Made available in DSpace on 2014-06-11T19:28:23Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-02-18Bitstream added on 2014-06-13T20:18:03Z : No. of bitstreams: 1 silva_vc_me_jabo.pdf: 1083755 bytes, checksum: 2d0de83ba52c01f35f8a0ede2c3b555e (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O uso de pastagens é a alternativa mais econômica para a alimentação de ruminantes. É de suma importância o conhecimento das características morfogênicas e estruturais dos pastos, uma vez que as mesmas determinam o índice de área foliar do relvado, refletindo diretamente no pastejo pelos animais. O experimento foi conduzido no período de janeiro/2010 a junho/2010, com o objetivo de avaliar as características morfogênicas, estruturais e a dinâmica do perfilhamento do capim tanzânia em diferentes índices de área foliar residual (IAFr), sob pastejo rotacionado por cabras Anglonubiano. Os tratamentos consistiram de três IAF residual (0,8; 1,6 e 2,4). O delineamento experimental utilizado foi o de blocos completos casualizados, em arranjo de parcelas subdividas no tempo, com seis repetições e um total de 18 unidades experimentais. Para determinação do período de descanso foi adotado o critério de 95% de interceptação luminosa (condição de pré-pastejo). Foram avaliadas, no pré e pós pastejo, as alturas do dossel, IL, IAF, massa de forragem e as características morfogênicas e estruturais dos pastos. A altura média, IL e IAF dos dosséis no pré pastejo decresceram com a diminuição do IAFr. No pós pastejo, os IAFr 0,8 e 2,4 apresentaram maior e menor valor de IL, de 35,93 e 62,50%, respectivamente. No pré-pastejo os valores dos componentes de massa dos pastos mantidos sob IAFr 2,4 foram superiores (P<0,10), quando comparados aos pastos sob IAFr 0,8. Houve um aumento nos valores de massa verde seca (8696,85 kg/MS/ha) e massa seca total (12082,00 kg/MS/ha), conforme o ciclo de pastejo, devido principalmente à contribuição da massa seca de colmo (MSC). O período que compreendeu o último ciclo de pastejo teve a TApF 32% menor quando comparada aos primeiro e segundo ciclos de pastejo. O último ciclo de pastejo (Abr/Mai) apresentou TAlF inferior comparadas aos... / The use of pastures is the most economical way to feed ruminants. It is of paramount importance the knowledge of the morphogenetic and structural characteristics of the pasture, since they determine the leaf area index of the sward, is directly reflected by the grazing animals. The experiment was carried from janeiro2010 to June/2010, in order to evaluate the morphogenesis, structure and dynamics of tillering of Guinea grass in different residual LAI under rotational grazing by goats Anglo Nubian. The treatments consisted of three residual rLAI (0.8, 1.6 and 2.4). The experimental design was a complete randomized block, with a split plot arrangement, with six replication and a total of 18 plots. For the determination of rest period has been adopted the criterion of 95% light interception (under pre-grazing). There were evaluated before and after grazing, the sward heights, IL, LAI, herbage mass and the morphogenetic and structural characteristics of the pastures. The average height, canopy LAI and IL pre grazing decreased with decreasing rLAI. In the post grazing, the rLAI 0.8 and 2.4 showed higher and lower LI of 35.93 and 62.50% respectively. In the pre-grazing values of the components of the mass of swards under 2.4 rLAI were higher (P<0,10) when compared to pastures under rLAI 0.8. There was an increase in the values of green dry mass (8696,85 kg / DM / ha) and total dry mass (12082,00 kg / DM / ha) as the grazing cycle, mainly due to the contribution of the dry mass of stem (DMS). The period that included the last period of grazing had LAI 32% lower when compared to the first and second grazing cycles. The last grazing cycle (Apr / May) had markedly lower compared to previous cycles (Mar / Apr). The lifespan of leaves (VPD) was affected by treatments (rLAI) and the grazing season (P<0.10). The rLAI 2.4 resulted in longer life compared to rLAI 0.8 and 1.6. No significant rLAI ... (Complete abstract click electronic access below)

The main challenge in studying genetics has evolved from identifying variations and their impact on traits to comprehending the molecular mechanisms through which genetic variations affect human biology, including disease susceptibility. Despite having identified a vast number of variants associated with human traits through large scale genome wide association studies (GWAS) a significant portion of them still lack detailed insights into their underlying mechanisms [1]. Addressing this uncertainty requires the development of precise and scalable approaches to discover how genetic variation precisely influences phenotypes at a molecular level. In this study, we developed a pipeline to automate the annotation of structural variant feature effects. We applied this pipeline to a dataset of 33,942 variants from the ClinVar and GnomAD databases, which included both pathogenic and benign associations. To bridge the gap between genetic variation data and molecular phenotypes, I implemented Non-negative Matrix Factorization (NMF) on this large-scale dataset. This algorithm revealed 6 distinct clusters of variants with similar feature profiles. Among these groups, two exhibited a predominant presence of benign variants (accounting for 70% and 85% of the clusters), while one showed an almost equal distribution of pathogenic and benign variants. The remaining three groups were predominantly composed of pathogenic variants, comprising 68%, 83%, and 77% of the respective clusters. These findings revealed valuable insights into the underlying mechanisms contributing to pathogenicity. Further analysis of this dataset and the exploration of disease-related genes can enhance the accuracy of genetic diagnosis and therapeutic development through the direct inference of variants that are likely to affect the functioning of essential genes.

Biomineral composites, consisting of intercrystalline organics and biogenic minerals, have evolved unique structural designs to fulfill mechanical and other biological functionalities. Aside from the intricate architectures at the composite level and 3D assemblies of the biomineral building blocks, the individual mineral blocks enclose intracrystalline structural features that contribute to the strengthening and toughening at the intrinsic material level. Therefore, the design strategies of biomineralized composites can be categorized into two structural levels, the individual building block level and the composite level, respectively. This dissertation aims at revealing the material design strategies at both levels for the bioinspired designs of advanced structural ceramics. At the building block level, there is a lack of comparative quantification of the mechanical properties between geological and biogenic minerals. Correspondingly, I first benchmark the mechanical property difference between biogenic and geological calcite through nanoindentation techniques. The selected biogenic calcite includes Atrina rigida prisms and Placuna placenta laths, corresponding to calcite {0001}, and {101 ̅8} planes. The natural cleavage plane {101 ̅4} of geological calcite was added to the comparative study. Under indentation load, geological calcite deforms plastically via twinning and slips under low loads, and shifts to cleavage fracture under high loads. In comparison, the P. placenta composites, composed of micro-sized single-crystal laths and extensive intercrystalline organic interfaces, exhibit better crack resistance. In contrast, the single-crystal A. rigida prisms show brittle fracture with no obvious plastic deformation. Secondly, how the internal microstructures and loading types affect the mechanical properties of individual building blocks is investigated. The prismatic building blocks are obtained from the bivalves A. rigida and Sinanodonta woodiana, where the former consists of single-crystal calcite and the latter consists of polycrystalline aragonite. The comparative investigation under different loading conditions is conducted through micro-bending and nanoindentation. The continuous mineral matrix in A. rigida prisms leads to comparable modulus under tensile and compressive loadings in the elastic regime, while the high-density intracrystalline nanoinclusions contribute to the conchoidal fracture behaviors (instead of brittle cleavage). In comparison, the interlocking grain boundaries in S. woodiana prisms correlate with easier tensile deformation (smaller tensile modulus) than compression, as well as the intergranular fracture morphologies. The third topic in the biomineral-level investigation focuses on how biomineral utilizes residual stress at the macroscopic scale. The selected model system is the spine from the sea urchin Heterocentrotus mamillatus, which has a bicontinuous porous structure and mesocrystalline texture. It is confirmed that the spine has a macroscopic stress field with residual tension in the central medulla and compression in the radiating layers. The multimodal characterizations on the spine conclude that the structural origins are not associated with the gradient distribution of the intracrystalline defects, including Mg substitution in the calcite matrix, intracrystalline organics, and amorphous calcium carbonates (ACC). It is hypothesized that the residual stress is generated due to the volume expansion during ACC crystallization at the compacted growth front. At the composite level, even though enhanced crack resistance is expected in biomineralized composites due to their hierarchical structures, the correlation between their 3D composite structures and damage/crack evolution is quite limited in the literature. I developed in-situ testing devices integrated with synchrotron-based X-ray tomography to capture the crack propagation in the materials, including the four-point bending and compression/indentation configurations. Two representative models are chosen to demonstrate the deformation of biomineralized composites under bending and compression, respectively, including the calcium carbonate-based gastropod shell (Melo diadema) and the hydroxyapatite-based fish teeth (Pogonias cromis). Also, the two composites are designed to achieve different functional requirements, i.e., enhanced fracture toughness vs. wear resistance. The comprehensive characterizations of these two composites revealed how biological structural composites are designed accordingly to their functional needs. For the crossed-lamellar M. diadema shell, directional dependence of the shell property was revealed, where the transversal direction (perpendicular to the growth line) represents both the stronger and tougher direction, but the longitudinal direction is more resistant to notches and defects. For the P. cromis teeth, the enhanced wear resistance of the near-surface enameloid originates from the intricate designs at the microscale, with c-axes of hydroxyapatite crystals and micro-sized enameloid rods coaligned with biting direction and F and Zn doping. In addition, the fracture morphologies of the fish teeth correlate with the microstructures; the enameloid exhibits corrugated fracture paths due to the interwoven fibrous building blocks, and the dentin exhibits clean planar fracture surfaces. / Doctor of Philosophy / Ceramic materials have wide applications in daily life and advanced technologies, and examples range from kitchenware (e.g., cups and plates) to spacecraft (e.g., thermal coating). These materials have indispensable applications due to their advantages of high strength and hardness, high heat and corrosion resistance, lightweight, chemical inertness, etc. Yet, intrinsic brittleness usually limits their applications. Typical ways to enhance the toughness of ceramics involve microstructure design (by refining the sizes and shapes of grains) and transformation toughening (phase transition) at the individual grain level, composite reinforcement (or ceramic matrix composites) at the composite level, and introducing residual stress to impede crack initiation and propagation. The engineering methods usually involve high energy input, chemical treatment, and usually significant waste and non-ecofriendly emissions. Therefore, learning the design strategies from biological ceramic solids constructed by organisms wound provide valuable insights into enhancing the performance of ceramics while reducing the harmful impact on the environment. In this dissertation, I investigated the mechanical design strategies from natural 3D biomineralized composites from two structural levels, i.e., building-block and composite levels, analogous to individual grains and composite reinforcement in engineering ceramics. For the building-block level research, the model systems include bivalve shells Atrina rigida, Placuna placenta, and Sinanodonta woodiana. The three bivalve shells contain different building blocks with intrinsic microstructures, corresponding to monolithic prisms with controlled nanoinclusions, diamond-shaped thin laths, and polycrystalline prisms with interlocking grains, respectively, presenting different structural designs of individual grains in ceramic materials. The sea urchin Heterocentrotus mamillatus spine represents a natural porous material with compressive residual stress on the surface, and the investigation of the structural origins aims to provide insights into the cost-effective synthesis of stressed ceramics with residual stress for engineering applications. In addition, the composite-level studies focus on the composite structures of the crossed-lamellar shell Melo diadema and the fish teeth from Pogonias cromis. These two model systems correspond to natural ceramic matrix composites with nano-scale fibrous building blocks arranged in 3D specialized for enhanced crack resistance and wear resistance, respectively. The comprehensive investigation of the deformation behaviors and mechanisms allows for a better understanding of the intricate strategies specialized for different functional requirements, which apply to bio-inspired designs in ceramic composites.

Objetivou-se com esse trabalho avaliar o efeito das doses de nitrogênio sobre as características morfogênicas, estruturais, crescimento da cultura e no desempenho de novilhos de corte em pastagem de Panicum maximum cv. Mombaça no norte de Tocantins. Os tratamentos consistiram nas aplicações de: 114,2, 228,3 e 342,5 kg/ha de nitrogênio aplicado na forma de sulfato de amônio no período das águas, nos meses de dezembro a abril de 2016. A pastagem foi adubada ainda com 50 kg/ha de P2O5 na forma de superfosfato simples previamente ao experimento, e K2O na forma de KCl, aplicado juntamente com o nitrogênio na proporção 1:0,5. Utilizou-se 24 novilhos Nelore com nove meses de idade e 173 kg de peso vivo médio inicial para avaliação de desempenho e 36 animais reguladores para manter a altura de saída da forragem. A pastagem foi manejada em pastejo rotacionado, com sete dias de pastejo e 21 dias de descanso. Para as medidas relacionadas a morfogênese, estrutura e composição química, foi utilizado o delineamento em blocos casualizados, com medidas repetida no tempo, três tratamentos, dois blocos por tratamento com quatro ciclos e quatro repetições (piquetes) por bloco, avaliando-se a interação entre tratamentos e ciclos. Para avaliação do desempenho animal utilizou-se delineamento inteiramente casualizado, com medidas repetidas no tempo, com três tratamentos, quatro ciclos de pastejo e oito repetições (animais) por tratamento, avaliando a interação entre tratamentos e ciclos. As variáveis foram submetidas a análise de variância a 5% de significância pelo teste t de Student. As maiores doses de nitrogênio não influenciaram a taxa de alongamento foliar, taxa de aparecimento foliar, taxa de alongamento de haste, filocrono e densidade populacional de perfilhos (p>0,05), no entanto, sofreram influência dos ciclos de pastejo (p<0,05), com exceção do filocrono. Com o aumento da dose de N de 114,2 para 342,5 kg o índice de área foliar pré-pastejo aumentou de 8,86 para 13,84 m2. O comprimento final das folhas expandidas sofreu incrementos de 9,6% com a maior dose (p<0,05). A maior dose de nitrogênio aumentou a taxa de crescimento cultural (p<0,05) com valores de 254,74 e 188,41 kg/ha/dia na maior e menor dose, respectivamente. A massa seca de forragem total, das lâminas foliares e de colmo verde prépastejo foram afetadas com a dose de 342,5 kg/ha de N (p<0,05), aumentando em 19,2; 20,7 e 32,6%, respectivamente, em relação a menor dose. Houve redução dos teores de FDN e FDA e aumento da PB (p<0,05) com a elevação das doses de 114,2 para 342,5 kg. O ganho médio diário dos animais não foi influenciado pelos tratamentos (p>0,05), com valor médio de 0,470 kg/animal/dia, no entanto, o ganho por área e a taxa de lotação foram incrementados pela maior dose, sobretudo nos dois ciclos intermediários (2º e 3º), apresentando valores médios de 5,51 e 6,38 kg/ha/dia e taxa de lotação de 5,5 e 7,0 UA/ha nas doses de 114,2 e 342,5kg de nitrogênio, respectivamente. Os parâmetros sanguíneos não foram afetados pelas doses de nitrogênio (p>0,05). Conclui-se que em pastagem de capim-Mombaça as características morfoestruturais relacionadas ao índice de área foliar, comprimento final das folhas e taxa de crescimento cultural aumentam com a elevação das doses de nitrogênio de 114,2 para 342,5 kg/ha/ano de nitrogênio. A massa seca de forragem total e de seus componentes morfológicos é incrementada com doses de 342,5 kg/ha de nitrogênio. A utilização da maior dose nitrogênio melhora a qualidade nutricional do Mombaça, reduzindo os teores de FDN e FDA e elevando a fração de proteína bruta na matéria seca. O aumento das doses de 114,2 para 342,5 kg/ha de nitrogênio não melhora o desempenho individual dos animais, no entanto, aumenta a produtividade por área. / The objective of this study was to evaluate the effect of nitrogen doses on morphogenetic characteristics, structural, crop growth and performance of beef steers grazing Panicum maximum cv. Mombasa in northern Tocantins. The treatments consisted of the application: 114.2, 228.3 and 342.5 kg/ha of nitrogen applied in the form of ammonium sulfate in the rainy season (December to April 2016). The pasture was also fertilized with 50 kg/ha P2O5 in the form of superphosphate prior to the experiment, and K2O as KCl, applied together with the nitrogen in the ratio 1: 0.5. Twenty-four Nellore steers with nine months of age and 173 kg average weight for performance evaluation and 36 animals regulators to maintain forage output high. The pasture was managed in a rotational grazing, with seven days of grazing and 21 days rest. For measures related to morphogenesis, structure and chemical composition, was used a randomized block design, with measurements repeated in time, three treatments, two blocks per treatment with four cycles and four replications (paddocks) per block, evaluating the interaction and between treatment cycles. For evaluation of animal performance was used completely randomized design with repeated measurements over time, with three treatments, four grazing cycles and eight repetitions (animals) per treatment, evaluating the interaction between treatments and cycles. The variables were subjected to analysis of variance at 5% significance by Student's t test. Higher doses of nitrogen did not affect the leaf elongation rate, leaf appearance rate, stem elongation rate, phyllochron and tiller population density (p>0.05), however, they suffered influence of grazing cycles (p<0.05), with the exception of phyllochron. With increasing N rate of 114.2 to 342.5 kg pre-grazing the leaf area index increased from 8.86 to 13.84 m2. The final length of the expanded sheets suffered increments of 9.6% with the highest dose (p<0.05). The higher dose of nitrogen increased the cultural growth rate (p<0.05) values of 254.74 and 188.41 kg/ha.day at higher and lower dose, respectively. The dry weight of the total forage, the leaf blades and pre-grazing green stem were affected with the dose of 342.5 kg/ha of N (p<0.05), increasing by 19.2; 20.7 and 32.6%, respectively, compared to lower doses. There was a decrease of NDF and ADF contents and increased BP (p<0.05) with increasing doses of 114.2 to 342.5 kg. The average daily gain of the animals was not affected by treatments (p>0.05), with an average of 0.470 kg/animal.day, however, the gain per area and the stocking rate were increased by the higher dose, particularly in two intermediate cycles (2 and 3), with average values of 5.51 and 6.38 kg/ha.day and stocking rate of 5.5 and 7.0 AU/ha in doses of 114.2 and 342,5kg nitrogen, respectively. The blood parameters were not affected by nitrogen levels (p>0.05). We conclude that in Mombaçagrass grazing the morphostructural characteristics related to leaf area index, final length of the leaves and cultural growth rate increase with the elevation of 114.2 doses of nitrogen to 342.5 kg/ha nitrogen. The dry weight of the total forage and its morphological components is increased with doses of 342.5 kg/ha of nitrogen. The use of higher nitrogen dose improves the nutritional quality of Mombasa, reducing NDF and ADF contents and increasing the crude protein fraction in dry matter. Increasing doses of 114.2 to 342.5 kg/ha of nitrogen does not improve the performance of individual animals, however, increases productivity per area.

Orientador: Ana Cláudia Ruggieri / Banca: Carlos Augusto de Miranda Gomide / Banca: Ricardo Andrade Reis / Resumo: O uso de pastagens é a alternativa mais econômica para a alimentação de ruminantes. É de suma importância o conhecimento das características morfogênicas e estruturais dos pastos, uma vez que as mesmas determinam o índice de área foliar do relvado, refletindo diretamente no pastejo pelos animais. O experimento foi conduzido no período de janeiro/2010 a junho/2010, com o objetivo de avaliar as características morfogênicas, estruturais e a dinâmica do perfilhamento do capim tanzânia em diferentes índices de área foliar residual (IAFr), sob pastejo rotacionado por cabras Anglonubiano. Os tratamentos consistiram de três IAF residual (0,8; 1,6 e 2,4). O delineamento experimental utilizado foi o de blocos completos casualizados, em arranjo de parcelas subdividas no tempo, com seis repetições e um total de 18 unidades experimentais. Para determinação do período de descanso foi adotado o critério de 95% de interceptação luminosa (condição de pré-pastejo). Foram avaliadas, no pré e pós pastejo, as alturas do dossel, IL, IAF, massa de forragem e as características morfogênicas e estruturais dos pastos. A altura média, IL e IAF dos dosséis no pré pastejo decresceram com a diminuição do IAFr. No pós pastejo, os IAFr 0,8 e 2,4 apresentaram maior e menor valor de IL, de 35,93 e 62,50%, respectivamente. No pré-pastejo os valores dos componentes de massa dos pastos mantidos sob IAFr 2,4 foram superiores (P<0,10), quando comparados aos pastos sob IAFr 0,8. Houve um aumento nos valores de massa verde seca (8696,85 kg/MS/ha) e massa seca total (12082,00 kg/MS/ha), conforme o ciclo de pastejo, devido principalmente à contribuição da massa seca de colmo (MSC). O período que compreendeu o último ciclo de pastejo teve a TApF 32% menor quando comparada aos primeiro e segundo ciclos de pastejo. O último ciclo de pastejo (Abr/Mai) apresentou TAlF inferior comparadas aos ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The use of pastures is the most economical way to feed ruminants. It is of paramount importance the knowledge of the morphogenetic and structural characteristics of the pasture, since they determine the leaf area index of the sward, is directly reflected by the grazing animals. The experiment was carried from janeiro2010 to June/2010, in order to evaluate the morphogenesis, structure and dynamics of tillering of Guinea grass in different residual LAI under rotational grazing by goats Anglo Nubian. The treatments consisted of three residual rLAI (0.8, 1.6 and 2.4). The experimental design was a complete randomized block, with a split plot arrangement, with six replication and a total of 18 plots. For the determination of rest period has been adopted the criterion of 95% light interception (under pre-grazing). There were evaluated before and after grazing, the sward heights, IL, LAI, herbage mass and the morphogenetic and structural characteristics of the pastures. The average height, canopy LAI and IL pre grazing decreased with decreasing rLAI. In the post grazing, the rLAI 0.8 and 2.4 showed higher and lower LI of 35.93 and 62.50% respectively. In the pre-grazing values of the components of the mass of swards under 2.4 rLAI were higher (P<0,10) when compared to pastures under rLAI 0.8. There was an increase in the values of green dry mass (8696,85 kg / DM / ha) and total dry mass (12082,00 kg / DM / ha) as the grazing cycle, mainly due to the contribution of the dry mass of stem (DMS). The period that included the last period of grazing had LAI 32% lower when compared to the first and second grazing cycles. The last grazing cycle (Apr / May) had markedly lower compared to previous cycles (Mar / Apr). The lifespan of leaves (VPD) was affected by treatments (rLAI) and the grazing season (P<0.10). The rLAI 2.4 resulted in longer life compared to rLAI 0.8 and 1.6. No significant rLAI ... (Complete abstract click electronic access below) / Mestre

Dans le futur, différentes sources d'énergies renouvelables comme les énergies de seconde génération produites à partir de déchets lignocellulosiques seront nécessaires pour palier à l'épuisement des énergies fossiles. Parmi ces énergies de seconde génération, le biohydrogène, le méthane et l'hythane produits à partir de procédés fermentaires anaérobies représentent des alternatives prometteuses. Cependant la production de biohydrogène et de méthane à partir de résidus lignocellulosiques est limitée par leurs structures récalcitrantes et une étape de prétraitement en amont des procédés fermentaires est souvent nécessaire. Ce travail a pour but d'étudier l'impact des facteurs biochimiques et structurels des résidus lignocellulosiques sur les performances de production d'hydrogène et de méthane, pour pouvoir par la suite développer des stratégies de prétaitements adaptées. Tout d'abord, sur un panel de vingt substrats lignocellulosiques, les potentiels hydrogène et méthane ont été corrélés aux paramètres biochimiques et structurels. Les résultats ont mis en évidence que le potentiel hydrogène est uniquement corrélé positivement à la teneur en sucres solubles. La production de méthane quant à elle est négativement corrélée à la teneur en lignine et, à un moindre degré, à la cristallinité de la cellulose, mais positivement à la teneur en sucres solubles, holocelluloses amorphes et protéines. Par la suite, des stratégies de prétraitements ont été établies pour améliorer la production d'hydrogène et de méthane. Le couplage prétaitements alcalins/enzymatique ainsi que les prétraitements à l'acide dilué, efficaces pour solubiliser les holocelluloses en sucres solubles ont été appliqués en amont de la production d'hydrogène. En combinant le pretraitement alcalin avec une hydrolyse enzymatique, le potentiel hydrogène des tiges de tournesol fut multiplié par quinze. En revanche, suite aux prétraitements acides, la production d'hydrogène fut inhibée à cause de la libération de sous-produits (furfural, 5-HMF et composés phénoliques) engendrant un changement d'espèces bactériennes vers des espèces non productrices d'hydrogène. Pour la production de méthane, cinq prétraitements thermo-chimiques (NaOH, H2O2, Ca(OH)2, HCl and FeCl3) efficaces pour délignifier ou solubiliser les holocelluloses ont été étudiés. Parmi ces prétraitements, la meilleure condition fut 55°C à une concentration de 4% NaOH pendant 24 h, résulant en une augmentation du potentiel méthane variant de 29 à 44 % en fonction des tiges de tournesol. Cette condition fut par la suite validée en réacteurs anaérobies continusavec une augmentation de 26.5% de la production de méthane. Un procédé à deux étages couplant la production d'hydrogène en batch suivi de la production de méthane en continu fut aussi étudié. Néanmoins, aucune différence significative en termes d'énergie produite ne fut observée entre les procédés à deux étages (H2/CH4) et à un étage (CH4). / In the future, various forms of renewable energy, such as second generation biofuels from lignocellulosic residues, will be required to replace fossil fuels. Among these, biohydrogen and methane produced through fermentative processes appear as interesting candidates. However, biohydrogen and/or methane production of lignocellulosic residues is often limited by the recalcitrant structure and a pretreatment step prior to fermentative processes is often required. Up to date, informations on lignocellulosic characteristics limiting both hydrogen and methane production are limited.Therefore, this work aims to investigate the effect of compositional and structural features of lignocellulosic residues on biohydrogen and methane performances for further developping appropriate pretreatments strategies. Firstly, a panel of twenty lignocellulosic residues was used to correlate both hydrogen and methane potentials with the compositional and structural characteristics. The results showed that hydrogen potential positively correlated with soluble carbohydrates only. Secondly, methane potential correlated negatively with lignin content and, in a lesser extent, with crystalline cellulose, but positively with the soluble carbohydrates, amorphous holocelluloses and protein contents. Pretreatments strategies were further developed to enhance both hydrogen and methane production of sunflower stalks. Dilute-acid and combined alkaline-enzymatic pretreatments, which were found efficient in solubilizing holocelluloses into soluble carbohydrates, were applied prior to biohydrogen potential tests. By combined alkaline-enzymatic pretreatment, hydrogen potential was fifteen times more than that of untreated samples. On the contrary, hydrogen production was inhibited after dilute-acid pretreatments due to the release of byproducts (furfural, 5-HMF and phenolic compounds) that led to microbial communities shift toward no hydrogen producing bacteria. Similarly, methane production, five thermo-chemical pretreatments (NaOH, H2O2, Ca(OH)2, HCl and FeCl3) found efficient in delignification or solubilization of holocelluloses, were considered. Among these pretreatments, the best conditions were 55°C with 4% NaOH for 24 h and led to an increase of 29-44 % in methane potential of sunflower stalks. This pretreatment condition was validated in one stage anaerobic mesophilic continuous digester for methane production and was found efficient to enhance from 26.5% the total energy produced compared to one stage-CH4 alone. Two-stage H2 (batch) / CH4 (continuous) process was also investigated. Nevertheless, in term of energy produced, no significant differences were observed between one-stage CH4 and two-stage H2 /CH4.

Although the descriptive representation of women in parliaments is continuously improving, sexist practices such as sexual harassment and domination techniques continue to permeate the inner workings of parliaments. No workplace is immune to sexual harassment but its prevalence in parliaments has serious implications, not only for those exposed but for democracy itself – conveying a message of who belongs in politics. While previous research has established the scope of the issue and its gendered and intersectional manifestations, little is known about parliamentary responses to sexual harassment. This study thus seeks to address this gap through a qualitative case study of the Swedish Parliament’s anti-harassment work, encompassing both Members of Parliament and parliamentary staff. By conducting qualitative text analysis on parliamentary documents and material gained through interviews with Swedish Members of Parliament and parliamentary staff, three dimensions of the Parliament’s anti-harassment work are explored. Initially, perceptions of sexual harassment are addressed, partly through the use of intersectional theory. Building on pioneer work in the field, de facto measures against sexual harassment are thereafter attended to. Lastly, by approaching parliaments as a specific form of gendered workplace with certain structural features, the difficulties inherent to the Swedish Parliament’s anti-harassment work are explored. Findings from the study indicate an awareness of sexual harassment as a gendered issue in the Parliament, albeit as a problem of limited scope and without recognition of how interactions between different social identity characteristics can further exposure. The mapping of different responses to sexual harassment through the three categories of regulations, complaint mechanisms and preventative/accompanying measures, reveals that measures are substantially more well developed for parliamentary staff and highlights that although there is active anti-harassment work in the Swedish Parliament, progressive efforts for Members of Parliament are continuously halted. While several difficulties are identified, the establishment of an independent complaint mechanism for Members of Parliament appears particularly pressing. Altogether, the findings indicate that the structural features of employment status, power and recurrent processes of socialising newcomers, integral to the parliamentary workplace, are important to consider when attempting to understand the disparities in measures between Members of Parliament and parliamentary staff and the difficulties in coming to terms with the issue.

Understanding the molecular structure of DNA was considered as greatest achievement in modern biology. It helped in understanding fundamental cellular processes such as replication of DNA, nature of the genetic code and transcription. It also led to technological advancements such as DNA sequencing, genetic engineering and gene cloning. The DNA molecule is highly polymorphic in nature and its structure is dependent on environment, base composition and sequence context. B-DNA, A-DNA, Z-DNA and curved or kinked DNA are some of the well characterized double helical polymorphs. B-DNA is the most prevalent structure in vivo and it can undergo small local variations and global variations. In this thesis we refer to distinct structural property of any particular DNA sequence as deviation from fibre model B-DNA structural parameters or random sequence DNA. Structural properties of DNA are an outcome of the linear arrangement of the 4 chemically different nucleotide bases and the characteristic features of the two grooves (minor and major) arising due to the asymmetric position of glycosidic bonds of base pairs. DNA structure and properties are expected to vary along its length. Several structural features have been defined for DNA duplex, while DNA stability, bendability and intrinsic curvature are well studied and found to be biologically relevant. These three sequence dependent properties differ in their nature and information content and can be studied both at local and global levels, depending on the length of DNA fragment being examined. Majority of the work in this thesis focuses on the analysis of these three DNA structural features in promoter regions of different eukaryotic systems and their relationship with gene expression. The thesis work is divided in to five sections briefly described below. The sections discuss prevalence of the three structural features, DNA stability, bendability and intrinsic curvature in the promoter regions of six eukaryotic systems namely S. cerevisiae, D. melanogaster, C. elegans, zebrafish, mouse and human. The relationship between DNA structural features of promoter regions of S. cerevisiae with gene expression variability is discussed, followed by application of the structure-based promoter prediction algorithm ‘PromPredict’ in annotating promoter regions of six different eukaryotes. Finally, an analysis of structural features of the flanking sequences of transcription factor binding sites (TFBSs) of six transcription factors and their relationship with the DNA binding affinity is discussed. Each of the projects described below will appear as a separate chapters in the thesis. An overview of the eukaryotic transcription machinery, promoter elements and different DNA structural properties are discussed in the introduction of the thesis (chapter 1). The structural properties of DNA in the promoter regions of eukaryotic genes (chapter 2)Earlier studies in the lab reported that, apart from sequence motifs, promoter re- gions have distinct structural properties, such as lower stability, lesser bendability and more curvature compared to other genomic regions. But those studies were on small datasets and few model systems. Advancement in high-throughput tech- niques has made availability of transcription start site information for many model systems. This work was initiated with the aim of investigating the structural fea- tures in different eukaryotic systems belonging to different domains of life. The quantitative analysis of three different structural features of promoter regions of six different model systems S. cerevisiae, C. elegans, D. melanogaster, zebrafish, mouse and human has been carried out. Further, the composition of different k-mers (k=3, 4 and 6) A-tracts and G-quadruplexes has been studied. The analysis allowed us to understand the similarities and differences in struc- tural features of promoter sequences in different model systems. The core promoter sequences of S. cerevisiae, C. elegans, D. melanogaster, zebra fish, mouse and hu- man have been observed to be less stable and have lower preference for nucleosome formation. S. cerevisiae, C. elegans and D. melanogaster promoter sequences have been shown to be less bendable whereas zebrafish, mouse and human promoter se- quences are flexible in terms of bendability towards major groove as predicted fDNase 1 sensitivity model. S. cerevisiae, C. elegans, D. melanogaster core promoter regions have AT rich oligomers, whereas mouse and human core promoter regions have GC rich oligomers and G-quadruplex motifs. DNA structural features of TATA-containing andTATA-less promoters (chapter 3)Eukaryotic genes can be broadly classified as TATA-containing and TATA-less based on the presence of TATA-box in their promoter sequences. Experiments on both classes of genes have reported that, they have differences in regulation of gene ex- pression and cellular functions. In this chapter, the differences in compositional and structural features of TATA-containing and TATA-less promoters in the above mentioned model systems are discussed. The results suggested that DNA structural features of TATA-containing and TATA-less promoters are distinctly different in all eukaryotes. The TATA-containing promoters are less stable, more flexible and more curved compared to TATA-less promoters in lower eukaryotes. In mouse and hu- man genes, DNA duplex stability and G-quadruplex motifs are very distinguishing features in the two classes of promoters. DNA structural properties of eukaryotic promoter regions and gene expression variability (chapter 4) Gene expression is regulated by various external (environment and evolution) and internal (genetic) factors. Presence of sequence motifs, such as TFBSs and TATA- box, as well as DNA methylation has been implicated in the regulation of expression of some genes in vertebrates, but a large number of genes lack these sequences. Ear- lier analyses (described in previous sections) in S. cerevisiae, have shown that their promoter sequences have special structural properties, such as low stability, less bendability and more curvature compared to other genomic regions. These strutural features may play a role in transcription initiation and regulation of gene expression. This project was carried out to understand 1. What is the relationship between DNA structural features and gene expres- sion? 2. What is the relationship between gene expression and bidirectionality of a pro- moter region? For this purpose, the information of seven different gene expression variability measures, stochastic noise, responsiveness, stress response, trans variability, mu- tational variance, interstrain variation and expression divergence have been com- pared with structural features in the promoter regions. It is observed that a few of the variability measures of gene expression are linked to DNA structural prop- erties, along with nucleosome occupancy, TATA-box presence and bidirectionality of promoter regions. Interestingly, gene responsiveness is shown to be most, inti- mately correlated with DNA structural features and promoter architecture. The study highlights the importance of sequence dependent structural features in gene regulation. Promoter prediction in eukaryotes using DNA duplex stability (chapter 5) Structural property-based algorithms can discriminate promoter sequences from non-promoter sequences and are far better than sequence motif-based predictors. Compared to other structural features, low stability is found to be the most preva- lent feature in promoter regions. “PromPredict” (in-house algorithm) uses the din- ucleotide free energy values obtained from differential melting stability of DNA du- plexes as a predictor of promoters and has been successfully used earlier to annotate promoter sequences in prokaryotes and rice. Comprehensive analysis of the perfor- mance of PromPredict in S. cerevisiae, D. melanogaster, C. elegans, zebrafish, mouse and human as well as TATA-containing and TATA-less promoter regions of S. cere visiae with TSS data and 48 eukaryotic systems with translation start site (TLS) data revealed that differential stability is a good criterion for promoter prediction. DNA structure in flanking sequences of consensus motifs modulate transcription factor binding (chapter 6) Sequence specific DNA-protein interactions are essential for specific expression pat- terns during the development. There are several factors contribute to DNA-binding specificities of transcription factors (TFs). They include structure and flexibility of TFs, cofactors, chromatin environment and DNA sequence. Along with actual tran- scription factor binding sites (TFBSs), their sequence context (flanking sequences) is also shown to play a major role in gene regulation. Most of the studies have ad- dressed the sequence context at global level but very little is understood about the role of sequences flanking TFBSs in binding of transcription factors. This project was initiated with the aim of understanding the effect of flanking sequences of TFBSs in transcription factor binding affinity. In vitro DNA binding information of six different transcription factors (with three types of DNA bind- ing domains, Zinc finger (GATA4), home domain (AbdA, AbdB and Ubx) and bZIP (fos-jun and Nfil3)) was provided by Aseem Ansari’s lab. The compositional and structural features (minor groove width, propeller twist, wedge and free energy) are compared with the DNA binding profiles of 12mers (or 8mers) of six different transcription factors. It has been observed that some of the DNA structural proper- ties of flanking sequences are strongly correlated with binding affinity. For GATA4 sequences, binding affinity is negatively correlated to GC content or minor groove width at their 5′ -flanking region, showing the significance of narrow minor groove at 5′ -region. On the other hand, the binding affinity of bZIP proteins is negatively correlated to wedge angles, whereas in case of homeodomain proteins, it is posi- tively correlated to propeller twist and GC content. Thus, this study highlights the differential preference for flanking sequences outside the core binding motifs of six different TFs, which interact with DNA through α-helix. ‘The relationship between transcription pre-initiation complexes and gene ex- pression variability in S. cerevisiae’ is briefly described in the appendix section of the thesis. General conclusion Overall, the results presented in this thesis indicate that DNA sequence based structural features are unique to promoter regions and play an important role in gene regulation. Local structural features of flanking sequences of transcription factor binding sites are also instrumental in determining the DNA binding affinity of transcription factors.

Made available in DSpace on 2014-08-20T13:44:36Z (GMT). No. of bitstreams: 1 dissertacao_alberto_bohn.pdf: 586241 bytes, checksum: 0568eec20a5d22d087fb11ebc9a8fb75 (MD5) Previous issue date: 2014-03-17 / The experiment was conducted at the Experimental Station of Embrapa Clima Temperado/Lowlands and Seed Analysis Laboratory of the Department of Plant Science, UFPel. Different densities in the soil seeds (T1 - 777.70 kg.ha-1; T2 - 736.63 kg.ha-1; T3 - 624.59 kg.ha-1 and T4 - 234.42 kg.ha-1) were tested in annual ryegrass (Lolium multiflorum Lam.) in succession to soybean crop. Forage harvesting has occurred twice and after the second defoliation, were tested different levels of urea (null; 45; 90 and 135 kg.ha-1). The highest densities produced more rapid crop establishment and greater mass of harvested forage, both at first and in the second cut. In this sense, from the application of different doses of urea was found, only significant effect of nitrogen on seed yield, so the addition of a unit of urea increased by 1.7 units seeds. Occurred relationship between levels of SPAD when the assessment was conducted before flowering. Prior to harvest seed regression models between SPAD and urea levels were not significant. The seed physiologic quality was not affected by the levels of in the soil seeds and urea. / O experimento foi conduzido na Estação Experimental da Embrapa Clima Temperado/Terras Baixas e no Laboratório de Análises de Sementes do departamento de Fitotecnia da Universidade Federal de Pelotas - UFPel. Foram avaliadas diferentes densidades de sementes no solo (T1 - 777,70 Kg.ha-1; T2 - 736,63 Kg.ha-1; T3 - 624,59 Kg.ha-1 e T4 - 234,42 Kg.ha-1) de azevém anual (Lolium multiflorum Lam.) em sucessão a cultura da soja. Ocorreu a colheita de forragem em duas ocasiões e, após a segunda desfolha, utilizada diferentes doses de ureia (zero; 45; 90 e 135 kg.ha-1). As maiores densidades proporcionaram mais rápido estabelecimento da cultura e maior massa de forragem colhida, tanto no primeiro, quanto no segundo corte. Neste sentido, a partir da aplicação das diferentes doses de ureia verificou-se, apenas, efeito significativo do nitrogênio sobre o rendimento de sementes, de modo que o acréscimo de uma unidade de ureia aumentou 1,7 unidades de sementes. Através do clorofilômetro foi possível predizer o rendimento de sementes pelos níveis de SPAD, quando comparadas antes do florescimento. Previamente a colheita da semente os modelos de regressão entre SPAD e níveis de nitrogênio não foram significativos. A qualidade fisiológica da semente não influenciada pelos fatores avaliados.

This paper concerns methods of verification of person's signature and handwriting. Some of commonly used techniques are resumed and described with related literature being referred. Next aim of this work is design and implementation of a simple handwriting verification application. Application is based on edge detection and comparison of a set of structural and statistical features. As a support classification tool a SVM classifier of the LIBSVM software is employed. The Application is written in C language using OpenCV graphics library. Testing and training set was extracted from samples found in the IAM Handwriting Database. Application was created and tested in the Windows XP operating system.