Development in multicellular organisms relies on establishing and maintaining gene expression profiles that give cells identity. Transcription factors establish gene expression profiles by integrating positional, temporal, and environmental cues to regulate genes essential for a cell's identity. These signals are often short lived while the differentiated state may persist for a long time. Epigenetic factors maintain these gene expression profiles by making heritable chemical alterations to target gene chromatin to stabilize transcriptional patterns. Here we explore the evolution and function of an epigenetic regulator, the Polycomb Repressive Complex 2 (PRC2), and a transcription factor, ASYMMETRIC LEAVES 1 (AS1) , in the lower eudicot Aquilegia. PRC2 is an important and deeply conserved epigenetic regulator, which is critical to many plant developmental processes, including the regulation of major developmental transitions and lateral organ development. We find that Aquilegia has a relatively simple complement of PRC2 genes that are expressed throughout development. Contrary to findings in other plant species, two members of the Aquilegia PRC2, AqSWN and AqCLF, are not imprinted in Aquilegia endosperm. Using virusinduced gene silencing (VIGS), we determined that Aquilegia PRC2 regulates aspects of lateral organ development, including branching within the leaf and lamina expansion, along with caroteinoid production in floral organs. PRC2 targeting of several floral MADS box genes may be conserved in Aquilegia, but other known targets such as the class I KNOX gene are not. AS1 is a transcription factor that plays a conserved role in controlling differentiation and polarity of lateral organs. In species with simple leaves, AS1 promotes cell determination by suppressing the expression of the class I KNOX genes in leaf primordia and regulates abaxial-adaxial polarity in the developing leaf. However, in species with compound leaves, KNOX genes and AS1 often work together to control leaflet initiation and arrangement. In Aquilegia, AqAS1 appears to primarily contribute to proper regulation of class I KNOX genes with a more minor role in leaflet polarity and positioning. Most interestingly, these combined datasets suggest that contrary to the widely held model, class I KNOX genes are neither necessary nor sufficient for leaf complexity in Aquilegia.

Temperate Midwestern oak savannas are considered imperiled ecosystems with < 1 % remaining since the time of European settlement and are identified as critical areas for preservation. Restoration of Midwestern oak savannas is challenging due to the lack of accurate historical data, few intact remnants remaining to study, and lack of restoration ecology studies. A plant trait-based approach was used to evaluate the ability of six C3 and three C4 native bunchgrasses to restore functionality to a remnant savanna–woodland of the Bluegrass Region of Kentucky. The response and effect framework was used to assess the response of the nine native grasses according to the habitat filters of interannual precipitation, inter- vs. intra-specific competition, and simulated grazing. The effect traits associated with plant-soil nitrogen and carbon cycling were also assessed. The response traits of interannual competition and inter- vs. intra-specific competition along with the effect traits plant-soil nitrogen and carbon cycling were measured in a monoculture experiment conducted at Griffith Woods WMA. The simulated grazing or clipping experiment was conducted over three months in a heated greenhouse experiment. Four of the C3 species were of the genus Elymus which had significant differences in life history traits compared to the other species and made them particularly well adapted to the Bluegrass Savanna-Woodland. The Elymus species were not well adapted to the most intense clipping treatment. For the other two C3 species, C. latifolium would be a better competitor than D. clandestinum under normal conditions. D. clandestinum had the most number of plastic traits and was the only species to exhibit all three grazing strategies. Comparing the C4 species, T. flavus and P. anceps grew well in the monoculture but A. virginicus did not. The life history traits of A. virginicus does not make this species a good candidate for restoration at this site. The three C4 species were well adapted to clipping. The results of this study suggest that the C3 species, particularly the Elymus, are well adapted to the eutrophic mesic conditions of the Bluegrass Savanna-Woodland, and that the C4 species are better adapted to disturbance.

Soybean [Glycine max (L.) Merr.] is an important crop worldwide. It has been widely consumed for protein, oil and other soy products. To develop soybean cultivars with greater resistance against pests and improved meal quality, it is important to elucidate the molecular bases of these traits. This dissertation aims to investigate the biochemical and biological functions of soybean genes from four gene families, which are hypothesized to be associated with soybean defense against pests and soybean meal quality. There are three specific objectives in this dissertation. The first one is to determine the function of components in the salicylic acid (SA) signaling pathway in soybean resistance against soybean cyst nematode (Heterodera glycines, SCN). The second one is to determine whether insect herbivory induce the emission of volatiles from soybean, and if so, how these volatiles are biosynthesized. The third objective is to identify and characterize soybean mannanase genes that can be used for the improvement of soybean meal quality. The soybean genome has been fully sequenced, which provides opportunities for cross-species comparison of gene families of interest and identification of candidate genes in soybean. The cloned cDNAs of putative genes were expressed in Escherichia coli to produce recombinant enzymes. Through biochemical assays, these proteins were proved to be soybean salicylic acid methyltransferase (GmSAMT1), methyl salicylate esterase (GmSABP2-1), α[alpha]-farnesene synthase (GmTPS1) and E-β[beta]-caryophyllene synthase (GmTPS2), and endo-β[beta]-mannanase (GmMAN1). Through a transgenic hairy root system harboring overexpression of GmSAMT1 and GmSABP2-1, both of these two genes were evaluated for their biological function related to resistance against SCN. The results showed that the over-expression of GmSAMT1 and GmSABP2-1 in the susceptible soybean background lead to enhanced resistance against SCN. Among four putative soybean mannanase genes, one gene was cloned and characterized. GmMAN1 showed the endo-β[beta]-mannanase hydrolyse activity and can hydrolyze cell walls isolated from soybean seeds. In summary, using comparative and functional genomics, a number of genes involved in soybean defense and meal quality were isolated and characterized. This study provides novel knowledge and molecular tools for the genetic improvement of soybean for enhanced resistance and improved meal quality.

The symbiosis between plants of the legume family and nitrogen-fixing rhizobia underpins global food security. Legume crops are a major source of protein in human diets, either directly or indirectly as feed for livestock. Application of inoculant rhizobial strains is common practice in many areas, as plant growth is often nitrogen limited and the symbiosis can significantly enhance yields. However, rhizobial strains and outcomes of the symbiosis vary widely. This variation has also been studied by evolutionary biologists interested in the stability of mutualisms. They proposed that plants may prevent establishing symbioses with ineffective strains (partner choice), or provide them with fewer resources (sanctioning). I studied both mechanisms, combining modelling and experimental approaches. Mathematical modelling was used to predict how plants should allocate resources to maximise growth rates, depending on rhizobial nitrogen provision and carbon requirements and on soil nitrogen conditions. The use of marked mutant strains – easily distinguishable and differing in a single rhizobial characteristic – overcame previous experimental difficulties. It was found that pea (Pisum sativum L.) plants are not able to exert partner choice, but do sanction in a more complex way than was previously established. In line with model predictions, resources were preferentially allocated to the single – best available – strain, so that resources allocated to an intermediate-fixing strain depended on whether or not a strain providing more nitrogen was available. Contrary to model predictions, there was no indication of discrimination based on rhizobial carbon requirements. The results cannot be explained by resource allocation in proportion to nitrogen received, and indicate systemic integration of information from different nodules. I formulate a hypothesis about the underlying plant regulatory mechanisms, and discuss implications of the results for selecting inoculant strains and enhancing yields in the field. Future work will rely on further integration of theoretical and applied methods and perspectives.

abstract: Climate change has the potential to affect vegetation via changes in temperature and precipitation. In the semi-arid southwestern United States, heightened temperatures will likely lead to accelerated groundwater pumping to meet human needs, and altered storm patterns may lead to changes in flood regimes. All of these hydrologic changes have the potential to alter riparian vegetation. This research, consisting of two papers, examines relationships between hydrology and riparian vegetation along the Verde River in central Arizona, from applied and theoretical perspectives. One paper investigates how dominance of tree and shrub species and cover of certain functional groups change along hydrologic gradients. The other paper uses the Verde River flora along with that river's flood and moisture gradients to answer the question of whether functional groups can be defined universally. Drying of the Verde River would lead to a shift from cottonwood-willow streamside forest to more drought adapted desert willow or saltcedar, a decline in streamside marsh species, and decreased species richness. Effects drying will have on one dominant forest tree, velvet ash, is unclear. Increase in the frequency of large floods would potentially increase forest density and decrease average tree age and diameter. Correlations between functional traits of Verde River plants and hydrologic gradients are consistent with "leaf economics," or the axis of resource capture, use, and release, as the primary strategic trade-off for plants. This corresponds to the competitor-stress tolerator gradient in Grime's life history strategy theory. Plant height was also a strong indicator of hydrologic condition, though it is not clear from the literature if plant height is independent enough of leaf characteristics on a global scale to be considered a second axis. Though the ecohydrologic relationships are approached from different perspectives, the results of the two papers are consistent if interpreted together. The species that are currently dominant in the near-channel Verde River floodplain are tall, broad-leaf trees, and the species that are predicted to become more dominant in the case of the river drying are shorter trees or shrubs with smaller leaves. These results have implications for river and water management, as well as theoretical ecology. / Dissertation/Thesis / M.S. Plant Biology 2011

xii, 83 p. : ill. A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / My dissertation research has centered on understanding how nuclear encoded proteins affect chloroplast gene expression in higher plants. I investigated the functions of three proteins that belong to families whose members function solely or primarily in mitochondrial and chloroplast gene expression; the Whirly family (ZmWHY1) and the pentatricopeptide repeat (PPR) family (ZmPPR5 and ZmPPR10). The Whirly family is a plant specific protein family whose members have been described as nuclear DNA-binding proteins involved in transcription and telomere maintenance. I have shown that ZmWHY1 is localized to the chloroplast where it binds nonspecifically to DNA and also binds specifically to the atpF group II intron RNA. Why1 mutants show reduced atpF intron splicing suggesting that WHY1 is directly involved in atpF RNA maturation. Why1 mutants also have aberrant 23S rRNA metabolism resulting in a lack of plastid ribosomes. The PPR protein family is found in all eukaryotes but is greatly expanded in land plants. Most PPR proteins are predicted to localize to the mitochondria or chloroplasts where they are involved in many RNA-related processes including splicing, cleavage, editing, stabilization and translational control. Our results with PPR5 and PPR10 suggest that most of these activities may result directly from the unusually long RNA binding surface predicted for PPR proteins, which we have shown imparts two biochemical properties: site-specific protection of RNA from other proteins and site-specific RNA unfolding activity. I narrowed down the binding site for PPR5 and PPR10 to ∼45 nt and 19 nt, respectively. I showed that PPR5 contributes to the splicing of its group II intron ligand by restructuring sequences that are important for splicing. I used in vitro assays with purified PPR10 to confirm that PPR10 can block exonucleolytic RNA decay from both the 5' and 3' directions, as predicted by prior in vivo data. I also present evidence that PPR10 promotes translation by restructuring its RNA ligand to allow access to the ribosome. These findings illustrate how the unusually long RNA interaction surface predicted for PPR proteins can have diverse effects on RNA metabolism. This dissertation includes both previously published and unpublished co-authored material. / Committee in charge: Eric Selker, Chairperson, Biology; Alice Barkan, Advisor, Biology; Victoria Herman, Member, Biology; Karen Guillemin, Member, Biology; J. Andrew Berglund, Outside Member, Chemistry

xviii, 160 p. : ill. (some col.) / Salt marshes are intertidal communities dominated by halophytic vascular plants that are subjected periodically to tidal inundation. These species have developed various adaptations to this stress, including tolerances of fluctuating salinity, extended periods of inundation and intervals of anoxic conditions. The marshes are divided into zones of different plant communities based on species' tolerances of ambient estuarine conditions. Abiotic stresses change along the estuarine salinity gradient (marine to riverine), potentially altering development and composition of plant communities. Abiotic gradients associated with tides are not the only factors that contribute to development of plant community composition in salt marshes. Both negative (competition) and positive (facilitation) biological interactions are also important. Factors that influence community structure in salt marshes, particularly on the eastern North American seaboard, have been well studied. In contrast, salt marshes along the Oregon coast are smaller and more discrete and have received comparatively little attention. The community structure and seed bank composition of six marshes along an estuarine salinity gradient were evaluated. Four major community types dominated marshes that varied in the salinity of inundating tidal waters. Community types were relatively consistent throughout the estuary despite the distances between the marshes. Unlike the emergent plant communities, marsh seed bank composition was more similar within a marsh than within a community type. The low and high marsh community types were separated by a distinct boundary in the marine marshes. Although abiotic factors influence the physical separation of communities, competitive interactions commonly determine the upper limit of a species. In Metcalf marsh, however, the upper boundary for two dominant low marsh species was not determined by competition with the high marsh dominant species. Positive biotic interactions between seedlings and existing vegetation in a community are important factors in determining species distributions, particularly in stressful estuarine environments. In salt marshes, where abiotic stress can be harsh, presence of existing vegetation can ameliorate these conditions and enhance germination and seedling establishment. However, interaction between seedlings and the emergent marsh community was highly competitive, though germination of one species was enhanced in the presence of existing vegetation. This dissertation includes un-published co-authored material. / Committee in charge: Dr. Scott Bridgham, Chairperson; Dr. Richard Emlet, Advisor; Dr. Steven Rumrill, Member; Dr. Alan Shanks, Member; Dr. Gregory Retallack Outside Member

abstract: Amsonia kearneyana is an endangered herbaceous plant endemic to a small area of the Baboquivari Mountains in southern Arizona. It exists in two distinct habitat types: 1) along the banks of a lower elevation ephemeral stream in a xeroriparian community, and 2) a higher elevation Madrean oak woodland on steep mountain slopes. Half of the largest known montane population (Upper Brown Canyon) was burned in a large fire in 2009 raising questions of the species capacity to recover after fire. This research sought to understand how the effects of fire will impact A. kearneyana's ability to recruit and survive in the burned versus unburned areas and in the montane versus xeroriparian habitat. I compared population size, abiotic habitat characteristics, leaf traits, plant size, and reproductive output for plants in each habitat area for three years. Plants in the more shaded unburned montane area, the most populated population, presented with the most clonal establishment but produced the least amount of seeds per plant. The unshaded burned area produced more seeds per plant than in the unburned area. Lower Brown Canyon, the xeroriparian area, had the fewest plants, but produced the most seeds per plant while experiencing higher soil temperature, soil moisture, photosynthetically active radiation, and canopy cover than the montane plants. This could indicate conditions in Lower Brown Canyon are more favorable for seed production. Despite ample seed production, recruitment is rare in wild plants. This study establishes germination requirements testing soil type, seed burial depth, temperature regimes, and shade treatments. Trials indicate that A. kearneyana can germinate and grow in varied light levels, and that soil type and seed burial depth are better predictors of growth than the degree of shade. Finally, this study examined the law, regulation, policy, and physiological risks and benefits of a new management strategy and suggests that "conservation by dissemination" is appropriate for A. kearneyana. Conservation by dissemination is the idea that a protected plant species can be conserved by allowing and promoting the propagation and sale of plants in the commercial market with contingent collection of data on the fate of the sold individuals. / Dissertation/Thesis / Masters Thesis Plant Biology 2015

abstract: Though cities occupy only a small percentage of Earth's terrestrial surface, humans concentrated in urban areas impact ecosystems at local, regional and global scales. I examined the direct and indirect ecological outcomes of human activities on both managed landscapes and protected native ecosystems in and around cities. First, I used highly managed residential yards, which compose nearly half of the heterogeneous urban land area, as a model system to examine the ecological effects of people's management choices and the social drivers of those decisions. I found that a complex set of individual and institutional social characteristics drives people's decisions, which in turn affect ecological structure and function across scales from yards to cities. This work demonstrates the link between individuals' decision-making and ecosystem service provisioning in highly managed urban ecosystems. Second, I examined the distribution of urban-generated air pollutants and their complex ecological outcomes in protected native ecosystems. Atmospheric carbon dioxide (CO₂), reactive nitrogen (N), and ozone (O₃) are elevated near human activities and act as both resources and stressors to primary producers, but little is known about their co-occurring distribution or combined impacts on ecosystems. I investigated the urban "ecological airshed," including the spatial and temporal extent of N deposition, as well as CO₂ and O₃ concentrations in native preserves in Phoenix, Arizona and the outlying Sonoran Desert. I found elevated concentrations of ecologically relevant pollutants co-occur in both urban and remote native lands at levels that are likely to affect ecosystem structure and function. Finally, I tested the combined effects of CO₂, N, and O₃ on the dominant native and non-native herbaceous desert species in a multi-factor dose-response greenhouse experiment. Under current and predicted future air quality conditions, the non-native species (<italic>Schismus arabicus</italic>) had net positive growth despite physiological stress under high O₃ concentrations. In contrast, the native species (<italic>Pectocarya recurvata</italic>) was more sensitive to O₃ and, unlike the non-native species, did not benefit from the protective role of CO₂. These results highlight the vulnerability of native ecosystems to current and future air pollution over the long term. Together, my research provides empirical evidence for future policies addressing multiple stressors in urban managed and native landscapes. / Dissertation/Thesis / Doctoral Dissertation Plant Biology 2014

As pesquisas com os peptídeos hormonais de plantas se iniciaram na década de noventa com a descoberta da sistemina. Hoje existem diversos peptídeos identificados, e alguns deles já em avançado estágio de caracterização. O envolvimento desta classe de moléculas em diversas funções básicas e específicas da biologia dos vegetais despertou o interesse da comunidade científica. Dentre os peptídeos em fase de caracterização, destacam-se os representantes da família RALF. Os peptídeos RALF estão presentes em basicamente todo o reino vegetal, desde o musgo Physcomitrela pattens até as plantas superiores mono e dicotiledôneas. A conservação destes peptídeos no reino vegetal sugere um importante papel na fisiologia vegetal, e evidências recentes indicam a participação de RALF em processos básicos do desenvolvimento das plantas. O mecanismo pelo qual o peptídeo RALF atua e é percebido pela célula constitui etapa fundamental para sua caracterização funcional. Para tanto, no presente trabalho foram empregadas técnicas para identificação de proteínas de interação com RALF. Os resultados indicam que este peptídeo possivelmente tem sua atividade regulada pelo íon cálcio, através da interação com uma proteína de ligação a cálcio que, assim como o RALF, é secretada para o apoplasto. Estes dados colocam RALF em um cenário até o momento inédito no mecanismo de ação hormonal em plantas. A exemplo de animais e leveduras, observou-se também que o processamento de RALF ocorre em um sítio dibásico. A mutação de um dos aminoácidos deste sítio foi suficiente para impedir processamento do peptídeo in vivo e in vitro. A utilização de extratos protéicos da fração microsomal de Arabidopsis no ensaio in vitro indica que esta atividade é desempenhada por uma protease presente no sistema de endomembranas celular, provavelmente da classe das convertases. Os resultados publicados marcam o início dos estudos de caracterização do processamento de prohormônios em plantas. / The peptide hormone research has begun during the 90s decade with the systemin discovery. Nowadays several peptides have already been identified, and some of them are further characterized. The involvement of these molecules with a range of basic and specific biological functions has raised the scientific communitys interest. Among the peptides being studied, the RALF family is particularly intriguing. The RALF peptides can be found throughout the plant kingdom, from the moss Physcomitrella patens to the mono and dicot plant groups. The conserved occurrence of these peptides along the plant kingdom suggests an important role in the plant physiology field. Recent evidences indicate that RALF plays a role in basic mechanisms of plant development. The RALF mechanism of action and its perception by the cell are fundamental information in order to characterize this peptide function. In the present work experiments to identify RALF interacting proteins were employed. The results indicate that RALF peptides activity is possibly regulated by the calcium ion. This regulation is mediated by the interaction with a calcium binding protein. This calcium binding protein was found to be secreted to the apoplast. Presented data suggests that RALF is regulated by a mechanism never described before in the plant hormone research field. As previously described in animals and yeast the RALF propeptide processing takes place in a dibasic site. A single amino acid site specific mutation disrupted peptide processing in vivo and in vitro. The correct processing is mediated by proteases of the Arabidopsis microsomal fraction. This processing seems to occur at the endomembrane system, possibly catalized by a convertase class enzyme. The published results points the beginning of the peptide processing studies in plants.