Plant Sciences Commons^™

Leveraging Mass Spectrometry-Based Proteomics And Post-Translational Modifications For System-Wide Understanding Of Bioenergy Plants And Their Environment, Him K. Shrestha

Doctoral Dissertations

Bioenergy research focuses on utilizing renewable biomass feedstocks to produce biofuels and bioproducts to address growing concerns about energy security and climate change. To better understand the details of bioenergy crop production and conversion to bioproducts, it is essential to characterize bioenergy plants and their environments at a molecular systems level. Mass spectrometry has emerged as a promising technique for detailed proteomic information, including post-translational modifications (PTMs), of molecular processes and cellular functions of biological systems. In this dissertation, proteomic approaches have been optimized and implemented to deepen our understanding of the interaction of plants and their environment in a …

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 …

Genome Evolution In The Salicaceae: Genetic Novelty, Horizontal Gene Transfer, And Comparative Genomics, Timothy Yates

Doctoral Dissertations

Genome evolution is a powerful force which shapes genomes over time through processes like mutation, horizontal transfer, and sexual reproduction. Although questions which aim to explore genome evolution are broad, they are all understood through the discovery and comparison of genetic variation. For example, genetic diversity may explain differences in phenotypes, etiology of disease, and is essential for phylogenomic analysis. Recently, the democratization of next generation and third generation DNA sequencing technologies have allowed for genomics to produce large amounts of sequence data. This has facilitated the capture of genetic variation at species and population scales.

Populus and Salix are …

Native Soil Virus Abundance, Composition, And Mobility Under Natural And Managed Agricultural Conditions, Regan Mcdearis

Doctoral Dissertations

Soil viruses are ubiquitous in the environment and important for their influence on host community composition and function. Viral infection influences host evolution, metabolism, function, diversity, community evenness, and more. As host bacteria play critical roles in agricultural systems, including nutrient cycling and soil aggregate formation, the influence which soil viruses have on their hosts makes them key players in these systems. However, many important questions remain regarding virus abundance and distribution under human imposed and natural conditions in agricultural systems. Understanding how these conditions impact virus abundance, transport, and community structure is critical for a broader understanding of soil …

Multi-Omic Systems Biological Analysis Of Host-Microbe Interactions, Piet Jones

Doctoral Dissertations

Systems biology offers the opportunity to understand the complex mechanisms of various biological phenomena. The wealth of data that is produced, at an increasing rate, provides the potential to meet this opportunity. Here we take an applied approach to integrate multiple omic level data sources in order to generate biologically relevant hypotheses. We apply a novel analysis pipeline to model both, in concert, the microbial and transcriptomic signature from COVID-19 positive patients. We show patients may suffer from an increased microbial burden, with an increased pathogen potential. Gene expression evidence further shows patients may exhibit a compromised barrier immunity, owing …

Community Assembly And Stress Response Of Grassland Phyllosphere Bacteria, Emily Bechtold

Doctoral Dissertations

Grasslands are an important ecosystem with potential to help stabilize food security and reduce greenhouse gas levels. As global temperatures rise, weather patterns are predicted to drastically change. The resulting increase in intensity, duration, and frequency of drought in important grassland areas will not only affect agricultural production, but also increase grassland susceptibility to fire, disease, and soil erosion. Thus, developing ways to sustainably promote grassland health and production is essential to increase food security and reduce environmental strain. Microbes in the phyllosphere, or aerial surface of plants, promote host fitness through phytohormone and nutrient production, increased stress tolerance, and …