Interstitial and intracavitary brachytherapy plays an essential role in management of several malignancies. However, the achievable accuracy of brachytherapy treatment for prostate and cervical cancer is limited due to the lack of intraoperative planning and adaptive replanning. A major problem in implementing TRUS-based intraoperative planning is an inability of TRUS to accurately localize individual seed poses (positions and orientations) relative to the prostate volume during or after the implantation. For the locally advanced cervical cancer patient, manual drawing of the source positions on orthogonal films can not localize the full 3D intracavitary brachytherapy (ICB) applicator geometry. A new iterative forward projection matching (IFPM) algorithm can explicitly localize each individual seed/applicator by iteratively matching computed projections of the post-implant patient with the measured projections. This thesis describes adaptation and implementation of a novel IFPM algorithm that addresses hitherto unsolved problems in localization of brachytherapy seeds and applicators. The prototype implementation of 3-parameter point-seed IFPM algorithm was experimentally validated using a set of a few cone-beam CT (CBCT) projections of both the phantom and post-implant patient’s datasets. Geometric uncertainty due to gantry angle inaccuracy was incorporated. After this, IFPM algorithm was extended to 5-parameter elongated line-seed model which automatically reconstructs individual seed orientation as well as position. The accuracy of this algorithm was tested using both the synthetic-measured projections of clinically-realistic Model-6711 125I seed arrangements and measured projections of an in-house precision-machined prostate implant phantom that allows the orientations and locations of up to 100 seeds to be set to known values. The seed reconstruction error for simulation was less than 0.6 mm/3o. For the physical phantom experiments, IFPM absolute accuracy for position, polar angle, and azimuthal angel were (0.78 ± 0.57) mm, (5.8 ± 4.8)o, and (6.8 ± 4.0)o, respectively. It avoids the need to match corresponding seeds in each projection and accommodates incomplete data, overlapping seed clusters, and highly-migrated seeds. IFPM was further generalized from 5-parameter to 6-parameter model which was needed to reconstruct 3D pose of arbitrary-shape applicators. The voxelized 3D model of the applicator was obtained from external complex combinatorial geometric modeling. It is then integrated into the forward projection matching method for computing the 2D projections of the 3D ICB applicators, iteratively. The applicator reconstruction error for simulation was about 0.5 mm/2o. The residual 2D registration error (positional difference) between computed and actual measured applicator images was less than 1 mm for the intrauterine tandem and about 1.5 mm for the bilateral colpostats in each detector plane. By localizing the applicator’s internal structure and the sources, the effect of intra and inter-applicator attenuation can be included in the resultant dose distribution and CBCT metal streaking artifact mitigation. The localization accuracy of better than 1 mm and 6o has the potential to support more accurate Monte Carlo-based or 2D TG-43 dose calculations in clinical practice. It is hoped the clinical implementation of IFPM approach to localize elongated line-seed/applicator for intraoperative brachytherapy planning may have a positive impact on the treatment of prostate and cervical cancers.

Patterns of the expansion of woody cover into grasslands on barrier islands of the Virginia coast were investigated. Seed dispersal of the dominant shrub Morella spp., was sampled deploying seed traps (n = 82) throughout a landscape under shrub encroachment pressure on Hog Island, VA. Traps were placed underneath: fruiting Morella, non-fruiting Morella, co-occurring species (Iva frutescens and Baccharis halimifolia) and in grass land, (no shrub cover). Environmental filters that act upon dispersed seeds and subsequently determine establishment patterns were also investigated. Dispersal distribution throughout the encroachment zone was leptokurtic and dispersal among cover types suggest co-occurring shrub species facilitate dispersal by functioning as bird perches. Interaction of biotic and abiotic factors mediate a complex process of establishment by influencing dispersal, germination and seedling survival to ultimately determine distribution patterns of woody plants in coastal environments.

Les cellules épidermiques des téguments des graines d’Arabidopsis thaliana, espèce myxospermique, libèrent un halo de mucilage polysaccharidique lors de leur imbibition. Les polysaccharides du mucilage sont produits et accumulés au cours du développement de la graine, selon un processus de différenciation déjà largement décrit (Western et al. 2006). Au laboratoire, une mutation naturelle a été mise en évidence chez l’accession Djarly, dont les graines ne libèrent pas de mucilage au cours de leur imbibition. Le clonage positionnel a démontré que le locus affecté chez Djarly code pour un inhibiteur de pectine méthylestérase (PMEI6). Les PMEIs exercent un contrôle négatif sur l’activité des pectines méthylestérases (PME), enzymes qui déméthylestérifient les homogalacturonanes, par la formation d’un complexe PME-PMEI (Di Matteo et al., 2005 ; Hothorn et al., 2004). Des études génétiques, cytologiques et biochimiques ont prouvé que PMEI6 régule la méthylestérification des homogalacturonanes du mucilage et des parois cellulaires distales des cellules épidermiques de la graine retardant la libération du mucilage séminal. L’expression de PMEI6 dépend des régulateurs de transcription GLABRA2 et MUM1. L’activité PME dans les cellules épidermiques des graines est aussi modulée par la subtilisine serine protéase AtSBT1.7, et le phénotype additif du mutant pmei6 atsbt1.7 indique que PMEI6 régule d’autres PMEs. Djarly fait partie d’un groupe de vingt accessions, dont les graines flottent à cause de modifications des propriétés du mucilage séminal. Ces accessions portent au moins dix mutations indépendantes, qui affectent au moins 4 locus différents. Cette étude nous a permis de proposer que la modification des propriétés du mucilage est impliquée dans l’adaptation à l’environnement local, permettant la dispersion à longue distance des graines par l’eau. / Upon imbibition, the myxospermous seeds of Arabidopsis thaliana, form a mucilage from hydrated polysaccharides released from the epidermal cells of the seed coat. These polysaccharides are produced and accumulated during seed development in a differentiation process that has been described in detail (Western et al. 2006). A screen of Arabidopsis accessions identified Djarly as a natural mucilage mutant affected in mucilage release on imbibition. The locus defective in Djarly was identified by map-based cloning as encoding a pectin methylesterase inhibitor (PMEI6). Theseproteinaceous inhibitors negatively control the activity of pectin methylesterases (PME), enzymes that demethylesterify HG, through the formation of a PME-PMEI complex (Di Matteo et al., 2005; Hothorn et al, 2004). Genetic, cytological and biochemical studies demonstrated that PMEI6 regulates methylesterification of homogalacturonans present in mucilage and the outer cell wall of seed coat epidermal cells. Delayed seed mucilage release in pmei6 mutants results, therefore, from the reduced level of homogalacturonan methylesterification. Expression of PMEI6 required the transcription regulators GLABRA2 and MUM1. PME activity in seed coat epidermal cells is also modulated by the subtilisin serine protease AtSBT1.7, and the additive phenotype of pmei6 atsbt1.7 mutants indicates that PMEI6 regulates different PMEs. Djarly is one of twenty accessions where seeds float due to modifications of mucilage properties. At least ten independent mutations are responsible for the mucilage modifications in these accessions, affecting at least 4 different loci. This study has led us to propose that these mucilage modifications are local adaptations that allow longdistance seed disperal on water.

Angiosperm seed development requires co-ordinated development of the embryo and a second zygotic tissue, the endosperm. In Arabidopsis thaliana, the endosperm is ephemeral and is largely consumed by the embryo during seed development. In addition to a role in embryo nutrition, it is also likely that the endosperm may play a more direct role in signalling to the embryo to regulate development. Despite their importance for embryo development, these processes are very poorly understood. The ZHOUPI (ZOU) gene provides an important tool to address these problems. Firstly, ZOU likely regulates endosperm breakdown. Whereas wild-type seed have a single layer of endosperm at maturity, zou seed has a large persistent endosperm and a correspondingly small embryo. The small zou embryo does not fill the seed so that the seed shrivels as it desiccates during maturation. Secondly, zou embryos have defects in their cuticle, so that the endosperm adheres to the embryo throughout seed development. After seed germination, zou cotyledons develop holes in their epidermis as they expand, probably due to the defects in the cuticle. ZHOUPI (ZOU) encodes a bHLH transcription factor and is expressed in the embryo surrounding region (ESR) of endosperm but not in the embryo itself. The role of ZOU in cuticle development is partly mediated by the ABNORMAL LEAF SHAPE1 (ALE1) gene. Thus, ale1 mutants also show defects in embryonic cuticle development and ALE1 is specifically expressed in ESR in a ZOU-dependent fashion. It was unclear whether the effects of ZOU upon embryo development are an indirect consequence of the persistent endosperm mechanically impeding embryo expansion, or rather reflect a more direct role of the ESR in signalling to the embryo. The main aims of this thesis were 1) to provide evidence that ZOU regulates endosperm cell death and 2) to test whether ZOU function in controlling endosperm cell death could be separated from that in embryonic epidermal cuticle development. To achieve this goal, 1) TUNEL assays were performed in the seeds to confirm the zou endosperm cell death phenotype, 2) ALE1 expression in the ESR in zou mutants was rescued using the ZOU-independent AtSUC5 promoter to investigate whether one or both of zou phenotypes were complemented, 3) Candidate ZOU target genes were validated and characterized to determine their functions in endosperm cell death and/or embryonic epidermal cuticle development. The TUNEL assays revealed that zou mutants display less DNA fragmentation in the ESR than that of the wild-type, but that zou did not have defects in cell death outside the seeds suggesting ZOU specifically regulated endosperm cell death. The AtSUC5::ALE1 transgene partially rescued zou defects in epidermal cuticle but not in endosperm cell death. This shows that the defects in the zou cuticle are not caused by the defective endosperm, rather zou has distinct, separable functions. Lastly, I characterised several novel ZOU targets and showed that RGP3 may be a direct ZOU target as it is expressed in ESR in ZOU dependent fashion, whereas RGP4 is likely indirect as it is expressed in the testa and up-regulated in zou mutants. In conclusion, ZOU has independent roles in endosperm cell death and embryonic epidermal cuticle development. Because ALE1, which largely mediates the role in cuticle development, is less widely conserved than is ZOU, the role in promoting endosperm cell death may be the ancestral function of ZOU.

Master of Science / Department of Agronomy / Kraig Roozeboom / Nitrogen fixation by Bradyrhizobium japonicum in soybean [Glycine max] is highly beneficial in soybean crop production. Nodulation issues have been encountered on fields new to growing soybeans in recent years in Kansas. The purpose of this research was to evaluate soybean nodulation performance under various situations and seed handling practices in order to educate producers on how to achieve reliable nodulation consistency in the field. The objectives of the study were to: 1) compare inoculant products using single and double rates and in combination with one another on fields with varying soybean history; 2) determine if there was a negative interaction between inoculant products and common seed treatments; and 3) discover the influence of inoculated seed storage conditions before planting on the rhizobia’s ability to successfully nodulate soybean roots. Field experiments were conducted on diverse Kansas sites in 2011 and 2012. Inoculant treatment and seed treatment interaction trials had ten and seven experimental sites respectively. Inoculated seed storage conditions were evaluated in a greenhouse experiment during the spring of 2013. All studies used a randomized complete block design with four replications. The Novozymes inoculant products generally provided superior nodulation performance over other company products in the study where soybean had not been in recent rotation with an average increase of 167% in nodule number verses the control. The combination of dry and liquid inoculant products provided a significant increase in root nodule number at five of the environments out of recent rotation with a 76% increase over single inoculant rates. Although there were early season nodulation differences between treatments in new soybean ground, these did not carry through to seed yield differences in the majority of research sites. Hot and dry summer conditions reduced yields, making detection of treatment differences difficult. There were no negative effects on nodulation performance with any of the seed treatments. Although soybean seed yield was 634 kg ha[superscript]-[superscript]1 greater for the Novozyme combination treatment compared to the check at one location in 2011, the control yielded as well or better than all other treatment/inoculant combinations, implying that yield differences were likely not related to inoculant treatments. At other sites, yield was not influenced by seed treatment and inoculant combinations. Results indicate that seed treatment formulations did not significantly impact bacterial inoculant product performance, soybean nodulation, or yield. Storage conditions had no effect on nodulation performance in the greenhouse study, likely due to survival of Bradyrhizobium japonicum in the heat-treated growth medium.

Doctor of Philosophy / Department of Biology / David C. Hartnett / Grazing and drought are instrumental in the development and maintenance of perennial grasslands. In this research I tested the belowground bud bank contribution to tallgrass prairie resistance and resilience when perturbed by grazing and drought. First, I tested the bud bank role in vegetation response to and recovery from severe drought (Chapter 2). I compared above- and belowground responses of experimentally droughted plots to ambient controls and irrigated plots during two years of severe drought and two years of recovery. I found that although aboveground net primary productivity declined 30-60% during drought, bud bank density and demography were insensitive to drought. These results suggest that grassland resistance and resilience when perturbed by drought may be mediated by stability of belowground bud banks. Second, I investigated vegetation and soil nutrient legacies following release from long-term grazing (Chapter 3). I documented a relatively rapid shift in aboveground vegetation within four years of grazer exclusion, with productivity, stem density, and diversity becoming relatively more similar to ungrazed than grazed prairie. The density and composition of the belowground bud bank and soil seed bank shifted more slowly, remaining more similar to grazed than ungrazed prairie. Responses of soil nutrients to removal of grazers varied, and in some cases was affected by recent fire history. These results demonstrate the contribution of belowground propagules to the maintenance of a diverse plant community both during grazing and after grazers are removed. Finally, I examined short-term vegetation responses to both drought and grazing (Chapter 4). Despite extreme drought and simulated grazing that reduced productivity and increased mortality of individual stems, the dominant C4 grasses maintained a stable bud bank. Aboveground net primary productivity and bud bank density of sedges and forbs, however, were reduced by both drought and grazing. This differential response of species to extreme drought and grazing led to shifts in community composition and species diversity over one growing season. Across drought and grazing treatments, live rhizome biomass was highly correlated with bud bank density and may be a useful, more easily measured index of bud bank density.

Doctor of Philosophy / Department of Agronomy / Johanna A. Dille / Kochia (Kochia scoparia L. Schrad.), one of the most problematic weeds in the Great Plains of United States, has evolved resistance to some herbicides including glyphosate (5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) inhibitor) which was first reported in western Kansas in 2007. The objectives of this research were to (1) characterize six kochia populations from western Kansas on the basis of glyphosate resistance or multiple herbicide resistance, (2) determine germination characteristics of the populations and evaluate their growth and fecundity in the field, and (3) determine if EPSPS gene amplification responsible for glyphosate resistance in kochia was associated with growth and fecundity cost in the plants. Six kochia populations were from Scott, Finney, Thomas, Phillips, Wallace, and Wichita counties. Based on shikimate assay for glyphosate and recommended field rates for four tested herbicides, three kochia populations (Scott (SC-R), Finney (FN-R), and Thomas (TH-R)) were grouped into glyphosate-resistant (GR) and three populations (Phillips (PH-S), Wallace (WA-S) and Wichita (WI-S)) were grouped into glyphosate-susceptible (GS). All populations were resistant to dicamba (synthetic auxin) and chlorsulfuron (acetolactate synthase inhibitor), however, atrazine (PS II inhibitor) resistance in FN-R was noted as exceptional among the GR populations. Across the three germination temperatures (5, 10 and 15 C), the GR populations consistently had less total cumulative germination and at 15 C, they consistently required more time to attain 50% of maximum cumulative germination than the GS populations. Both the field study and evaluation of relationship between EPSPS gene amplification and plant performance showed that differences in plant height, biomass accumulation and fecundity among populations were not in respect to glyphosate resistance but rather, differences in their inherent ability to grow and produce seeds in the presence or absence of neighbors. This research suggests that fitness differences between GR and GS kochia populations could be identified in germination characteristics but not in their growth or fecundity.

Premise of research. Dust particles and pollen grains are similar in size. Dust deposition might therefore influence the pollination and reproduction of flowering plants. Little is known about such effects, however, despite more general interest in ecological effects of dust. Methodology. We used observational and experimental methods to explore whether dust generated by traffic on unpaved roads affects the amounts of pollen received and numbers of seeds produced by four species of native wildflowers in the western United States. Pivotal results. Flowers of Nuttall's larkspur (Delphinium nuttallianum), scarlet gilia (Ipomopsis aggregata), Lewis flax (Linumlewisii), and sulphur paintbrush (Castilleja sulphurea) growing 1-2mfrom a road received substantially more dust and less pollen than those growing 40-50 m away. We observed the same pattern when we transplanted individuals of the first two species into pots and placed pots near to compared with far from a road. Experimental "hand dusting" of scarlet gilia and Lewis flax plants also reduced stigma pollen loads to a degree that resembled the average effect of road proximity for those species. On the other hand, numbers of seeds per flower ("seed set") did not vary consistently for any species as a function of road proximity or hand-dusting treatment. Conclusions. Several mechanisms might contribute to the different effects of dust on pollen loads and seed set. Wediscuss four possible mechanisms, which we refer to as pollen excess, pollen quality, resource limitation, and compensatory herbivory. These mechanisms suggest avenues for further study of dust, pollination, and plant reproduction with this and other systems.

Apesar da capacidade regenerativa da dentina já ser bem estabelecida, este processo pode ser insuficiente no caso de injúrias decorrentes de traumas e/ou lesões cariosas extensas, podendo levar à exposição pulpar e perda de sua vitalidade. Assim, pesquisas recentes no campo da engenharia tecidual têm identificado materiais e substâncias que poderiam ser utilizadas como biomodificadores da dentina e auxiliares na regeneração do complexo dentina-polpa. Entre eles estão os extratos ricos em proantocianidina, um composto fenólico bioativo presente no extrato de semente de uva (GSE). Assim, o objetivo deste trabalho foi avaliar o potencial estimulatório de quatro concentrações crescentes do GSE na atividade funcional de células odontoblastoides. Foram utilizadas células de camundongo da linhagem MDPC-23, cultivadas em garrafas de cultura até a subconfluência. Em seguida, as células foram cultivadas em placas de 24 poços em uma concentração de 104/poço e divididas em cinco grupos: células sem adição do GSE, células + 0.1 µg/mL de GSE; células + 1 µg/mL de GSE; células + 10 µg/mL de GSE; células + 20 µg/mL de GSE. Após 3, 7 e 10 dias, foram analisados os seguintes parâmetros: proliferação e viabilidade celular, detecção e atividade de fosfatase alcalina, quantidade de proteína total, detecção e quantificação de nódulos mineralizados, expressão quantitativa dos genes Alp, Col1a1 e Dmp1 por meio de PCR em tempo real e sua expressão proteica correspondente por meio de imunolocalização. Os dados obtidos foram analisados quanto à normalidade e submetidos aos testes estatísticos ANOVA e Kruskal-Wallis, com nível de significância estabelecido em 5%. Os resultados mostraram proliferação e viabilidade celular com as concentrações mais baixas de GSE (0,1 e 1 µg/mL), assim como a atividade de síntese de proteínas totais e da fosfatase alcalina. A deposição de nódulos mineralizados foi significativamente maior com a concentração de 1 µg/mL do extrato. Esta mesma concentração favoreceu a expressão quantitativa dos genes Alp, Col1a1 e Dmp1 e a secreção das proteínas correspondentes vistas por imunolocalização. Conclui-se que baixas concentrações do extrato de semente de uva podem influenciar e favorecer a atividade de células odontoblastoides, contribuindo para a regeneração dentinária, devido à suas características antioxidantes e biomineralizadoras / The process of dentinogenesis generally involves several steps of cell differentiation, culminating with an extracellular matrix very similar to bone tissue. Dentin regeneration may be necessary in cases of pulp exposure, root resorption and carious lesions. Studies on functional regeneration of lost tissues are being carried on recently, based on the presence of cells, scaffolds and/or substances that induce cell proliferation and differentiation. Among the several substances which can interact with cell metabolism are the extracts rich in proanthocyanidin, bioactive phenolic compounds present in fruits, vegetables and seeds. The purpose of this project is to evaluate the stimulatory potential of four different concentrations of grape seed extract (GSE) in the functional activity of odontoblast-like cells. MDPC-23 cell line was seeded in culture flasks until subconfluence followed by cell seeding in 24-well culture plates in the concentration of 104/well and divided in five groups: 1) cells without GSE, 2) cells + 0,1 µg/mL of GSE; 3) cells + 1 µg/mL of GSE; cells + 10 µg/mL of GSE and cells + 20 µg/mL of GSE. After 3, 7 and 10 days, there were evaluated the following parameters: cell proliferation and differentiation, ALP detection and activity, total protein content, mineralization detection and quantification, as well as the expression of genes Alp, Col1a1 and Dmp1 through Real Time PCR and their corresponding proteins by means of immunolocalization. Data were analyzed by ANOVA and Kruskal-Wallis statistical tests, with significance level set at 5%. The results demonstrated cell proliferation and viability with low GSE concentrations (0,1 and 1 µg/mL), as well as total protein content and ALP activity. Deposition of mineralized nodules was significantly increased with the GSE concentration of 1 µg/mL. The same concentration favoured the expression of genes Alp, Col1a1 and Dmp1 as well as the corresponding proteins. It is concluded that low concentrations of grape seed extract may influence functional activity of odontoblast- like cells, contributing to dentin regeneration by means of its antioxidant and biomineralizing properties

The content of this thesis was to draw up the literary owerview around Japanese quail breeding and fattening and to execute the practice experiment whitch aim was to analyse the efect of the inclusion of extruded flax seed to the diet for quails.