Development of early leafspot, caused by Cercospora arachidicola Hori, was monitored on' Florigiant' peanut (Arachis hypogaea L.) at two field sites in Suffolk, Virginia. In one study, plants in 27-cm-diameter plots were inoculated with 20,000 conidia and inoculation dates were replicated in five randomized complete blocks. At location one in 1985 and 1986, lesions/leaf at two weeks after inoculation correlated significantly (P ≤ 0.05) with infection indices (IND) developed by the Virginia leafs pot advisory and hours of relative humidity (RH) ≥ 95%. At location two, correlations between lesions/leaf and IND as well as hours of RH ≥ 95% were significant in 1986, but not in 1985. Certain site specific factors were believed to have altered plant susceptibility to leafspot at this site in 1985. In another study, pots with greenhouse-grown peanut were placed between unsprayed rows of field plants, heavily colonized by C. arachidicola. Plants were removed after 3, 5, and 7 days of field exposure for six consecutive weeks in 1986 and returned to the greenhouse. Lesions/leaf at two weeks after initial exposure were correlated with IND values computed by five versions of the leaf spot advisory. Significant correlations were found between lesions/leaf on plants with field exposures of 5 and 7 days and cumulative IND values and hours of RH ≥ 90% and 95%. The low incidence of lesions resulting with field exposures of only 3 days coupled with a lack of significant correlations between disease and cumulative IND values for 3 days after inoculation in both studies suggests that infection processes require several days, and that fungicides may be applied to achieve disease control during this time. / M.S.

Switchgrass (Panicum virgatum L.) is a candidate bioenergy crop. Somatic embryogenic (SE) calli are used for genetic transformation in switchgrass. A superior switchgrass line, HR8, was developed using recurrent tissue culture selection from cv. Alamo. HR8 SE calli were genetically transformable using Agrobacterium at an efficiency of ~12%. We used HR8 somatic embryogenic calli for genetic improvement of switchgrass. The lignin content of feedstock has been proposed as one key trait impacting biofuel production. 4-Coumarate: Coenzyme A ligase (4CL) is one of the key enzymes involved in the monolignol biosynthetic pathway. Two homologous 4CL genes, Pv4CL1 and Pv4CL2, were identified in switchgrass. Gene expression patterns and enzymatic activity assays suggested that Pv4CL1 is involved in monolignol biosynthesis. Stable transgenic plants were obtained with Pv4CL1 down-regulated. RNA interference of Pv4CL1 reduced extractable 4CL activity by 80%, leading to a reduction in lignin content with decreased guaiacyl unit composition. The transgenic plants had uncompromised biomass yield. After dilute acid pretreatment, the low lignin transgenic biomass had significantly increased cellulose hydrolysis (saccharification) efficiency for biofuel production. Erect leaf is a desirable trait to adjust the overall plant architecture to perceive more solar energy and thereby to increase the plant biomass production in a field population. We overexpressed an Arabidopsis NAC transcriptional factor gene, LONG VEGETATIVE PHASE ONE (AtLOV1), in switchgrass. Surprisingly, AtLOV1 induced smaller leaf angle by changing morphologies of epidermal cells in the leaf collar region, affecting lignin content and monolignol composition, and also causing delayed flowering time in switchgrass. Global gene-expression analysis of AtLOV1 transgenic plants demonstrated an array of genes has altered expressions. Potential downstream genes involved in the pleiotropic phenotypic traits of the transgenic plants are discussed. / Ph. D.

Rice bacterial leaf streak disease caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most important rice bacterial diseases. Xanthomonas type III effector gene avrRxo1 is conserved in diverse Xoc strains and its homologues have been identified from several other gram-negative bacteria species such as Burkholderia and Acidovorax. In this research, we studied the protein structure of AvrRxo1 and illustrated its virulence mechanism.We determined the three-dimensional structure of the complex of AvrRxo1 and its cognate chaperone Arc1 (AvrRxo1 required chaperone 1). The AvrRxo1: Arc1 complex is structurally similar to the Zeta-epsilon family of toxin: antitoxin systems from the human bacterial pathogen Streptococcus pyogenes. AvrRxo1 and Arc1 have toxin: antitoxin-like activity in bacteria, and the toxin activity of AvrRxo1 is required for its virulence function in planta. These findings suggest that AvrRxo1 evolved from an endogenous bacterial toxin-antitoxin system.Furthermore, AvrRxo1 was shown to have virulence functions in diverse host plants including Arabidopsis thaliana. The ectopic expression of wild type avrRxo1 in Arabidopsis suppresses plant basal defense. AtVOZ (Arabidopsis vascular one zinc-finger transcription factor), which has two homologues in the Arabidopsis genome, VOZ1 and VOZ2, was identified as one of AvrRxo1 candidate interactor. The knockout of voz1/voz2 renders the plants more susceptible to the virulent pathogen Pseudomonas syringae pv. tomato (Pst) DC3000, but compromises the virulence function of AvrRxo1. The expression profiling of transgenic Arabidopsis plants expressing the avrRxo1 gene allowed us to identify Arabidopsis genes regulated by AvrRxo1 and VOZ1/2. AvrRxo1 interacts with and stabilizes VOZ2 in vivo and directly binds to the promoter region of AtCYS2 (Arabidopsis phytoCYStatin 2) to induce its expression. The overexpression of CYS2 in increased stomatal aperture size, and enhanced plant susceptibility to Pst. Therefore one of AvrRxo1 virulent functions is to regulate the expression of CYS2 by manipulating VOZ2, resulting in increased stomatal aperture. Presumably, this renders the host leaf more susceptible to colonization via the stomata. Another component of my dissertation was based on a genome-wide survey of Arabidopsis papin-like cysteine protease genes (PLCPs). The Arabidopsis genome has 31 PLCP and 7 cystatin genes, and they often worked in pairs to regulate signaling pathways in response to biotic and abiotic stress. The coordinated transcriptional regulation of all Arabidopsis PLCP and cystatin genes has never been systematically investigated. In order to unveil the mechanism of stomata-related plant immunity regulated by CYS2, we analyzed the expression patterns of 28 PLCPs and 7 cystatins in Arabidopsis in response to biotic or abiotic stress, by reprocessing and integrating microarray data from the AtGenExpress database. We also performed enzyme assays and evaluated the inhibition specificity of seven cystatins to the five most abundant PLCPs in Arabidopsis. Finally, we utilized the SVMs (support vector machines) package in R software to predict a functional network of PLCP-cystatin interplay in Arabidopsis. We identified the PLCP protein PAP4 as one of the putative targets of CYS2. The co-expression profiling indicated that the expression patterns of PAP4 and CYS2 were strongly correlated during virulent bacterial infection, and weakly correlated under drought stress. Therefore, PAP4 was determined to be a promising gene in regulating stomatal aperture size. Further research on the interplay of PAP4-CYS2 could be important for understanding AvrRxo1's virulence mechanism and regulation of plant stomatal immunity. / Ph. D.

Land-use practices have long been associated with alterations in stream ecosystem structure and function, however, 'exurbanization' and its impact on streams is poorly understood. This study compares the ecosystem structure and function of 9 southern Appalachian streams of differing land-use (forested, exurban, agricultural). Impacts of land-use on leaf breakdown are examined in Chapter 1. Leaf breakdown rates were significantly related to land-use. Forested streams exhibited the slowest breakdown rates, followed by exurban streams, with agricultural streams having the fastest rates. Leaf breakdown was most strongly related to discharge (white oak) and some fine sediment metrics (red maple). Our results suggest that the altered hydrological regimes in agricultural streams, as well as the influx of fine sediments into streams from exurban development, can play a role in altering in-stream organic matter processing. The taxa and number of shredders present may play a role to a lesser extent. Impacts of land-use on macroinvertebrate assemblages are examined in Chapter 2. Shannon diversity, %EPT, and NCBI were significantly related to land-use regime. There were significant negative relationships between macroinvertebrate diversity and conductivity and temperature. In addition, biotic integrity had a significant negative relationship with conductivity. Canonical Correspondence Analysis (CCA) showed that agricultural streams were characterized by temperature and flow, forested streams by MPS and standing stock course particulate organic matter (SSCPOM), and two of three exurban streams by conductivity and temperature. Principal Coordinates Analysis (PCoA) revealed that while macroinvertebrate communities overlapped, some differences in community assemblage could be seen between land-use types. / Master of Science

El trabajo incluido en esta tesis está encuadrado en un proyecto cuyo objetivo general es el desarrollo de un vector viral eficiente de expresión o silenciamiento de genes, basado en el virus del manchado foliar de los cítricos (Citrus leaf blotch virus, CLBV). Para desarrollar un vector viral a partir del genoma de CLBV era necesario disponer de un clon infeccioso del virus y de métodos eficientes de inoculación del mismo en plantas de cítricos. Se construyó un clon infeccioso de cDNA del genoma completo de CLBV bajo el promotor T7 del fago lambda y se pusieron a punto protocolos para el aislamiento de protoplastos de N. benthamiana, N. occidentalis y cidro Etrog. CLBV replicó en protoplastos de las tres especies transfectados con viriones purificados, aunque el nivel de replicación fue muy bajo y sólo se detectó a partir de 4-5 días post inoculación (dpi), que es el tiempo máximo de supervivencia de los protoplastos en nuestras condiciones de trabajo. La multiplicación del virus en protoplastos inoculados con transcritos de CLBV fue menor, detectándose sólo en algunos experimentos de transfección de protoplastos de N. benthamiana. Finalmente, la inoculación mecánica directa de plantas de cítricos o de N. benthamiana y N. occidentalis con transcritos de RNA del virus fue infructuosa, a pesar de que estos transcritos eran capaces de infectar protoplastos. Antes de modificar el clon infeccioso de CLBV para convertirlo en un vector viral eficiente, era necesario conocer la estrategia de expresión del genoma viral y caracterizar las secuencias implicadas en el reconocimiento y promoción de la síntesis de los RNAs subgenómicos (sgRNAs) para poder duplicar un promotor y expresar genes o fragmentos de genes mediante la formación de un nuevo sgRNA. Para mapear el promotor del CP-sgRNA de CLBV se construyeron varios mutantes a partir del clon IC-CLBV (clon infeccioso del genoma completo de CLBV bajo el promotor 35S de CaMV) mediante supresión de nucleótidos y mutagénesis dirigida. / Renovell Ferrer, MÁ. (2010). El virus del manchado foliar de los cítricos: caracterización del promotor del RNA subgenómico del gen de la proteína de la cápsida y del supresor del silenciamiento de RNA [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/7324

The structure and function of stream ecosystems may be strongly influenced by land-use practices within watersheds. The magnitude of land-use impacts may depend upon the spatial arrangement of development in watersheds. This study examines the relationship between land-cover patterns and stream structure and function in 9 southern Appalachian headwater basins. Using a GIS/remote sensing approach, land-cover patterns were quantified at several spatial scales, including the entire watershed, riparian corridor, and riparian sub-corridors extending upstream in 200 m increments for 2 km. In-stream physico-chemical variables were related to land-cover patterns at different spatial scales. Dissolved constituents (e.g., TIN, alkalinity) were frequently related to physical features or land-cover patterns at the watershed scale. Conversely, mean substrate particle size and stream temperature were most strongly related to land-use practices at the entire riparian corridor scale. Finally, maximum stream temperature was best explained from land-cover patterns at the 200 m sub-corridor scale. The relationship between land-cover patterns and benthic macroinvertebrate communities is examined in Chapter 1. Macroinvertebrate assemblage structure was quantified using the slope of rank-abundance plots, and further described using standard diversity and evenness indices. Macroinvertebrate taxa richness ranged from 24 to 54 among sites, and the analysis of rank-abundance curves defined three distinct groups with high, medium, and low diversity. In general, other macroinvertebrate indices were in accord with rank-abundance groups, with richness and evenness decreasing among sites with maximum stream temperature. Macroinvertebrate indices were most strongly related to land cover patterns evaluated at the 200 m sub-corridor scale, suggesting local, streamside development effectively alters assemblage structure. The relationship between land-cover patterns and leaf breakdown is examined in Chapter 2. Breakdown rate for American sycamore (Plantanus occidentalis) leaf packs varied significantly among sites (k = 0.0051 to 0.0180 d-1), but fell within the range reported in the literature for sycamore. Leaf breakdown rate increased among sites with shredder density and biomass. Further, breakdown rate and shredder density and biomass were positively related to mean substrate particle size. Though several instream variables were related to watershed-scale features, leaf breakdown rate was not related to land cover at the watershed scale. Leaf breakdown rate was inversely related to % non-forest within riparian sub-corridors of approximately 1 km. Results suggest that the distribution of shredders is critical to leaf processing in these streams. In some streams, increased sediment inputs as a result of agricultural activity or residential development in riparian corridors may limit the distribution of shredders and thus influence leaf breakdown rates. Alternatively, near stream development may reduce the quantity and/or quality of allochthonous inputs to streams, and thus indirectly influence the distribution of shredders. / Master of Science

Drought is a major environmental stress factor that poses a serious threat to food security. The effects of drought on early reproductive tissue at 1-2 DAP (days after pollination) is irreversible in nature and leads to embryo abortion, directly affecting the grain yield production. We developed a working RNA-Seq pipeline to study maize (Zea mays) drought transcriptome sequenced by Illumina GSIIx technology to compare drought treated and well- watered fertilized ovary (1-2DAP) and basal leaf meristem tissue. The pipeline also identified novel splice junctions - splice variants of previously known gene models and potential novel transcription units. An attempt was also made to exploit the data to understand the drought mediated transcriptional events (e.g. alternative splicing). Gene Ontology (GO) enrichment analysis revealed massive down-regulation of cell division and cell cycle genes in the drought stressed ovary only. Among GO categories related to carbohydrate metabolism, changes in starch and sucrose metabolism-related genes occurred in the ovary, consistent with a decrease in starch levels, and in sucrose transporter function, with no comparable changes occurring in the leaf meristem. ABA-related processes responded positively, but only in the ovaries. GO enrichment analysis also suggested differential responses to drought between the two tissues in categories such as oxidative stress-related and cell cycle events. The data are discussed in the context of the susceptibility of maize kernel to drought stress leading to embryo abortion, and the relative robustness of actively dividing vegetative tissue taken at the same time from the same plant subjected to the same conditions. A hypothesis is formulated, proposing drought-mediated intersecting effects on the expression of invertase genes, glucose signaling (hexokinase 1-dependent and independent), ABA-dependent and independent signaling, antioxidant responses, PCD, phospholipase C effects, and cell cycle related processes. This work was supported by the National Science Foundation Plant Genome Research Pro- gram (grant no. DBI0922747), iPlant Collaborative (NSF DBI-0735191) and also NSF ABI1062472. / Master of Science in Life Sciences

Leaf litter is a major nutrient source for aquatic detrital food webs, fueling the microbes and macroinvertebrates that colonize it. Litter is especially important as a nutrient source for macroinvertebrates in headwater streams that tend to have lower primary production than higher-order stream systems. Understanding how litter decomposition and macroinvertebrates interact at large scales facilitates predictions about how stream ecosystems will change over space and time with regards to allochthonous nutrient inputs. We utilized a subset of the National Ecological Observatory Network's wadeable stream sites to deploy a litter pack study across the United States and Puerto Rico to determine the controlling factors for litter decomposition and associated macroinvertebrate assemblages, abundances, and species richness at a national scale. We found that litter species was the most important contributing factor to litter decomposition, and despite litter decomposition differences from stream to stream, the relative differences in decomposition rate between litter types was very similar. Stream identity, temperature, and flow also played roles in affecting decomposition patterns. In contrast to litter decomposition, litter species did not significantly contribute to variation in macroinvertebrate assemblages, abundance, or species richness, though environmental variables did impact abundance and species richness. These results suggest that there is functional redundancy in aquatic detritivore communities at large scales, and that the assemblages colonizing different species of leaf litter–despite being similar–might be functioning differently.

Trabalhos recentes vêm tentando resolver as relações filogenéticas na subordem Portulacineae. A família Portulacaceae, como tradicionalmente circunscrita, não constituía um grupo monofilético e recentemente foi desmembrada em diversas famílias menores. Algumas destas famílias, juntamente à família Cactaceae, formam o clado ACPT (Anacampsetotaceae, Cactaceae, Portulacaceae e Talinaceae), sustentado principalmente por dados moleculares, sendo poucos os caracteres morfológicos e anatômicos reconhecidos como sinapomorfias. A presente dissertação teve como objetivo documentar a anatomia e o desenvolvimento de folhas e da região da axila foliar em espécies de Portulacaceae e Talinaceae, discutindo os resultados com a literatura existente para outros grupos do clado ACPT. Técnicas usuais em anatomia vegetal foram usadas para analisar folhas e regiões nodais do ápice e base do caule. Como principais resultados, pudemos observar diversos caracteres presentes na região da axila foliar que representam homologias primárias dentro do clado ACPT. Além disso, descrevemos diferentes padrões de desenvolvimento foliar, relacionados especialmente com a atividade do meristema marginal, levando a diferentes morfologias foliares. Acreditamos que os dados aqui obtidos sejam relevantes para uma melhor compreensão da evolução das diferentes linhagens do clado ACPT, e que futuros estudos, abordando outros grupos com maiores detalhes, poderão testar estas hipóteses de homologias primárias aqui propostas. / Recent works attempt to resolve the phylogenetic relationships within suborder Portulacineae. The family Portulacaceae, as traditionally circunscribed, is not monophyletic, and was recently split into several smaller families. Some of these families, along with Cactaceae, form the ACPT clade (Anacampsetotaceae, Cactaceae, Portulacaceae and Talinaceae), sustained mainly by molecular data. Few morphological and anatomical synapomorphies are known for the group. This dissertation aims to investigate the anatomy and development of leaves and leaf axils in species of Portulacaceae and Talinaceae, discussing the results with existing literature for other groups of the ACPT clade. Usual techniques of plant anatomy were used to examine leaves and nodal regions of apical and basal portions of stems. As main results, we observed several characters present in the region of leaf axil that represent primary homologies within ACPT clade. In addition, we describe different patterns of leaf development, especially related to the activity of the marginal meristem leading to different leaf morphologies. We believe that these data are relevant to a better understanding of the evolution in different lineages of the ACPT clade. Future studies, addressing other groups in greater detail, will be able to test these hypotheses of primary homologies proposed here.

Orientador: Gustavo Habermann / Banca: José Pires de Lemos Filho / Banca: Rafael Vasconcelos Ribeiro / Resumo: As folhas são órgãos adaptados para a captação de energia luminosa e sua transformação em energia bioquímica. Entretanto, a irradiância interceptada pelas folhas é maior do que a irradiância que é de fato absorvida e aproveitada de forma eficiente, o que torna os mecanismos de fotoproteção essenciais. Esses mecanismos podem minimizar a absorção da irradiância ou ativar respostas metabólicas responsáveis pela proteção do sistema fotoquímico. Styrax camporum é uma espécie com ampla distribuição no cerrado sensu lato. Suas folhas possuem orientação horizontal ou vertical, mas também podem apresentar ângulos intermediários. Com a finalidade de observar a influência que a orientação foliar exerce sobre o desempenho fotossintético, foram avaliadas as curvas das taxas fotossintéticas em resposta ao aumento da disponibilidade de luz para ambas as faces (adaxial e abaxial) de folhas horizontais e verticais. Além disso, foi realizado um experimento de deficiência hídrica no qual as trocas gasosas, a fluorescência da clorofila a e as relações hídricas foram acompanhadas em ambas as faces dos dois tipos foliares. Os resultados mostraram que, em S. camporum, a orientação vertical de parte das folhas não está relacionada à fotoproteção estrutural e que, nessa espécie, o posicionamento vertical das folhas poderia estar relacionado à otimização da assimilação de CO2 em decorrência da potencial exposição de ambas as faces foliares à radiação direta / Abstract: Leaves are organs adapted to sunlight interception and conversion of light energy into biochemical energy. However, the irradiance that is intercepted by leaves is greater than the absorbed irradiance that is effectively used in photosynthesis, making photoprotective mechanisms essential. Such mechanisms may reduce the amount of absorbed irradiance or may activate metabolic activities that are responsible for protecting the photochemical system. Styrax camporum is a woody species that is widely distributed in the cerrado sensu lato areas. S. camporum leaves show horizontal or vertical orientation, but they may also have intermediate angles. We investigated whether the leaf angles of S. camporum have any influence on photosynthetic performance. Photosynthetic response curves in response to increasing light were measured on both surfaces (adaxial and abaxial) of horizontal and vertical leaves. In addition, a water deficiency experiment was performed. In this experiment, gas exchange rates, chlorophyll a fluorescence and plant water relations values were also monitored on both surfaces of both leaf types. Results showed that, in S. camporum, vertical leaf orientation is not related to structural photoprotection and that, in this species, such leaf orientation could be related to the optimization of CO2 assimilation since both leaf surfaces are potentially exposed to direct sunlight / Mestre