This work has examines the creation and use of chemical templates for nanocircuit and other nanodevice fabrication. Chemical templating can be useful in attachment, orientation and wiring of molecularly templated circuits. DNA origami provides a suitable method for creating molecularly templated circuits as DNA can be folded into complex shapes and functionalized with active circuit elements, such as semiconducting nanomaterials. Surface attachment of DNA origami structures can be accomplished by hybridization of dangling single-stranded DNA (ssDNA) on the origami structures with complementary surface-bound strands. Chemical templating provides a pathway for placing the patterned surface-bound attachment points needed for surface alignment of the molecular templates. Chemical templates can also be used to connect circuit elements on the surface by selectively metallizing the templates to form local wiring. AFM tip-directed nano-oxidation was selected as the method for patterning to create chemical templates. This project demonstrates new techniques for creating, continuous metallization of, and DNA attachment to nanochemical templates. Selective-continuous metallization of nanochemical templates is needed for wiring of circuit templates. To improve the metallization density and enable the continuous nano-scale metallization of amine-coated surfaces, the treatment of amine-coated surfaces with a plating additive prior to metallization was studied. The additive treatment resulted in a 73% increase in seed material, enabling continuous nano-scale metallization. A new method was developed to create amine nanotemplates by selective attachment of a polymer to surface oxide patterns created by nano-oxidation. The treatment of the templates with the additive enabled a five-fold reduction in feasible width for continuous metallization. Nano-oxidation was also used in the nanometer-scale patterning of a thiol-coated surface. Metallization of the background thiols but not the oxidized patterns resulted in a metal film that was a negative of the patterns. The resulting metal film may be useful for nanometer-scale pattern transfer. DNA-coated gold nanoparticles (AuNPs) were selectively attached to amine templates by an ionic interaction between the template and ssDNA attached to the particles. Only the ssDNA on the bottom of the AuNPs interacted with the template, leaving the top strands free to bind with complementary ssDNA. Attempts to attach origami structures to these particles were only marginally successful, and may have been hindered by the presence of complementary ssDNA in solution but not attached to the origami, or the by the low density of DNA-AuNPs attached to the templates. The formation of patterned binding sites by direct, covalent attachment of ssDNA to chemical templates was also explored. Initial results indicated that ssDNA was chemically bound to the templates and able to selectively bind to complementary strands; however, the observed attachment density was low and further optimization is required. Methods such as these are needed to enable nano-scale, site-specific alignment of nanomaterials.

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Crabgrass is a warm-season annual species that has the potential to provide high-quality summer forage for ruminants in the transition zone between subtropical and temperate regions of the United States. Growing annual lespedeza in association with crabgrass may be beneficial due to nitrogen transfer from the legume to the grass. The objectives of the research reported in this thesis were to (1) determine the effects of pH on establishment and growth of crabgrass; and (2) evaluate the effects of lespedeza seeding rate and N fertilization treatment on the yield, botanical composition, and nutritive value of crabgrass-lespedeza mixtures. A greenhouse study was conducted using three soil pH levels of 4.8, 5.5, and 6.3. Crabgrass germination and root and shoot yields were not affected by soil pH values. A field study was conducted to evaluate the influence of six lespedeza seeding rates (0-28 kg ha-1) and two N fertilization treatments (140 kg total N ha-1 or zero N) on crabgrass-annual lespedeza mixtures. In most cases, increasing lespedeza seeding rate increased lespedeza in the sward. However, lespedeza rate had limited effect on yield and nutritive value of the mixture. Nitrogen fertilization increased crabgrass in the sward and total yield by as much as 46%. Responses of nutritive value parameters to N fertilization were variable and appeared linked to weather factors. In vitro true digestibilities ranged from 750 to 875 g kg-1, and were largely unaffected by N fertilization and seeding rate The results of these studies indicate that crabgrass could provide moderate amounts of highly digestible forage while growing on acidic soils commonly found in the southeastern United States. Annual lespedeza may be grown in association with crabgrass, but limited improvement in yield and nutritive value were found for this practice. / Master of Science

There is growing interest in the development of biomimetic matrices that are simultaneously cell-friendly, allow rapid vascularization, exhibit enough mechanical integrity to be comfortably handled and resist mechanical stresses when implanted in the site of interest. Meeting all these requirements with a single component material has proved to be very challenging. The hypothesis underlying this work was that hybrid materials obtained by combining scaffolds with bioactive hydrogels would result in a synergy of their best properties: a construct with good mechanical properties, easily handled and stable thanks to the scaffold; but also, because of the gel, cell-friendly and with enhanced oxygen and nutrients diffusion, and promoter of cell colonization. Moreover, such a composite material would also be useful as a controlled release system because of the gel’s incorporation. Poly (ethyl acrylate) (PEA) scaffolds prepared with two different morphologies were envisaged to provide the mechanical integrity to the system. Both types of scaffolds were physicochemically characterized and the effect of the scaffolds production process on the PEA properties was examined. The scaffolds preparation methods affected the PEA properties; nevertheless, the modifications induced were not detrimental for the PEA biological performance. Two different bioactive gels were studied as fillers of the scaffolds’ pores: hyaluronan (HA), which is a natural polysaccharide, and a synthetic self-assembling peptide, RAD16-I. HA is ubiquitously present in the body and its degradation products have been reported to be angiogenic. RAD16-I is a synthetic polypeptide that mimics the extracellular matrix providing a favourable substrate for cell growth and proliferation. Given the hydrophobic nature of poly(ethyl acrylate), the combination of PEA scaffolds with aqueous gels raised a number of problems regarding the methods to combine such different elements, the ways to gel them inside the pores, and the procedures to seed cells in the new composite materials. Different alternatives to solve these questions were thoroughly studied and yielded protocols to reliably obtain these complex structures and their biohybrids. An extensive physico-chemical characterization of the components’ interaction and the combined systems was undertaken. As these materials were intended for cardiac tissue engineering applications, the mechanical properties and the effect of the fatigue on them were studied. The different composite systems here developed were homogeneously filled or coated with the hydrogels, were easy to manipulate, and displayed appropriate mechanical properties. Interestingly, these materials exhibited a very good performance under fatigue. The use of the composite systems as a controlled release device was based on the possibility of incorporating active soluble molecules in the hydrogel within the pores. A release study of bovine serum albumin (BSA), intended as a model protein, was performed, which served as a proof of concept. The biological performance of the hybrid scaffolds was first evaluated with fibroblasts to discard the materials cytotoxicity and to optimize the cell seeding procedure. Subsequently, human umbilical vein endothelial cells (HUVECs) cultures were performed for their interest in angiogenic and vascularization processes. Finally, co-cultures of HUVECs with adipose-tissue derived mesenchymal cells (MSCs) were carried out. These last cells are believed to play an important role for clinical regenerative medicine, and their cross-talk with the endothelial cells enhances the viability and phenotypic development of HUVECs. Through the different experiments undertaken, hybrid scaffolds exceeded the outcome achieved by bare PEA scaffolds. / Arnal Pastor, MP. (2014). New scaffolding materials for the regeneration of infarcted myocardium [Tesis doctoral]. Editorial Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/46129 / Premios Extraordinarios de tesis doctorales

Alzheimer's disease (AD) is a large and growing problem and while we today lack a full understanding of this disease, we know that the protein tau and the amyloid fibrils it forms play a central role in its development. We also know that these fibrils can have different morphologies in different diseases and that fibrils produced in vitro not necessarily adopt any of the morphologies found in patients. This means there is a need for more pathologically relevant fibrils in vitro to be able to understand this disease better. One approach to satisfy this need is to use fibrils found in patients as seeds and thus transfer their morphology to recombinantly purified protein. To facilitate this process this study has attempted to develop a way to differentiate between different fibril morphologies using a FRET based system. This involves fluorescent fusion proteins (tau-EXFPs) and fluorescent amyloid probes as well as seeding experiments with pseudo wild type tau (PWT) and tau with the P301L mutation. Greater differences in terms of fibrillation rates and ThT fluorescence between PWT and P301L was shown than previously reported between WT and P301L. They were also shown to differ in fibril morphology in TEM. The ThT fluorescence intensity was to a certain degree transferable from PWT to P301L by seeding. Furthermore, this study confirms that the tau-EXFP fusion protein can be incorporated into amyloid fibrils and strongly suggests that a FRET effect between EXFP and BTD14 (as well as X34 and ThT) can be achieved. It also demonstrates differences in FRET efficiency between PWT and P301L fibrils using FLIM. These results indicate that a FRET based approach could be a useful method to discern different fibril morphologies from each other, but further measurements and optimization are needed before this method could be reliably applied. The fusion proteins could also be used to investigate tau spreading in vivo, e.g. in D. melanogaster. To find suitable FRET partners to the fusion proteins, a ligand screen was conducted. This could be used as an alternative to the FRET method. With the right selection of fluorescent amyloid probes, a unique fingerprint for each fibril morphology could maybe be generated and fulfill the same intended function as the FRET method.

A doença vassoura-de-bruxa reduziu expressivamente a produtividade dos cacauais da região sul da Bahia, maior produtora nacional. O controle genético da enfermidade, com o uso de plantas tolerantes e com alto potencial produtivo, tem sido a principal estratégia para o convívio com essa doença. O plantio de mudas clonais, provenientes de estacas enraizadas, tem mostrado ser uma prática promissora para a renovação da lavoura. O Instituto Biofábrica de Cacau (IBC), criado em 1999, tem como um de seus objetivos produzir e comercializar essas mudas. Estudos preliminares mostraram a necessidade de aprimoramento do protocolo, pois foram observados distúrbios nutricionais, apesar do uso elevado de fertilizantes. Os objetivos deste trabalho foram: avaliar a perda de nutrientes; comparar metodologias de extração de nutrientes em substratos; identificar a folha mais adequada para ser utilizada como diagnóstica; comparar formas de adubação; definir níveis críticos (NC) e doses recomendáveis de P e de N. Foram realizados dois experimentos, ambos em viveiro de produção de mudas do IBC, onde se utilizou o clone PH 16, com 12 mudas por parcela útil (uma muda por tubete de 288 cm3), sendo avaliados: diâmetro, altura, área foliar, matéria seca, concentração e conteúdo de nutrientes na planta. O primeiro experimento, implantado em julho de 2005, foi um fatorial 5x5+1: cinco substratos (misturas de fibra de coco – FC e Plantmax®), cinco doses de P no plantio (de zero a 0,8 g dm-3) e um tratamento adicional (P aplicado aos 30 dias); o segundo experimento, instalado em julho de 2006, foi um fatorial 2x5: duas formas de adubação, no substrato e foliar, e cinco doses de uréia, aplicadas semanalmente após o 82º dia. A análise do lixiviado do primeiro experimento identificou variações do pH, da condutividade elétrica e dos nutrientes de acordo com os tratamentos e com o tempo. A terceira folha do primeiro lançamento maduro foi a mais indicada para ser utilizada como folha diagnóstica. Para a maioria dos nutrientes, não foram encontradas correlações significativas entre os teores extraídos dos substratos, por metodologias distintas, com os absorvidos pelas plantas, exceto para P, K, Ca e Cu. A adubação com P em cobertura aumentou sua disponibilidade e absorção, mas não afetou o crescimento das mudas. Os melhores substratos foram os que continham entre 30 a 55% de FC. As doses recomendáveis, calculadas para obtenção de 99% da produção máxima da matéria seca da parte aérea, variaram de 136 a 275 g m-3 de P, aplicadas em préestaqueamento, de acordo com o substrato; e, para N, em aplicação semanal pósenraizamento, foi de 63 mg dm-3 para a adubação no substrato ou de 11,7 g L-1 para a adubação foliar. Para o N, a adubação no substrato foi superior à foliar. O NC de P no substrato variou de acordo com o extrator e o substrato e os NCs foliares foram de: 1,75 g kg-1 de P e 23,1 g kg-1 de N. / The witches' broom disease decreased expressively the cocoa productivity in Bahia south region, the biggest national producer. The disease genetic control, using tolerant plants with high potential productivity, has been the main strategy to cope with this disease. The cloned cutting breeding, originated from rooted cuttings, has proved to be a promising practice for crop renovation. The "Instituto Biofábrica de Cacau" (IBC) or Cocoa Biofactory Institute, founded in 1999, has one of its aims to produce and commercialize these rooted cuttings. Preliminary studies have shown the need of protocol improvement, as it was observed nutritional problems, despite the high use of fertilizers. The objectives of this work were: Evaluate nutrients losses; compare nutrient extraction methodologies in potting mix; identify the most suitable leaf to be used as diagnostic; compare different fertilization practice; define P and N critical levels (CL) and recommendable doses. It was carried out two experiments, both in cloning breeding nurseries of IBC, where it was used clone PH 16, with 12 cuttings by useful plot (one cutting by container of 288 cm3), being evaluated: diameter, height, foliar area, dry matter, concentration and nutrient content in plants. The first trial, implanted in July 2005, was a factorial 5x5+1: five potting mix (mix of coconut fiber – CF and Plantmax®) five doses of P in the planting (from 0 to 0.8 g dm-3) and an additional treatment (P applied on the 30th day); the second experiment, installed in July 2006, there was a factorial 2x5: two fertilization treatments, in potting mix and foliar, and five urea doses, applied weekly after the 82nd day. The first experiment leaching analysis identified variations of the pH, electric conductivity and nutrients according to treatments and time. The third leaf from first ripen sprout was the most indicated to be used as the diagnostic leaf. For most nutrients were not found significant correlation between substrate extract levels by distinct methodologies and the absorbed ones by plants, except for P, K, Ca and Cu. The P fertilization in covering increased its availability and absorption, but did not affect cutting growth. The best substrates were those contained between 30 and 55% of CF. The recommendable doses, assessed to obtain 99% of the maximum production of shoot dry matter, varied from 136 to 275 g m-3 of P, applied in the precutting, according to the substrate; and for N, in weekly pos-rooting application, was 63 mg dm-3 for the substrate fertilization or 11.7 g L-1 for foliar fertilization. For the N, the substrate fertilization was superior to foliar. The CL of P in the potting mix varied according to extractor and substrate and the foliar CLs were: 1.75 g kg-1 of P and 23.1 g kg-1 of N.

O presente trabalho tem por objetivo propor um modelo para estimação da produtividade de grãos de milho para o Estado de São Paulo com base nos valores mensais de temperatura, radiação solar e chuva, no intuito de disponibilizar ferramenta para o planejamento regional (identificação das épocas do ano e dos locais mais indicados para o cultivo de milho). O uso de modelos de crescimento e desenvolvimento vegetal possibilita uma economia de tempo, trabalho e quantidade de recursos para tomada de decisões referentes ao manejo no setor agrícola por possibilitar uma previsão do processo de interesse e/ou um melhor entendimento do sistema em estudo. O conhecimento da quantidade de energia solar disponível às plantas, bem como da capacidade de conversão da mesma em energia química metabólica, possibilita prever produtividade de grãos, no caso do milho, quanto à eficiência de conversão em biomassa, através de um modelo geral mecanístico, levando em consideração aspectos agrometeorológicos, fisiológicos, genéticos e edáficos. A assimilação de CO2 pode ser convertida em massa de carboidrato, produzida durante o processo de fotossíntese, em função do índice de área foliar, temperatura e radiação solar absorvida. Estimando-se os valores de radiação solar absorvida, fotoperíodo, índice de área foliar e duração do ciclo, considerando as correções quanto à respiração de manutenção e crescimento, bem como a variação temporal da área foliar, pode-se transformar esse valor em massa líquida de carboidrato total final produzida durante o ciclo. O balanço hídrico foi utilizado com a finalidade de estimar a deficiência hídrica durante o ciclo da cultura de milho, sendo adotado o método de Thornthwaite & Mather (1955), sendo a evapotranspiração de referência estimada pelo método de Thornthwaite (1948). A produtividade deplecionada de grãos de milho foi estimada a partir dos dados de produtividade potencial predita pelo modelo, considerando-se a depleção em função da evapotranspiração relativa (relação entre evapotranspiração real e evapotranspiração da cultura). A partir de dados climáticos obtidos de estações e postos meteorológicos localizados em diversas partes do estado de São Paulo, foram elaborados mapas de superfície no programa TNTmips, com a identificação, por município, das localidades com potencial para o desenvolvimento da cultura de milho. Através destes mapas, é possível identificar restrições quanto à deficiência hídrica, temperatura, radiação solar, produtividade potencial e produtividade de grãos de milho no estado de São Paulo. / The present work has the objective to suggest a model to estimate potential yield and corn yield for São Paulo state based on monthly values of temperature, solar radiation and rainfall, in order to dispose a tool for regional planning (identification of sites and timing during the year more indicated for maize cropping). The use of growing and development models allows savings in time, work and resources needed for making decisions regarding agricultural management, by enabling a preview of the process of interest and/or a better understanding of the system being studied. The knowledge of the available amount of solar energy to plants and the capability of those to convert it into metabolic chemical energy, allows to preview grain yield, in the case of corn, regarding to biomass converting efficiency, through a general mechanistic model, considering agro-meteorological, physiological, genetical and edaphological aspects. The carbon dioxide (CO2) assimilation can be converted into mass of carbohydrates produced during photosynthesis process, as a function of leaf area index, air temperature and absorbed solar radiation. By estimating the values of solar radiation, the photoperiod, the leaf area index, and the cycle length, and considering the corrections related to growing and maintenance respiration, as well as the temporal variation of leaf area, it is possible to transform those value into final net mass of total carbohydrate produced during the cycle. The hydric balance, as proposed by Thornthwaite & Mather (1955), was used with the objective to estimate the hydric deficit during maize cycle, being the reference evapotranspiration being estimated by Thornthwaite (1948). Corn yield was estimated up from potential yield predicted by the model, considering the depletion from the relative evapotranspiration (relation between real evapotranspiration and crop evapotranspiration). Starting from climatic data obtained from several meteorological station located at different sites in São Paulo State, Brazil, surface maps were elaborated using TNTmips software, with the identification, by county, of those sites with maize development potential. Through those maps it is possible to identify restriction regarding hydric deficit, temperature, solar radiation, potential yield, and corn yield in São Paulo State.

O presente estudo teve como objetivo avaliar o efeito da inoculação com rizóbio no estabelecimento, crescimento inicial e em alguns aspectos da dinâmica de N em folhas de leguminosas (Fabaceae) arbóreas nativas plantadas por semeadura direta no campo, em área de mata ciliar no Estado de São Paulo. Foi avaliada a emergência de plântulas (% em relação ao número de sementes plantadas) até os 3 meses após a semeadura (MAS) e o crescimento em altura aos 13 MAS. O fracionamento isotópico do N foliar também foi avaliado, pelo método da abundância natural do 15N, além da concentração de N e a razão C/N foliar. Acacia polyphylla foi usada como planta-referência não-fixadora de N2. Em relação ao desenvolvimento inicial, houve grande variação entre as espécies estudadas. Acacia polyphylla e Enterolobium contortisiliquum apresentaram taxa de germinação mediana e rápido crescimento. Mimosa bimucronata e Parapiptadenia rigida tiveram crescimento relativamente rápido, porém baixo potencial germinativo. Erythrina speciosa e Poecilanthe parviflora, com crescimento lento, apresentaram germinação elevada no campo. As espécies fixadoras de N2 mostraram &#948;15 N médio de 2,7&#8240;, enquanto que a referência Acacia polyphylla se mostrou cerca de 4,0&#8240; mais enriquecida em 15N . Erythrina speciosa e Ormosia arborea apresentaram os menores valores de &#948;15N, enquanto que Parapiptadenia rigida, enriquecida em 15N, mostrou estar obtendo N exclusivamente do solo. Poecilanthe parviflora, Mimosa bimucronata e Enterolobium contortisiliquum apresentaram valores intermediários de &#948;15N, com grande variação entre os indivíduos amostrados. A concentração de N nos tecidos foliares variou entre 1,5% e 3,6%. De forma geral, esta variável não mostrou relação direta com o &#948;15N das plantas. A menor razão C/N foi observada em Enterolobium contortisiliquum e Erythrina speciosa, seguida por M. bimucronata. Nas condições experimentais locais, as plantas não responderam à inoculação com rizóbio em nenhum dos parâmetros avaliados (estabelecimento, crescimento inicial, &#948;15N, concentração de N e razão C/N). As espécies de crescimento mais lento e com alta incidência de herbivoria observados no campo (E. speciosa e O. arborea) foram também as que apresentaram &#948;15N na faixa considerada como de ocorrência da fixação biológica de nitrogênio. Os resultados indicam, para as outras espécies, maior aquisição de N proveniente do solo. / The aim of this work was to assess the effect of rhizobia inoculation on the establishment, early growth and some aspects of N dynamics in direct-seeded native legume (Fabaceae) trees in a riparian zone of São Paulo State, Southeastern Brazil. Seedling emergency (% of total planted seeds) was evaluated until three months after sowing (MAS), and the height of the trees were measured at 13 MAS. Isotopic N fractionation was also assessed by the 15N natural abundance method, as well as foliar N content and C/N ratio. Acacia polyphylla was used as a non-N2-fixing reference plant. Acacia polyphylla and Enterolobium contortisiliquum grew most rapidly, with moderate germination rate. Mimosa bimucronata and Parapiptadenia rigida were fast-growing but with low establishment rate. Erythrina speciosa and Poecilanthe parviflora showed low growing rate, but high germination potential. The N2-fixers showed an average foliar &#948;15N of 2,7&#8240;, while the reference-plant was 4,0&#8240; more <sup15>N enriched. Erythrina speciosa and Ormosia arborea showed the lowest &#948;15N values. The high &#948;15N of Parapiptadenia rigida probably indicated that it is obtaining N exclusively from the soil. Poecilanthe parviflora, Mimosa bimucronata and Enterolobium contortisiliquum showed intermediate &#948;15N values, with strong variations among the sampled individuals. Foliar N concentrations varied from 1,5% to 3,6%. In general, N concentrations were not correlated with foliar &#948;15N . The lowest C/N ratio was observed on E. contortisiliquum and E. speciosa , followed by M. bimucronata. In this field trial conditions, rhizobia inoculation did not show differences in all surveyed parameters (establishment, early growth, foliar &#948;15N, total N content and C/N ratio of trees). The slow-growing species, E. speciosa and O. arborea , that also had a high herbivore attack observed in the field, showed foliar &#948;15N in the biological N2 fixation range. The results suggested, for the other species, a larger soil N acquisition.