abstract: Over the past decade, several high-value proteins have been produced using plant-based transient expression systems. However, these studies exposed some limitations that must be overcome to allow plant expression systems to reach their full potential. These limitations are the low level of recombinant protein accumulation achieved in some cases, and lack of efficient co-expression vectors for the production of multi-protein complexes. This study report that tobacco Extensin (Ext) gene 3' untranslated region (UTR) can be broadly used to enhance recombinant protein expression in plants. Extensin is the hydroxyproline-rich glycoprotein that constitutes the major protein component of cell walls. Using transient expression, it was found that the Ext 3' UTR increases recombinant protein expression up to 13.5- and 6-fold in non-replicating and replicating vector systems, respectively, compared to previously established terminators. Enhanced protein accumulation was correlated with increased mRNA levels associated with reduction in read-through transcription. Regions of Ext 3' UTR essential for maximum gene expression included a poly-purine sequence used as a major poly-adenylation site. Furthermore, modified bean yellow dwarf virus (BeYDV)-based vectors designed to allow co-expression of multiple recombinant genes were constructed and tested for their performance in driving transient expression in plants. Robust co-expression and assembly of heavy and light chains of the anti-Ebola virus monoclonal antibody 6D8, as well as E. coli heat-labile toxin (LT) were achieved with the modified vectors. The simultaneous co-expression of three fluoroproteins using the single replicon, triple cassette is demonstrated by confocal microscopy. In conclusion, this study provides an excellent tool for rapid, cost-effective, large-scale manufacturing of recombinant proteins for use in medicine and industry. / Dissertation/Thesis / Ph.D. Plant Biology 2012

abstract: The Arizona State University Herbarium began in 1896 when Professor Fredrick Irish collected the first recorded Arizona specimen for what was then called the Tempe Normal School - a Parkinsonia microphylla. Since then, the collection has grown to approximately 400,000 specimens of vascular plants and lichens. The most recent project includes the digitization - both the imaging and databasing - of approximately 55,000 vascular plant specimens from Latin America. To accomplish this efficiently, possibilities in non-traditional methods, including both new and existing technologies, were explored. SALIX (semi-automatic label information extraction) was developed as the central tool to handle automatic parsing, along with BarcodeRenamer (BCR) to automate image file renaming by barcode. These two developments, combined with existing technologies, make up the SALIX Method. The SALIX Method provides a way to digitize herbarium specimens more efficiently than the traditional approach of entering data solely through keystroking. Using digital imaging, optical character recognition, and automatic parsing, I found that the SALIX Method processes data at an average rate that is 30% faster than typing. Data entry speed is dependent on user proficiency, label quality, and to a lesser degree, label length. This method is used to capture full specimen records, including close-up images where applicable. Access to biodiversity data is limited by the time and resources required to digitize, but I have found that it is possible to do so at a rate that is faster than typing. Finally, I experiment with the use of digital field guides in advancing access to biodiversity data, to stimulate public engagement in natural history collections. / Dissertation/Thesis / M.S. Plant Biology 2012

xiv, 166 p. : ill. A print copy of this title is available through the UO Libraries. Search the library catalog for the location and call number. / Restoration of imperiled ecosystems has emerged as a national priority, but there is little mechanistic understanding of how to restore ecosystems so as to sustain both species diversity and ecosystem function. The main objectives of my dissertation were (i) to develop an understanding of mechanisms that structure upland and wetland prairie plant communities in Oregon's Willamette Valley, with particular focus on edaphic and competitive controls over native and exotic species, and (ii) to apply this knowledge toward more effective restoration of prairie ecosystems. I used a combination of experiments and analysis of natural gradients to examine the effects of succession, competition, and environmental heterogeneity on plant community structure and ecosystem function within a restoration framework. I conducted a large, replicated field experiment and a retroactive study of previously restored wetland prairies to assess different site preparation techniques. These techniques had variable effectiveness in suppressing the existing vegetation and seed bank, thus providing different initial successional trajectories. However, over time plant community structure converged due to a loss of early-successional species and the increasing dominance of native bunchgrasses; hence, there was a negative relationship between cover of native species and diversity. Only the more extreme treatments, such as topsoil removal, had large impacts on soil functioning. These studies underscore the importance of using a successional framework to guide restoration efforts. Given the potential importance of competition between native and exotic grasses in structuring prairie vegetation, I used a paired study of field and greenhouse experiments to determine how abiotic factors influence the competitive hierarchies between native and exotic grasses commonly found in upland and wetland prairies. Exotic grasses dominated competitive interactions with the native grasses, but this depended upon nutrient and moisture availability. Finally, I used a laboratory experiment to determine the seasonal and edaphic controls over nutrient and carbon cycling within a spatially heterogeneous upland prairie. Manipulating moisture and temperature resulted in significant changes in nitrogen, phosphorus, and carbon cycling, particularly in the winter. Under projected future climate change, these changes will likely have large effects on plant community structure. This dissertation includes my previously published and co-authored materials. / Advisers: Scott D. Bridgham, Barbara "Bitty" A. Roy, Bart R. Johnson

The colonization of the arid continental surface by plants was one of the milestones in Earth's history. Morphological innovations, such as the origin of complex 3D tissues, allowed the successful colonization and radiation of plants on land. The epidermis is the outermost plant tissue that constitutes the interface between the plant and the environment. Thus, the evolution of epidermal cells was crucial for the adaptation of plants on the terrestrial arid environment. I undertook a combined approach that aims to understand the evolutionary trends that drove land plant colonization and the genetic mechanisms that underlie the development of the epidermis. This approach includes: 1) analyses of plant transcription factors (TFs) families distribution and diversification, with a particular focus on the basic Helix-Loop-Helix (bHLH) TF family, and 2) functional characterization of a putatively conserved bHLH TF subfamily involved in epidermal cell development in land plants. Here, I showed that there was a stepwise increase in the number of transcription factor (TF) families and bHLH subfamilies that predated the colonization of the terrestrial surface by plants. The subsequent increase in TF number on land was through duplication within pre-existing TF families and subfamilies. Moreover, a similar trend occurred in metazoan bHLH TF, suggesting that the majority of innovation in plant and metazoan TF families occurred in the Precambrian before the Phanerozoic radiation of land plants and metazoans. Furthermore, I demonstrated that the function of IIIf bHLH TFs in controlling the development of the epidermal cell layer is conserved between liverworts and angiosperms. This suggests that IIIf bHLH TFs are ancient and conserved regulators of epidermal cell development since the early colonization of the land by plants. Moreover, these bHLH TFs were recruited during the evolution of land plants to control the development of seemingly unrelated morphological characters in specific lineages of extant land plants. The recruitment of ancient developmental regulators to control distinct and unrelated developmental processes in land plants might underlie the huge morphological and taxonomic radiation of plants on land.

abstract: Stream flow permanence plays a critical role in determining floristic composition, abundance, and diversity in the Sonoran Desert, but questions remain about the effects of stream flow permanence on butterfly composition, abundance, and diversity. Understanding the effects of flow permanence on butterflies and relevant subsets of butterflies (such as butterflies whose host plants are present) and comparing them to these same effects on plants and relevant subsets of plants (such as butterfly nectar plants and larval host plants) provided insight into pollinator and riparian conservation and restoration. I surveyed four Sonoran desert stream sites, and found significant relationships between flow permanence and plant and butterfly species richness and abundance, as well as strong relationships between plant and butterfly abundance and between plant and butterfly species richness. Most notably, my results pointed to hosted butterflies as a break-out category of butterflies which may more clearly delineate ecological relationships between butterfly and plant abundance and diversity along Sonoran Desert streams; this can inform conservation decisions. Managing for hosted (resident) butterflies will necessarily entail managing for the presence of surface water, nectar forage, varying levels of canopy cover, and plant, nectar plant, and host plant diversity since the relationships between hosted butterfly species richness and/or abundance and all of these variables were significant, both statistically and ecologically. / Dissertation/Thesis / Masters Thesis Plant Biology 2015

abstract: The Upper Verde River of central Arizona flows through a landscape of complex geology at the meeting of seven biotic communities and three physiographic provinces. This has resulted in notably diverse flora and fauna and a hub of rare and endemic plant species. The river has sustained cultures since pre-history, however current regional water use is predicted to diminish streamflow over the next century. Prior to this project, no floristic inventory had been conducted along any section of the Verde. The purpose of this study was to develop a Flora of the Upper Verde River, with the goals of documenting rare and endemic species, the composition and abundance of wetland plants, and the factors shaping plant diversity in the region. I made a total of 1856 collections and reviewed past collections to produce a checklist of 729 vascular plant taxa in 403 genera and 98 families. The most species-rich family is the Poaceae, followed by Asteraceae and Fabaceae. The flora includes 159 wetland taxa, 47 endemics, and 26 taxa of conservation concern, eight of which are Federally listed. Several new populations were found in these categories and of rarely-collected taxa including one state record, three county records and several range extensions. I report on the local status of several endemics, wetland taxa with limited distributions, and relict populations of a tepary bean (Phaseolus acutifolius) that were likely transported to the region and cultivated by pre-Columbian cultures. I categorize thirteen distinct plant communities, the most abundant being Pinyon/Juniper Woodland, Chihuahuan/Apacherian Scrub, and Riparian Deciduous Forest. Four primary factors influence floristic diversity of the Upper Verde region: 1) a location at the junction of three physiographic and floristic provinces—represented by co-occurrence of species with affinities to the Sonoran, Intermountain and Madrean regions, 2) geologic diversity—as distinct groups of species are associated with particular geologic types, 3) topographic and habitat complexity—allowing species adapted to disparate environments to co-occur, and 4) human introductions—since over 15% of the flora is composed of introduced species from Eurasia and several taxa were introduced to the region and cultivated by pre-Columbian cultures. / Dissertation/Thesis / Masters Thesis Plant Biology 2015

As espécies de plantas classificadas no gênero Amaranthus são frequentemente encontradas infestando áreas agrícolas brasileiras, contudo existem poucos trabalhos que avaliaram as características biológicas e o controle destas espécies. Assim sendo, este trabalho foi conduzido com o objetivo de analisar a germinação, o crescimento e o desenvolvimento, estimar a área foliar, a competitividade e a susceptibilidade a herbicidas de cinco espécies de plantas daninhas do gênero Amaranthus As espécies de Amaranthus estudadas foram: A. deflexus (caruru-rasteiro), A. hybridus (carururoxo), A. retroflexus (caruru-gigante), A. spinosus (caruru-de-espinho) e A. viridis (caruru-de-mancha). O experimento que avaliou a germinação foi conduzido no Laboratório de Análise de Sementes e os demais em casa-de-vegetação do Departamento de Produção Vegetal da ESALQ/USP, Piracicaba - SP, no período compreendido entre março e dezembro de 2005. Com relação à germinação, constatou-se que variações na disponibilidade de luz e temperatura interferem em todas as espécies de Amaranthus, em que as maiores taxas de germinação foram obtidas em condição de fotoperíodo com alternância de temperatura (8h-luz-30°C / 16h-escuro-20°C). Em condições menos favoráveis, A. viridis e A. hybridus obtiveram maiores taxas de germinação que as demais espécies. Em geral, A. deflexus e A. spinosus foram as espécies de plantas daninhas que apresentaram os menores índices de velocidade de germinação. Sobre o crescimento e desenvolvimento, constatou-se que A. deflexus foi a espécie com ciclo vegetativo mais curto, menor acúmulo de massa seca e área foliar; por outro lado, A. retroflexus e A. hybridus foram aquelas que alcançaram os maiores valores para estas variáveis. A estimativa de área foliar demonstrou que a equação linear passando pela origem (Ar=a.(C.L)) foi adequada para ajustar a relação entre as medidas lineares do limbo e a área foliar real de todas as espécies. Com relação à competição, concluiu-se que a cultura do feijoeiro é melhor competidora que todas as espécies de plantas daninhas do gênero Aramanthus que foram utilizadas neste trabalho, quando cultivadas em igualdade de proporções. A. deflexus e A. viridis foram as espécies com a fenologia menos afetada pela competição com o feijoeiro; a competição intraespecífica foi a mais prejudicial à cultura do feijoeiro, o que sugere que os danos causados pelas plantas daninhas estão mais relacionados com as altas densidades em que estas ocorrem do que com a habilidade competitiva intrínseca das espécies. O controle químico obtido para as espécies de Aramanthus avaliadas neste trabalho demonstrou diferenças de susceptibilidade aos herbicidas aplicados em pósemergência, principalmente ao trifloxysulfuron-sodium e ao chlorimuron-ethyl, em que A. deflexus foi a espécie menos suscetível, seguido por A. spinosus, A. viridis, A. hybridus e A. retroflexus. / Plant species classified in the Aramanthus genus are frequently found infesting brazilian agricultural areas, although there are few researches that evaluated the biological characteristics and the control of these species. Therefore, this work was conducted with the objective of analyzing the germination, the growth and the development, estimating the leaf area, the competitiveness and the susceptibility to herbicides of five weed species of the Aramanthus genus. The species of Aramanthus studied were: A. deflexus, A. hybridus, A. retroflexus, A. spinosus and A viridis. The experiment that evaluated the germination was conducted in the Laboratory of Seed Analyses and the others in the greenhouse of the Crop Science Department of ESALQ/USP, Piracicaba - SP, in the period comprehended between March to December 2005. About the germination, it was established that variation in the availability of light and temperature interferes in all the species of Aramanthus and the highest levels of germination were obtained in condition of photoperiod with alternating temperature (8h-light-30°C / 16h-dark-20°C). In less favorable conditions, A. viridis and A. hybridus obtained higher germination levels than all the other species. In general, A. deflexus and A. spinosus were the weed species that presented the lowest rates of germination speed. About the growth and development, it was observed that A. deflexus was the species with shortest vegetative cycle, the lowest dry mass and leaf area accumulation; however, A. retroflexus and A. hybridus were the species which reached the highest values for these variables. The leaf area estimation showed that the linear equation crossing the origin (Ar=a.(C.L)) was adequate to adjust the correlation between the linear blade dimensions and the real leaf area for all the species. About competition, it was concluded that the crop of common bean is more competitive than all the weed species of the Aramanthus genus that were studied in this work, when grown in equivalent proportion; A. deflexus and A. viridis were the species which phenology was less affected by the competition with common bean; the intraspecific competition was the most damaging to the crop of common bean, what suggests that the damages caused by the weeds are more connected with its high density of infestation than the intrinsic competitive ability of the species. The control obtained for the Aramanthus species evaluated in this research presented differences of susceptibility to post-emergence applied herbicides, mainly to trifloxysulfuron-sodium and chlorimuron-ethyl, which A. deflexus was the least susceptible species, followed by A. spinosus, A. viridis, A. hybridus and A. retroflexus.

As non-vascular, early land plants with an aquatic ancestry, mosses do not regulate internal water conditions separate from that of their environment and as a result, evolved mechanisms to survive in a terrestrial world out of water. Yet, there is a widely accepted dogma that moss reproductive success is solely dependent on rainfall events carrying swimming, bi-flagellate sperm across the landscape to reproductively mature and receptive female mosses--but this classic view of moss reproduction may be too simplistic. In this dissertation I test the assumptions of reproductive limitation in mosses and present novel findings in a basal, yet understudied terrestrial plant mating system. I find evidence of environmental desiccation tolerance in moss sperm, thus offering the potential for stress-tolerant gametes on the landscape possibly suited for various transport vectors, reminiscent of a pollen grain. To investigate the broad evolutionary implications of this newfound complexity in moss sexual reproduction, I tested classic tenets of plant-pollinator theory on the ancient mosses and their ubiquitous microarthropod inhabitants. Experimental results show that mosses and microarthropods are engaged in a "pollination-like" syndrome guided by sex-specific volatile cues that differentially affect microarthropod behavior. These data indicate an existing complex mutualistic relationship and provides new evidence of sexually dimorphic investment by male and female mosses into reproductive success. Further, these data put forth the idea that female mosses challenge an inherent mate limitation by investing into reproductive assurance via maintaining a relationship with microarthropods. Experimental work further confirms a role for invertebrates in moss reproductive success and tests mutualism theory through ongoing experiments. Such experiments include an assessment of moss genetic diversity, paternity, and male fitness traits as it relates to mosses with or without the presence of microarthropods, thereby testing for fitness benefits gained by mosses possibly engaged in a transport mutualism with microarthropods. I further tested mutualism, community ecology and moss sexual reproduction concepts in extreme geothermal moss populations living at the edges of inhabitable Earth, and results show that even geothermal moss canopies are diverse and host differential and abundant life. In a first field test of mutualism I found that although extreme heat stress may constrain sexual reproduction in mosses, a correlation between within-population moss genetic diversity and microarthropod abundances exists. To further examine mosses in extreme environments, and how these environments may constrain sexual reproductive success, I evaluated the effects of simulated warming on Antarctic moss physiology and reproductive biology. Data indicates that simulated warming relieves mosses of physiological stress, and results in a greater investment into primary productivity and sexual reproduction. These data support the hypothesis that with less stress, sexual reproduction is increased. Mosses are an ideal system by which to understand organisms that exist in environments ranging from the mesic to the extreme, in the laboratory and the field and even in the classroom, where the small functioning ecosystem of mosses can be used for discovery-based biology education as described in the Mosscosms curriculum. This work contributes significantly to the field of bryophyte and plant biology by revealing novel insights into the biotic and abiotic drivers of sexual reproduction in mosses.

Environmental stressors such as nutrient deficiency and insect infestation can significantly impact tree health. Despite much research on the ecological effect on forests in the northeastern United States due to calcium depletion and hemlock woolly adelgid infestation, little is known regarding the physiological mechanisms altered by these stress factors. I tested the hypothesis that calcium depletion, associated with sugar maple decline, compromises water transport processes as a result of calcium-related reductions in cell growth and stabilization. A survey of forest-grown sugar maples from a long-term replicated calcium-manipulation study showed no significant impact of calcium deficiency on wood density, stem hydraulic conductivity (Ks), or vulnerability to cavitation (VC). In vitro removal of xylem-bound calcium showed no impact on VC or air seeding thresholds (Pt). Results suggest that sugar maple decline is not caused by compromises in xylem function due to calcium deficiency. I also tested the hypothesis that hemlock woolly adelgid (Adelges tsugae Annand) (HWA) infestations impact water transport processes and nutrient partitioning in eastern hemlock trees. HWA infestation resulted in higher Ks due to an increase in average tracheid lumen area associated with the proliferation of false rings. HWA-infested trees exhibited higher rates of net photosynthesis and significant changes in foliar nutrient partitioning. These results are the first to demonstrate increases in Ks and alterations in foliar cation levels in response to HWA infestation. In two additional studies, I investigated methods for evaluating the structure and function of xylem networks. Using sequential sectioning of aerial roots of epiphytic aroids, I directly quantified the topographic relation of vessels in a single organ with measurements of vessel length, diameter, vessel end overlap length, and vessel stelar orientation. In a separate study, I explored the relationship between vessel length and measurements of Pt. In establishing guidelines for estimating whole-stem cavitation with the use of single vessel air injection, I demonstrate that calculations of Pt are influenced by stem length measured and removal of native emboli prior to testing. Improvements in tools to quantify xylem structure and function will enhance our ability to understand the responses of forest trees to environmental stress.

Palms provide valuable commercial resources in the tropics and are dominant species in tropical lowland forests. While general biology of palms is well studied, there are gaps in the literature on palm growth through life stages and in response to environmental conditions. Literature gaps on palm growth could be caused by the slow growth of palms; it is difficult to monitor morphology and architecture for the periods of time necessary to capture changes. Acoelorrhaphe wrightii is a threatened palm native to southern Florida with an unusual adult architecture. The purpose of this dissertation was to study growth A. wrightii throughout its life stages and in response to changes in environmental conditions. In order to do study growth, I first had to understand the evolutionary history and types of vegetative branching in palms to identify vegetative branching possibilities in A. wrightii. I described branching types for 1903 species from all 181 genera using literature reviews and hands-on analysis. I then studied adult morphology and architecture in a common garden setting by monitoring leaf morphology, ramet growth and architecture of A. wrightii in two gardens in Miami, FL, over a two year period. I tested the effects of water and light on germination and growth of juvenile plants in a mesocosm where water and light were manipulated, following growth for a year. Finally, I compared leaf morphology and architecture of adult individuals in four populations in Belize and Florida. I found five branching types were present in the palms: lateral axillary branching, shoot apical division, false vivipary, abaxial branching and leaf-opposed branching. In the garden, Acoelorrhaphe wrightii displayed two types of lateral axillary branching: basal suckering and rhizomatous branching. The two branching types produced tiers in adult clones, which were used to model architecture. Ramets had an establishment period and growth varied seasonally in establishing and established phases. Low water levels and full sun yielded greater germination of A. wrighti and produced juveniles with a greater number of leaves, more root mass and more branches. Variability between populations and environmental conditions was observed in adult individuals in the field but differences were minimal.