Life Sciences Commons^™

Machine Learning-Based Soybean Yield Prediction And Optimizing Lidar-Mounted Uav Efficiency, Leticia Santos

LSU Master's Theses

The first chapter of this thesis explores the predictive capabilities of random forests algorithm on datasets obtained from field plot experiments on crop management systems in soybean. Furthermore, the chapter presents a complementary analysis of model performance according to dataset sizes and two techniques on how to impute and deal with missing data. Random forests are being compared with standard statistical techniques such as linear regression on a well-structured, information-rich agronomic experiment. The key findings of this chapter includes the best hyperparameters adjustment and the identification of the dataset threshold for optimal algorithms performance. The second chapter has a research …

Utilizing Soil Sensors To Assess Soil Health And Investigating Cover Crops Impact On Methane Emission, Shailesh Pandit

Electronic Theses and Dissertations

Soil health is influenced by climate change, cultural practices, topography, crop rotations, cover crops, soil parent materials, and soil biota. Interactions between these factors can improve or reduce soil health. This thesis investigates two topics, using soil sensors to provide a rapid assessment of soil health, and the impact of cover crops on soil biological activity and greenhouse gas emissions. Chapter 1 explores the use of two types of sensors to measure apparent electrical conductivity (ECa) and provides examples on the use of these sensors. Even though both sensors measure ECa using different processes, they provide useful information about temporal …

Investigating Birds As Dispersal Vectors Of Litylenchus Crenatae Subsp. Mccannii (Anguinidae), The Nematode Associated With Beech Leaf Disease, Spencer Rock Parkinson

Graduate Theses, Dissertations, and Problem Reports

Beech leaf disease (BLD) is an emerging forest pathogen primarily affecting American beech (Fagus grandifolia, Ehrh.) in North America and has been attributed to tree mortality of sapling sized trees within five to seven years of infection. Symptoms typically occur in regenerating American beech thickets sprouting from roots of trees killed by beech bark disease. Scientists first observed BLD in Ohio in 2012 and currently has spread to 15 states in the USA and one Canadian province. The nematode Litylenchus crenatae subsp. mccannii (Lcm) is highly associated with BLD symptoms, interveinal chlorosis and defoliation of leaves, and is currently …

Ms Environmental Biology Capstone Project, Sarah Luper

Regis University Student Publications (comprehensive collection)

Recreational trails and the presence of invasive species such as Bromus inermis can both disturb grassland community composition. Trails can act as dispersal corridors for plant material, but can also be a source of trampling and compaction. Invasive grasses like Bromus inermis can easily establish in grasslands and decrease species richness by increasing competition. Understanding these effects, this study aims to understand how both the presence of recreational trails as well as the presence of Bromus inermis affect species richness and overall community composition at Two Ponds National Wildlife Refuge. Belt transect sampling took place in fall 2019 and again …

Environmental Biology Masters Capstone, Antonio Gonzalez-Pita

Regis University Student Publications (comprehensive collection)

Human wildlife interactions (HWI) pose a complex challenge for wildlife managers. Human encroachment into wildlife habitat and the growing number of outdoor recreationists are increasing the frequency of contact and conflict, especially in regions such as the Front Range of Colorado. Geographic information systems (GIS), which use a combination of remote sensing and environmental survey data, allow for predictive spatial analyses of where human wildlife interactions are likely to occur. I used publicly reported observations of moose to create spatial predictive maps in a species distribution model framework. Slope and elevation were shown to be the strongest predictors of HWI, …

Assessing Endophyte Frequency Distributions And The Effect Of Epichloë Brachyelytri In The Chemotypic And Genotypic Diversity Of Brachyelytrum Erectum, Rachel Ann Sneed

Theses and Dissertations--Plant Pathology

Seed-transmissible epichloid fungal endophytes are best known for their roles as defensive mutualists in cool-season grasses. Historically, the discovery of fungal endophytes was driven by investigations of plant toxicity to livestock, followed by extensive study of their alkaloids and protection against insects and nematodes. Epichloae can produce four classes of alkaloids: ergot alkaloids, lolines (saturated aminopyrrolizidines), indole–diterpenes, and peramine. It is increasingly evident that these hereditary symbionts have much more diverse chemical profiles both in individual populations and between them. To this end, differences in chemotypic profiles of these symbionts may translate to different evolutionary and environmental advantages across plant …

Exploring The Impact Of Invasive On Grassland Diversity: A Study In Montana, Ella Gaffney

Undergraduate Theses, Professional Papers, and Capstone Artifacts

For the capstone project with the University of Montana Davidson Honors College, I investigated the diversity index of grassland and rangeland plots across the state of Montana. My study, conducted from June to August 2023, includes data collected by my team. The purpose of this research project was testing the hypothesis that the diversity index decreases in plots containing invasive grass species.

During the summer of 2023, the Spatial Analysis Lab surveyed over 1000 plots in rangelands and grasslands across the state of Montana to locate an invasive grass, Ventenata dubia. Data collected includes species identification, ocular estimates of …

Nitrogen Application Timing And Cereal Rye (Secale Cereale L.) Cover Crop Influence Greenhouse Gas Emissions, Graig Reicks

Electronic Theses and Dissertations

Dryland contributions to greenhouse gas (GHG) emissions are increased by N fertilizer applications and high soil water contents. Fertilizer timing and spring growth of cover crops prior to cash crop planting were investigated in separate studies to examine impacts on overall GHG emissions using a near continuous measurement system. There was a significant interaction between N fertilizer rate (0 vs. 224 kg N ha-1 surface-applied as urea) and application date (p= 0.01) for CO2 emissions. This interaction occurred because N fertilizer increased CO2 emissions by 35% for the 21 d interval following early spring application. When application was delayed until …

Developing Machine Learning Models For Selection Of Management Zones, Sravanthi Bachina

Electronic Theses and Dissertations

Soil sampling and analyses play a crucial role in optimizing nutrient management and enhancing crop productivity. However, collecting representative samples across diverse landscapes is challenging due to knowledge gaps about spatial variability of soil properties, large fields, multiple samples, and analysis costs. Collecting soil samples based on the management zones can help farmers gather precise information about soil properties with fewer samples. Recent developments in precision agriculture and machine learning. This study aimed to develop machine learning models that can learn, analyze, and refine landscape and soil properties data for automated selection of soil sampling zones and generating prediction maps. …

Portable X-Ray Fluorescence Spectrometry For Sensing Salinity And Sodicity In Glacial Northern Great Plains Soils With Machine Learning Models, Adam Devlin

Electronic Theses and Dissertations

Saline and sodic soils are an increasing concern across the Northern Great Plains (NGP) due to factors of climate change and land management that are drawing geologically derived salts to the land surface. Traditional laboratory assessments, such as electrical conductivity (EC) and sodium adsorption ratio (SAR), are time and resource consumptive. Portable X-ray fluorescence (PXRF) may be a viable proximal sensing alternative, as it is able to provide elemental data in minutes, in situ or ex situ, and can directly quantify salinity-associated elements like Ca, Mg, and S. PXRF paired with predictive models has proven useful for a range of …

Integrating Early Season Clover Cover Crops As A Living Mulch In Broccoli And Transitional Organic Winter Squash Production In Eastern South Dakota, Alexis Rose Barnes

Electronic Theses and Dissertations

Managing weeds, improving soil health, and reducing the use of plastic mulch continue to be priorities for South Dakota vegetable farmers. Farmers have expressed an interest in integrating cover crops into their farm systems. Clover cover crops used as a living mulch within and along cash crop rows may aid in weed suppression, nitrogen fixation, and prevent soil erosion. However, prior research has shown challenges of incorporating living mulch due to yield decreases. Research conducted in 2022 and 2023 in eastern South Dakota investigated the effects of four clover and four in-row soil management treatments on broccoli and organic winter …

The Hutton Project: Long-Term Agricultural Impacts On Soil Loss And Carbon Dynamics In Eastern South Dakota, Eli Halverson

Electronic Theses and Dissertations

Long-term and intensified agricultural land management has resulted in increased rates of soil erosion and has altered much of the carbon cycle at regional and global scales. Anthropogenic degradation of soil resources is a barrier to sustainable production, soil functioning, and ecosystem services. It is difficult to quantify the scope of pedogenic changes due to the lack of legacy data and short temporal scales. This study utilized decades to century-old soil information to quantify historical soil erosion losses and changes in soil carbon pools of eastern South Dakota soils. The results show that soils in the region have been significantly …

The Effects Of Potassium Fertilization Regime On High Tunnel Tomato Production, Sapana Pandey

Theses and Dissertations--Plant and Soil Sciences

A two-year field experiment (2022-2023) was conducted at the University of Kentucky Horticulture Research Farm in Lexington, KY to study the effects of potassium (K2O) fertilization rates on tomato yield and ripening disorders in determinate and indeterminate varieties (‘BHN-589’ and ‘Big Beef’, respectively). In the first year, K2O rates representing the soil test result-based commercial recommendation (0 lbs/acre) and sequentially greater rates (150, 300, and 450 lbs K2O/acre) were applied. In the second year, K2O rates were increased based on lack of fruit quality response and were 0, 300, 600, and 900 lbs K2O/acre. Leaf tissue nutrients, tomato yield, and …

Evaluation Of Winter Cereal Cover Crops Across Nitrogen Management Stragies For No-Till Corn Production, Robert Nalley

Theses and Dissertations--Plant and Soil Sciences

Rye (Secale cereale L.) is the most popular winter cereal cover crop utilized before corn, but wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) may provide a comparable value due to their similar fibrous root systems. Despite the benefits associated with winter cereal cover crops, drawbacks are possible for the subsequent corn crop. A field study was conducted with three site-years in Kentucky to measure the impact of the three winter cereals across nitrogen (N) management strategies. Wheat produced the most biomass compared with barley or rye cover crops. Wheat and rye needed approximately 100 more …

Evolutionary Origins Of Secondary Growth - The Periderm Perspective: Integrating Evidence From Fossils And Living Plants, Madison A.K. Lalica

Cal Poly Humboldt theses and projects

Periderm is a structural feature with roles in protection of inner plant tissues and wound healing. Knowledge of periderm occurrences in the fossil record and living lineages outside the seed plants is limited and its evolutionary origins remain poorly explored. Here, I review the known taxonomic distribution of canonical periderm (typical ontogenetic stage) and wound periderm (self-repair mechanism). To this sparse body of data I add new observations and experiments on living plant lineages and new occurrences from the fossil record. One of the latter, documented in the new early euphyllophyte species Nebuloxyla mikmaqiana, joins the oldest known periderm …

Building Detailed And Accurate Whole-Plant Concepts: A Morphometrics-Informed Reconstruction Of A Zosterophyll From The Lower Devonian Of Wyoming, Samar R. El-Abdallah

Cal Poly Humboldt theses and projects

The fragmentary state of plant fossils and the modular organization of plants make whole-plant reconstructions of fossil species desirable and feasible. Such reconstructions are key for integrating fossil species in systematic studies. The ca. 410 Ma Beartooth Butte Formation of Wyoming (USA) hosts the only rich Early Devonian plant assemblages in western North America, which fills a major gap in the phytogeography of this interval. I construct a whole-plant concept for a new zosterophyll from the Beartooth Butte Formation based on a detailed morphometric study. More than 600 fragments of the new zosterophyll were observed and 200 of those were …

Characterizing New Plant Fossils With Woody Growth From The Battery Point Formation Of Quebec (Canada), Emma T. Casselman

Cal Poly Humboldt theses and projects

The oldest woody growth has been recognized in several Early Devonian (ca. 410-395 Ma) euphyllophytes. Their taxonomic diversity is difficult to evaluate due to a lack of quantitative methods for comparing plants based on secondary xylem anatomy. In turn, this hinders understanding of their implications for the evolution of plant development. To develop metrics that quantify secondary xylem anatomy and allow for conclusive comparisons, I investigated extant taxa and Early Devonian fossil woody taxa. I developed multiple metrics for quantifying tracheid size as a function of position in the secondary xylem and tested them on a dataset of extant gymnosperms. …

Assessing Relocation Habitats And Assisted Migration Of The Lassics Lupine, An Endangered California Serpentine-Endemic, Caitlyn M. Allchin

Cal Poly Humboldt theses and projects

The Lassics lupine, Lupinus constancei, is a serpentine species endemic to the Lassics Mountains of northern California, listed as critically imperiled and federally endangered. Increased encroachment from reduced fire intervals has led to elevated herbivory from small mammals. While deployment of exclosure cages has decreased negative impacts, diminishing snowpack from shifting climate continues to threaten the Lassics lupine. To locate possible refugia, I evaluated alternative sites for assisted migration. I built a habitat suitability model (HSM) using MaxEnt software and WorldClim variables to predict optimal habitat. I then evaluated aerial imagery, topography, and geology to identify areas for microhabitat …

Environmental Implications Of Modern Food Production: An Analysis For The Conscious Consumer, Jessica T. Coming

Cal Poly Humboldt theses and projects

This project explores the pathways by which agriculture affects the environment and determines which foods have the greatest climate, water, and land impacts. Agricultural effects on the environment are extensive, from loss of habitat and declines in regional biodiversity to disruption of global nutrient cycles and climate change. Global food production accounts for 26-34% of annual anthropogenic greenhouse gas emissions, makes up 38-46% of habitable land, and is responsible for 70% of freshwater extraction. The effect of agriculture on the environment is most significantly dictated by what type of food is being produced. Animal-based food products consistently have the highest …

Quantitative Trait Loci Influencing Elemental Content In Grapevine Leaves, Jesse L. Krokower

MSU Graduate Theses

In grapevine, the influence of the plant’s elemental composition (the ionome) on fruit and wine quality is well established, but its genetic underpinnings have received limited scientific attention. In this study, I analyzed the leaf ionome of 131 interspecific F1 hybrid progeny plants from a cross between a Vitis rupestris Scheele (♀) and a Vitis riparia Michx (♂) parents, which were replicated in four different environments: Southwest Missouri, Central Missouri, South Dakota, and New York. I sampled leaves at three different times during the growing season at all four locations and had the concentration of 20 elements measured using ICP-MS. …

Investigating The Impacts Of Drought On Turfgrass (Festuca Arundinacea) Chlorophyll-A Fluorescence Emission, Ayanna S. Hatton

Honors Projects

When photons from sunlight are absorbed by plants, they can take paths of photosynthesis, fluorescence, or energy dissipation. Instruments to quantify fluorescence have expanded in scale to allow measurements from satellites and flux towers using Solar-Induced Chlorophyll Fluorescence (SIF). Studies have found a positive correlation between SIF and gross primary productivity (GPP; representative of photosynthesis), suggesting SIF is a proxy for GPP. This conclusion encourages the use of SIF to inform decisions about carbon budgets and responding to climate change. Studies of fluorescence on the single-leaf scale have revealed that SIF measurements do not account for all variables nor is …

A Histological Investigation Of Arceuthobium Pusillum Infections In Picea Rubens And Picea Glauca, Sade K. Mcclean

Honors Projects

Arceuthobium pusillum is a hemiparasite that infects select Picea species. The hosts of A. pusillum do not experience the same symptoms of infection. A. pusillum infections are more fatal to P. marinara, and P. glauca. P. rubens, on the other hand, can survive longer with sustained infection. This presents itself as a contemporary issue because P. glauca, one of the parasite’s most vulnerable hosts, was untethered from ecological competition when old growth forests were subjected to large scale anthropogenic disturbances. These disturbances allowed P. glauca to proliferate, with A. pusillum following. A deeper understanding of the host-species specific …

Quantifying The Ecological Effects Of Salix Fragilis On Riparian Habitat In Kittitas County, Washington, Landon Shaffer

All Master's Theses

Invasive species threaten plant community structure and function globally. Riparian areas, the zone near streams where water influences vegetation, are especially sensitive to invasive species colonization, suffering large-scale shifts in community composition. Salix fragilis (crack willow) is a nonnative riparian species abundant in the lower elevation tributaries of central Washington. Some speculate whether this willow should be listed as invasive in Washington, despite a lack of regional supporting evidence. I studied riparian communities dominated by either S. fragilis or native species in the Kittitas Valley and measured biodiversity, quantified differences in solar attenuation, and compared leaf decomposition rates to learn …

Habitat And Demography Of The Ozark Chinquapin (Castanea Ozarkensis) At Roaring River State Park In Barry County, Missouri, Danielle Evilsizor

Electronic Theses & Dissertations

The Ozark chinquapin, Castanea ozarkensis Ashe, is a chestnut tree with a range concentrated in the Interior Highlands of North America. Like other North American members of Castanea, it was reduced from an overstory tree to an understory shrub by the invasive chestnut blight fungus (Cryphonectria parasitica [Murrill] M.E. Barr) during the early 20^th century. However, relatively little is known about the habitat of this species or its health and reproductive capability post chestnut blight. Chapter one of this study analyzed the habitat of this species through a random forest species distribution model (SDM) to predict where …

Freezing Tolerance Of Herbaceous Legumes Within Southwestern Ontario: Evidence Of Disproportionate Freezing Sensitivity, Samuel L. Rycroft

Electronic Thesis and Dissertation Repository

Legumes (Fabaceae) represent a diverse and ecologically significant plant taxon; most described legumes form mutualisms with diazotrophic rhizobia, potentially fixing substantial quantities of nitrogen within habitats where they are well-established. Stressors causing lethal or sub-lethal impacts in legumes or rhizobial symbionts may therefore impact the nitrogen dynamics of such habitats. In recent decades, variability of winter temperatures, precipitation, and soil freeze-thaw cycling has increased in temperate regions. Without adequate snow cover to insulate roots and shoot bases, herbaceous plants will likely be exposed to more frequent or severe freezing. In southwestern Ontario, a pattern of disproportionate freezing sensitivity relative to …

Addressing Water Hyacinth (Pontederia Crassipes) Impacts On Aquatic Biota In Lake Okeechobee, Joseph Salerno

All HCAS Student Capstones, Theses, and Dissertations

The incursion of water hyacinth, Pontederia crassipes in Lake Okeechobee has resulted in management systems to be implemented to reduce the coverage of the invasive macrophyte. Its residence in the Lake Okeechobee ecosystem and the effects it has on organisms in the lake, whether it be positive or harmful is unknown. This study attempted to assess the potential effects that water hyacinth has on aquatic biota in Lake Okeechobee. Biotic data were collected on open water, water hyacinth covered, and native vegetation covered habitats via hook-and-line fishing, electrofishing, baited minnow traps, and the sampling of plant roots over a thirteen-month …

Evaluating Habitat Use By Nekton In Widgeon Grass (Ruppia Maritima), Shoal Grass (Halodule Wrightii), And Unvegetated Bottom Habitats In The Grand Bay National Estuarine Research Reserve, Jessica Woodall

Master's Theses

Seagrass beds support high biodiversity and animal abundance, serve as feeding grounds for a variety of animals, offer shelter from predation, and act as a nursery habitat for juveniles. The species composition of seagrass beds can impact their use as habitat by animals. Two common species of seagrass in the Gulf of Mexico are Ruppia maritima (widgeon grass) and Halodule wrightii (shoal grass). The shallow coastal waters of the Grand Bay National Estuarine Research Reserve (NERR) support both species, but the use of each seagrass as habitat by nekton is poorly understood, which can limit management decision-making. Nekton communities were …

Characterization Of Radiotolerance In Potato And Development Of A Gamma Radiation Phytosensor., Robert Graham Sears

Doctoral Dissertations

As humans pursue space travel and nuclear energy, the risk of harm from ionizing radiation increases. On Earth or in space, plants are essential to our personal and environmental health. Plants serve as sentinels, bioremediators and food sources in areas of high ionizing radiation, therefore it is essential to understand how ionizing radiation affects plant biology. This work aimed to understand plant responses to ionizing radiation in the potato chassis and apply that knowledge to generate novel phenotypes for nuclear energy and space applications. The first gamma radiation phytosensor was developed for monitoring at standoff distances greater than three meters. …

Characterization Of Lignin Structural Variability And The Associated Application In Genome Wide Association Studies, Nathan D. Bryant

Doctoral Dissertations

Poplar (Populus sp.) is a promising biofuel feedstock due to advantageous features such as fast growth, the ability to grow on marginal land, and relatively low lignin content. However, there is tremendous variability associated with the composition of biomass. Understanding this variability, especially in lignin, is crucial to developing and implementing financially viable, integrated biorefineries. Although lignin is typically described as being comprised of three primary monolignols (syringyl, guaiacyl, p-hydroxyphenyl), it is a highly irregular biopolymer that can incorporate non-canonical monolignols. It is also connected by a variety of interunit linkages, adding to its complexity. Secondary cell wall …

Regulation Of Protein Synthesis In Arabidopsis Thaliana Through A Bioinformatic And Mathematical Lens, Ricardo Andres Urquidi Camacho

Doctoral Dissertations

Organisms exist under constantly varying environmental and internal conditions, which necessitate the differential regulation of gene expression. To synthesize proteins, the ribosome translates the information encoded in the nucleotide sequence of an mRNA into the final, functional amino acid sequence. Knockouts of ribosomal proteins lead to lethality. One such protein is the ribosomal protein 6 of the small subunit (eS6/RPS6). We confirmed that the knockout of either one of two eS6 paralogs in Arabidopsis leads to stunted growth and chlorosis. Here, these phenotypes have been further characterized in seedlings by precisely quantifying the ribosome loading of mRNAs as well as …