass Accumulation And Total Nitrogen Uptake For Cover Crops In Arkansas, Mila Victório Pessotto

Graduate Theses and Dissertations

Including cover crops in agricultural production systems is an important management practice. Cover cropping can improve soil health, increase plant-available nitrogen (N), provide surface residue to prevent erosional soil loss, increase water infiltration, and increase weed suppression. Cover crops growth can be predicted using thermal days or growing degree days [GDD] similar to commodity crops such as corn (Zea mays L.) or rice (Oryza sativa). Growing degree day calculations are a well-known tool to predict crop growth stage or development stage and can be adapted for use in any plant species, including cover crops. Identifying and developing the relationship between …

Potato Processing In The Home: Sustainability And Nutritional Impacts, Aubin Payne

Biological and Agricultural Engineering Undergraduate Honors Theses

Potatoes are the world's fourth most consumed crop. Their versatility and long shelf-life make them a staple food for millions of people worldwide. Still, the increasing consumption of highly processed potato products in developed countries has damaged the public's appreciation of potatoes as a valuable source of essential nutrients. Additionally, as public awareness of environmental sustainability increases, the average consumer is more likely to value processing methods that mitigate environmental damage.

Researchers simulated several home storage and processing conditions to find out how nutrition and environmental impact are affected by the home processing timeline. Then, a nutrient analysis, life cycle …

Climate Change And Conservation Of Milkweed: Evidence Of Extensive Admixture Between Common Milkweed And Poke Milkweed, Elizabeth Davies

Undergraduate Honors Theses

Global climate change can drive many changes in species interactions. One primary way it affects species is by changing climates, causing species to expand their ranges and allowing them to interact with species from whom they were previously isolated. In plants, new species interactions can result in hybridization – the creation of hybrid offspring between two separate species. This hybridization can increase gene flow between the species and lead to introgression, the transfer of genetic material from one species to another through hybrid backcrossing with the parent species. My thesis investigates hybridization in the model system Asclepias (milkweed) by analyzing …

Using A Machine Learning Model To Predict Plant Inflorescences Based Upon Its Soil Microbiome, Luke Denoncourt

Undergraduate Honors Theses

The UN estimates that the global population could reach 9.7 billion by 2050 (United Nations). As a result, the amount of food required to feed humanity is thought to double by 2050 (Ray et al., 2012). Humanity must find a way to increase crop production without increasing fertilizer usage and eutrophication, which can be done using the soil microbiome. Using potted plants with soils inoculated with Pseudomonas alcaligenes, Pseudomonas denitrificans, Bacillus polymyxa, and Mycobacterium phlei, both the shoot and root growth of pea and cotton plants was significantly increased (Egamberdieva & Höflich, 2004). In this study, utilizing a random forest …

Floating Treatment Wetlands For Brackish Waters: Plant Selection And Nutrient Uptake Potential., Andrea Landaverde

All Theses

Brackish water bodies in coastal regions provide critical ecosystem services that support human and environmental health. Anthropogenic activities such as agricultural and industrial activities, construction, urban settlements, and tourism contribute to increased inputs of nitrogen (N) and phosphorus (P) in brackish coastal ecosystems. Excess nutrients can lead to impaired water quality and affect marine organisms. Floating treatment wetlands (FTWs) are a vegetated-base technology used to remove contaminants from water column, that has been mainly studied and applied in freshwater systems. Application of FTWs in brackish systems requires further investigation, as high salinity in brackish waters could result in toxicity to …

Fighting Food Insecurity In New York City: What Role For Street Trees?, Kristen Cooney

Environment and Sustainability Honors Papers

There is growing recognition that urban forests have the potential to combat food insecurity via their edible parts, namely fruits, berries, and nuts. I researched New York City’s street trees, by locating trees with edible parts within food insecure communities, to analyze this potential.

A Comparison Of Natural, Living, And Hardened Shorelines Ability To Prevent Coastal Erosion And Maintain A Healthy Ecosystem, Gabrielle Spellmann

Master's Theses

It is important to find a suitable method to protect the U.S. Gulf Coast shoreline, since its’ low elevation and the Loop current make it vulnerable to sea level rise. I focused on two manmade methods, hardened, and living shorelines, of coastal protection for when the natural marsh suffers excess erosion rates. Living shorelines are a suite of shoreline conservation and restoration techniques that usually involve some sort of hardened structure that dampens wave energy so that the native vegetation behind it can take root and stabilize the shoreline. This study looked at six different sites, all containing a natural, …

Examining Soil Microbial Diversity In Transition Zones Between Corn Fields And Restored Prairie In The Upper Midwest, Anna M. Burns

Scripps Senior Theses

Prairies were once the largest ecosystem in North America, but agriculture and settlement has destroyed up to 99% of their pre-colonization extent. Prairie restorations are a strategy to recover the biodiversity and carbon sequestration functions of these grasslands, but typically occur in isolated strips between agricultural fields. My thesis analyzes how effective prairie restorations in the Liberty Prairie (northeastern Illinois) are at recovering the diversity of the prairie soil microbiome, focusing on verrucomicrobia abundance, alpha diversity, and soil physical characteristics.

Evolution Of Drought And Low Temperature Responses In Temperate Pooideae Grasses: Timings, Determinants, And Intersections, Aayudh Das

Graduate College Dissertations and Theses

Anthropogenically-mediated rises in atmospheric CO2 and global average temperatures is leading to increasingly severe drought and extreme weather events, the latter including unseasonal bouts of low and high temperatures. In order for plant breeders and conservation biologists to predict future responses to global warming, they must understand the ecological and evolutionary processes that shaped plant tolerance to stressful environments in the past. This is particularly true for grasses (Poaceae) that dominate approximately one-third of the Earth's vegetative cover, live in some of the world's harshest terrestrial environments, and are tremendously important, both ecologically and economically. One of the largest subfamily …

Genomic Analysis Of Pollen Grains For Forensic Applications, Luz Kelley

Electronic Theses and Dissertations, 2020-

With over 300,000 plant species on the planet and more than 90% of them relying on pollen for reproduction, palynology, the study of pollen grains plays a vital role in many research fields. One of them is forensic palynology, which uses pollen as a proxy to link individuals or objects to a location or instance. It relies on the fact that (1) pollen is an ever-present feature of the environment; (2) different locations have different pollen signatures, allowing for inference related to spatial tracking; (3) plants bloom at different times, allowing for temporal inference; and (4) pollen is exceptionally durable …

Footprints On The Prairie: Examining The Interlocking Land Histories Of The Liberty Prairie Reserve, Illinois, Anna M. Burns

Scripps Senior Theses

This thesis begins with the local history of the Liberty Prairie, the land where I conducted the ecological field-work that I later discuss in my second thesis on soil microbiome diversity (“Examining Soil Microbial Diversity in Transition Zones Between Corn Fields and Restored Prairie in the Upper Midwest"). I examine the Indigenous histories of the land, and the conflicts between the Bodwéwadmi and Euro-American settlers that resulted in the land being farmed for cattle, corn, and soy for over a hundred and fifty years. I then take a step back and analyze the broader historical contexts of Midwestern Corn Belt …

"Demeter" Soil Monitoring System, Ryan Matthews, Rachel Rummer, Temilolu Fayomi, Alex Fuller

Williams Honors College, Honors Research Projects

The purpose of this project is to develop a soil monitoring system that can remotely sense and relay soil conditions back to a user. The deMETER soil probe, Demeter is the Greek goddess of the harvest, is designed to aid hobbyist gardeners, small-scale farms, and nurseries to monitor their dynamic soil conditions and maximize their harvest. The probe is a self-powered system that can monitor the moisture and essential nutrients of the soil profile to determine which areas should receive water and fertilizer. This would significantly cut water and fertilizer waste. The solution will include an embedded system with sensors …

Response Of Soil Biochemical And Physical Properties To Long Term Prairie Cordgrass And Kura Clover Intercropping System, Vaishnavi Varikuti

Electronic Theses and Dissertations

Prairie cordgrass (Spartina pectinata) (PCG) is a warm-season perennial grass that can be used as a biofuel feedstock and can be grown on marginal lands. Previous studies on intercropping of a perennial legume i.e., kura clover (Trifolium ambiguum) (KC) with PCG can improve soil biochemical properties, increase biomass production, mitigate greenhouse gas (GHG) emissions while reducing the chemical fertilizer requirement. However, there is a lack of evidence about the effects of PCG production on soil biochemical and physical properties during the cropping season and at deeper soil depths in reference to support plant growth, environmental implications and enhance the soil …

Largemouth Bass In The Upper Mississippi River: An Evaluation Of Management Strategies And Understanding Potential Factors Influencing Dynamic Rate Functions, Kylie Beth Sterling

MSU Graduate Theses

The Upper Mississippi River (UMR) supports ecologically and economically important commercial and recreational fisheries. One recreational fishery in the UMR is the Largemouth Bass fishery. Recreational fisheries can be effectively managed using information on population dynamics, though little is known about Largemouth Bass population dynamics in large river ecosystems. Therefore, the objectives of this study were to 1) evaluate recruitment, growth, and mortality of three Largemouth Bass populations in the UMR, specifically within Pools 4, 8, and 13, and 2) to use those estimates of recruitment, growth and mortality to inform exploitation models to evaluate best management practices for each …

Ms Environmental Biology Capstone Project, Dylan Brown

Regis University Student Publications (comprehensive collection)

Chapter 1- Revisiting Tamarisk Invasion in Riparian Ecosystems: An Argument Against Single Species Management of the Southwestern Willow Flycatcher (Empidonax traillii extimus)

Chapter 2- Temporal Trends of Tamarisk Remediation to Native Vegetation Establishment

Chapter 3- Assessing Effectiveness of Tamarisk Removal Treatments Through a Meta Regression Analysis

Chapter 4- Legal Challenges of Tamarisk Removal in the Southwestern United States

Northern Great Plains Saline Sodic Soil Development, Classification, Remediation, And Management., Shaina Westhoff

Electronic Theses and Dissertations

Soil salinity and sodicity are issues of growing concern in the United States (U.S.) and globally. Knowledge gaps for glaciated, dryland salt-affected soils exist because much original salinity and sodicity research focused on irrigated systems. Land managers are being asked to produce food, feed, fiber, and fuel for an expanding global population. The number of land managers and crop advisors who are affected by these soils is increasing. Addressing salinity and sodicity knowledge gaps will be critical for their success. Salinity and sodicity have been impeding crop productivity since the advent of cultivation. Saline and sodic soils form via multiple …