Proteomics is defined as a tool to explore how proteins control and regulate important molecular and physiological processes. Further, peptide-centric approaches, or bottom-up methods, provide more comprehensive coverage of a proteome compared to whole-protein approaches. This body of work assesses the technical feasibility of several bottom-up proteomics technologies applied to Arabidopsis thaliana, including gel-based methods, those that require peptide derivitization, and those that do not. Selected-reaction monitoring (SRM) for targeted proteomics, and data-independent acquisition (MSE) was also evaluated. In addition to assessing the capabilities of these technologies, we then applied them to the context of uncovering new insights into the flavonoid biosynthetic pathway and the auxin and ethylene signaling pathways. Chapter one provides background information related to secondary metabolism, phytohormone signaling, and the status of proteomics in plants. In Chapter 2 and Appendix A, we establish the methodology to apply traditional and DiGE-based 2D-GE strategies to global proteomics in Arabidopsis. Our results suggest that while 2D-GE is applicable to Arabidopsis, there are practical and conceptual limitations that must be understood. Further, our results suggest that pertubations in the flavonoid pathway do not affect the abundance of proteins in Arabidopsis seedlings, roots, or flowers that can be studied using 2D-GE and DiGE. Additionally, we demonstrated the first parallel comparison of the effects of auxin and ethylene on the Arabidopsis root proteome and observed no overlap among the proteins regulated by the two phytohormones, at least for the most abundant proteins observed by 2D-GE. Chapter 3 explores the efficacy of selected reaction monitoring for relative peptide quantification in Arabidopsis roots. Our results suggest that while the technology parallels application in yeast and humans, there are substantial analytical challenges that much be addressed. In Chapter 4 we explore the MSE data acquisition scheme for global proteomics in Arabidopsis. We observe that treatment with exogenous auxin affects the abundance of many proteins representing diverse biological processes. Interestingly, we observe minimal overlap among genes and proteins regulated by exogenous auxin. Appendix B explores the efficacy of iTRAQ labeling for relative peptide quantification in Arabidopsis roots. / Ph. D.

It is our purpose here to investigate the method of solving equations for real roots by Newton's Method and to indicate a generalization arising from this method.

Use of soil amendments at planting is one of the time-honored traditions in horticulture, although their effectiveness has been questioned by many. Recently, humate and humate-based products, generally known as biostimulants, have been marketed to increase transplant success. In this study, three experiments were conducted to examine the effects of soil amendments and biostimulants on post-transplant growth of landscape trees. The first experiment, conducted in a greenhouse, determined the effects of several biostimulant treatments (granular humate, water-soluble humate, liquid humate, liquid humate+ = humic acid, hormones, and vitamins) and fertilizer levels (low, medium, high) on the growth of container-grown Corylus colurna L. (Turkish hazelnut) seedlings. Biostimulants did not increase top growth compared to control treatments, but root growth was increased by granular humate at a medium fertilizer rate. The second experiment examined the effects of biostimulants (granular humate, water-soluble humate, liquid humate+) on the post-transplant root growth and sap-flow of landscape-sized balled and burlapped Acer rubrum L. (red maple) grown in root observation compartments (rhizotrons). Biostimulants did not increase root growth over control treatments, but sap-flow was increased. The third experiment, conducted in the field (Groseclose silt loam soil) investigated the effects of soil amendments (peat, and compost) and biostimulants (granular humate, and liquid humate+) on the post-transplant growth of Crataegus phaenopyrum (Blume) Hara (Washington hawthorn) and red maple transplanted bare-root, and grown under combinations of irrigated vs non-irrigated and fertilized-at-planting vs non-fertilized-at-planting regimes. Hawthorn controls generally had less top growth than the other soil treatments as a whole. No soil treatment was higher than control for top growth of red maple. However, root growth of red maple was highest in the peat-treated trees. Stem diameter and dry mass for the control and compost treatments were higher than the biostimulant treatments in irrigated plots, but no differences were observed in non-irrigated plots. Granular humate-treated trees resulted in higher stem diameter and dry mass than the liquid humate+-treated trees in non-irrigated plots. There were no effects of fertilizer, or irrigation on growth after two growing seasons for either species. / Master of Science

Hairy roots are a syndrome of the plant pathogen Agrobacterium rhizogenes, which induces the aggressive growth of roots in the plants it infects. Hairy roots are shown to have increased production of secondary metabolites when compared to roots that are not transformed, especially when they are exposed to plant signaling hormones called elicitors. Two popular elicitors are Methyl Jasmonate (MeJA) and Salicylic Acid (SA), which are also potent plant signaling compounds involved in plant defense and immunity. Many studies have reported on the secondary metabolites of hairy roots and their production of metabolites after exposure to elicitors. However, there is a gap in current knowledge of how hairy roots and non-transformed roots of Helianthus annuus (the common sunflower) compare in their secondary metabolite profiles, which include the volatile terpenoids they produce. This experiment used solid-phase microextraction gas chromatography-mass spectrometry (SPME GC-MS) to compare the volatile terpenoid profiles of hairy roots and non-transformed roots of H. annuus after their exposure to 0.2 mM MeJA and MeSA, the methyl ester of SA. The experiment identified several differences in the production of volatile compounds across elicitor treatments and time points yet hairy roots largely maintained the properties of their native counterparts. This project provides information on the secondary metabolism and volatile terpenoid profiles of hairy roots and explores the biotechnological applications of such insights.

Drought resistance among genotypes of Port-Orford-cedar (Chamaecyparis lawsoniana (A. Murr.) Pan., Cupressaceae) seedlings was evaluated both in the field and in the greenhouse. Field water potentials (��) of 5-year-old seedlings were measured at two high-elevation plantation sites where summer drought occurs. Measurements of �� were compared to survival two years prior at the same site. The north coastal breeding zone 1 had significantly lower mid-day �� and lower survival than the southern interior breeding zone 6. Percent survival at 3 years was significantly correlated with mid-day ��. A second assessment of drought resistance was performed in the greenhouse on 1-0 seedlings. Root growth potential (RGP) was measured in the winter under non-stress conditions and following a drought in the summer. Differences among breeding zones were opposite in pattern from outplanting measurements of survival and water potential; therefore, RGP may not be a good predictor of drought resistance or survival among different genotypes within a single species. Low-elevation, coastal families had greater root growth than inland, high elevation sources. Greater root growth occurred in seedlings with more shoot mass. Little regional specialization in RGP across the species' range was indicated as there was greater variation among families than among breeding zones. In the summer RGP test following drought, only the two extremes of the range were evaluated; both north coastal and southern interior families showed decreased root growth compared to the winter RGP under non-stress conditions. Despite significantly higher predawn �� in inland, high elevation families, lower elevation coastal families had significantly more roots. Change in chlorophyll fluorescence yield measured on foliage of droughted plants was positively correlated with the absolute value of predawn ��; however, it was not a sensitive predictor of predawn �� (R��=0.06) at the levels used in this study. Lower levels of �� may be necessary to produce severe stress to damage Port-Orford-cedar foliage. / Graduation date: 2003

Graduation date: 1997

Thesis (Ph. D.) in Forest Resources--University of Maine, 2002. / Includes vita. Includes bibliographical references (leaves 216-241).

No description available.

The importance of root systems for soil-based resource acquisition by plants has long motivated researchers to quantify the complexity of root system structures. However, most of those studies proceeded from 2-D spatial data, and thus lacked the relevance of a 3-D analysis. In this project, helical CT scanning was applied to study root systems with an unprecedented level of accuracy, using non-destructive and non-invasive 3-D imaging that allowed for a spatio-temporal analysis. The appropriate CT scan parameters and configuration were determined for root systems of maize seedlings grown in sand and loamy sand. It was found that the soil conditions allowing for better visualization were sand before watering and loamy sand after watering. Root systems were CT scanned and visualized either at a single moment in time or repeatedly on successive days. Complexity analysis was performed by estimating the fractal dimension on skeletonized 3-D images of root systems.

Thesis (M. Sc.)--University of Canterbury, 2006. / Typescript (photocopy). Includes bibliographical references (leaves 100-108). Also available via the World Wide Web.