The spring bloom of microalgae within the bottom of sea ice provides a significant contribution to primary production in the Arctic Ocean. The aim of this research was to improve observations of the ice algae bloom using a transmitted irradiance technique to remotely estimate biomass, and to examine the influence of physical processes on biomass throughout the sea ice melt season. Results indicate that bottom ice temperature is highly influential in controlling biomass variability and bloom termination. Snow depth is also significant as it buffers ice temperature from the atmosphere and largely controls transmission of photosynthetically active radiation (PAR). The relationship between snow depth and biomass can change over the spring however, limiting biomass accumulation early on while promoting it later. Brine drainage, under-ice current velocity, and surface PAR in the absence of snow cover are also important factors. Overall this research helps to characterize the spring ice algae bloom in the Arctic by improving in situ biomass estimates and identifying primary factors controlling it.

The spring bloom of microalgae within the bottom of sea ice provides a significant contribution to primary production in the Arctic Ocean. The aim of this research was to improve observations of the ice algae bloom using a transmitted irradiance technique to remotely estimate biomass, and to examine the influence of physical processes on biomass throughout the sea ice melt season. Results indicate that bottom ice temperature is highly influential in controlling biomass variability and bloom termination. Snow depth is also significant as it buffers ice temperature from the atmosphere and largely controls transmission of photosynthetically active radiation (PAR). The relationship between snow depth and biomass can change over the spring however, limiting biomass accumulation early on while promoting it later. Brine drainage, under-ice current velocity, and surface PAR in the absence of snow cover are also important factors. Overall this research helps to characterize the spring ice algae bloom in the Arctic by improving in situ biomass estimates and identifying primary factors controlling it.

Many biosurfactants show antimicrobial activity and some are found to be superior for isolating membrane proteins. This study was aimed towards a general understanding of the interactions of biosurfactants with lipid membranes on a molecular level. To this end, a new, fluorescence lifetime-based membrane leakage assay has been established that does not only quantify membrane permeabilization more precisely but reveals also the leakage mechanism. This mechanism, referred to as graded or all-or-none leakage, is crucial for interpreting potential biological activities and modes of action. Lipopeptides of the surfactin, fengycin, and iturin families as produced by Bacillus subtilis were studied along with synthetic surfactants. Their membrane permeabilizing activity and selectivity mirrored, to some extent, the active concentrations and fungicidal selectivity of the compounds in vivo. Furthermore, the effects of co-surfactants and co-solvents (glycerol, urea, DMSO) have been investigated to better understand and predict means of improving the performance of fungicidal products as well as conditions for membrane protein solubilization.

Many biosurfactants show antimicrobial activity and some are found to be superior for isolating membrane proteins. This study was aimed towards a general understanding of the interactions of biosurfactants with lipid membranes on a molecular level. To this end, a new, fluorescence lifetime-based membrane leakage assay has been established that does not only quantify membrane permeabilization more precisely but reveals also the leakage mechanism. This mechanism, referred to as graded or all-or-none leakage, is crucial for interpreting potential biological activities and modes of action. Lipopeptides of the surfactin, fengycin, and iturin families as produced by Bacillus subtilis were studied along with synthetic surfactants. Their membrane permeabilizing activity and selectivity mirrored, to some extent, the active concentrations and fungicidal selectivity of the compounds in vivo. Furthermore, the effects of co-surfactants and co-solvents (glycerol, urea, DMSO) have been investigated to better understand and predict means of improving the performance of fungicidal products as well as conditions for membrane protein solubilization.

All biological processes are fundamentally inter-molecular interactions. In order to understand, and hence control, biomolecular structure and function, methods are required that probe biological systems at the molecular level, ideally with those molecules being in their native environment. The research summarized herein has at its core the development and application of ultra violet (UV)-visible spectrophotometric techniquies for this prupose, in particular circular dichrosim (CD) and linear dichrosim (LD) but also absorbance, fluorescence and resonance light scattering. The spectroscopy is complemented by fundamental theoretical work on molecular structure and reactivity that forms the basis for designing molecules to bind to biomolecules for a particular structural or functional effect. A brief summary of the contributions of the listed publications to our understanding of 'Molecular aspects of biololecule structure and function' is given below under five headings: Circular dichroism theory Molecular geometry and reactivity Small molecule-macromolecule interactions: spectroscopic probes of inter-molecular geometries Molecular design for nucleic acid structure and control Spectroscopic probes of biomolecule structure: instrumentation and application In general terms these correspond to successive phases of the research programme, however, all areas have been present since the first publications in 1983 and can be traced weaving through all subsequent activity.

A imprecisão das estimativas de carbono estocado em florestas naturais no ciclo global de carbono vem criando uma demanda de desenvolvimento e padronização de métodos indiretos para modelagem deste ciclo e de emissões de CO2 provenientes de mudanças de uso da terra e florestas. O trabalho teve como objetivo estabelecer as relações empíricas existentes entre a biomassa e o estoque de carbono de uma Floresta Ombrófila Mista (FOM) e os dados ópticos provenientes de sensores remotos de média resolução espacial (ASTER, LiSSIII e TM) por meio de análise de regressão. Além disso, criou-se um cenário hipotético de Redução de Emissões por Desmatamento, Degradação Florestal e Aumento de Estoque de Carbono (REDD+). O estudo foi desenvolvido na Estação Experimental de São João do Triunfo, no estado do Paraná. As equações de regressão envolveram como variáveis dependentes (y): a biomassa e o carbono florestal, obtidos indiretamente do inventário florestal contínuo do Programa de Pesquisas Ecológicas de Longa Duração (PELD), e como variáveis independentes (x) as bandas espectrais e os índices de vegetação (IV). O tratamento estatístico envolveu a análise da matriz de correlação (r) entre as variáveis x e y; a análise de regressão linear simples, não linear e múltipla, com as seguintes estatísticas: R², R²aj., Syx, Syx% e dispersão dos resíduos, Por fim, elaboraram-se mapas temáticos para estas variáveis biofísicas. Como as correlações (r) entre as variáveis biofísicas e espectrais do sensor ASTER (15m) foram baixas, a imagem foi degradada para 30m e 45m. Na resolução de 30m, o uso dos dados ASTER foi superior ao seu uso na resolução original. Não houve diferenças significativas nos valores de r entre o uso das bandas ou dos IVs para predizer as variáveis biofísicas. Regressões lineares simples se mostraram mais adequadas do que as regressões não lineares (exponenciais e logarítmicas) e múltiplas para estimar as variáveis biofísicas, apresentando erros inferiores aos estabelecidos nas campanhas de inventários tradicionais (α < 5%). Os mapas gerados a partir do sensor ASTER 30m foram mais fidedignos ao retratar a distribuição espacial destas variáveis na área de estudo devido à alta correspondência destes com os valores observados no inventário (PELD). Assim, a equação de regressão de carbono florestal a partir do ASTER foi usada na criação do projeto REDD+. A estimativa de biomassa e de carbono florestal da FOM mediante uso de dados de sensores ópticos foi adequada, com possibilidades de ser expandida para extensas áreas. A metodologia, portanto, se mostrou apropriada para ao monitoramento, relatório e verificação de estoques de carbono em florestas. / The imprecision of the estimates of carbon stock in natural forests in the global carbon cycle has created a demand for development and standardization of indirect methods for modeling this cycle and CO2 emissions from land use change and forestry. The work had as objective to establish empirical relationships between biomass and carbon stock of an Araucaria Forest (FOM) and medium spatial resolution remote sensing data (ASTER, and LiSSIII TM) through regression analysis. In addition, we created a hypothetical scenario of Reducing Emissions from Deforestation and Forest Degradation and Enhanced Carbon Stocks (REDD+). The study was developed at the Experimental Station of São João do Triunfo, state of Paraná. The regression analysis involved the forest biomass and forest carbon obtained from continuous forest inventory of the Long Term Ecological Research Program (LTER) as dependent variables (y) and spectral bands and vegetation indices (VIs) as independent variables (x). The statistical analysis comprised correlation analysis (r) between the variables x and y; regression analysis from linear, nonlinear and multiple regressions with the following statistics: R², R²adj, Syx, Syx% and residual dispersion. Furthermore thematic maps were made. Correlations between the biophysical variables and the spectral ASTER data were weak therefore ASTER was scaling up to 30m and 45m. The resolution of 30m, using ASTER data was higher than its use in the original resolution. There were not significant differences in r values between use of bands or VIs to predict the biophysical variables. Linear regressions were more suitable than nonlinear regressions (exponential and logarithmic) and multiple to estimate the biophysical variables, with errors lower than established in traditional inventories campaigns (α <5%). Maps generated from ASTER 30m were more reliable in portraying the spatial distribution of these variables in the study area due to the high correlation of these with the values observed in the inventory (LTER). Thus, the forest carbon equation from ASTER data was used in the creation of REDD+. The estimated biomass and forest carbon by using optical sensors data was adequate, with possibilities to be expanded to large areas. The methodology thus proved suitable for the monitoring, reporting and verification of carbon stocks in forests.

In this thesis, we investigate the mechanisms driving the self-assembly of peptides and proteins using computational and theoretical tools, always validating our results with experimental measures when possible. In the first part, Chapters 2-5, we focus on the Aβ system, a peptide whose aggregation is intimately linked with the development of Alzheimer's Disease. We begin by simulating the major alloforms of the peptide, Aβ_40 and Aβ_42, demonstrating that the two populate similar disordered ensembles and matching experimental data. Next we investigate how disordered Aβ_42 monomers interact with each other, finding that oligomerisation into amorphous aggregates is driven largely by hydrophobic, non-specific forces. We then move on to probing the aggregation of Aβ_42 into amyloid structures using a native-centric coarse-grained model, and explain the results with a novel Markov state analysis from which we are able to extract structural, kinetic and thermodynamic information on elongation reactions. Finally, we probe the interactions of Aβ_42 monomers with Aβ_42 fibrillar surfaces using a specially designed enhanced sampling scheme, which allows us to obtain enthalpy-driven binding thermodynamics consistent with experiments and to propose major polar binding modes. In the second part of the thesis, Chapters 6 and 7, we model the aggregation of two other self-assembling systems, viruses and a truncated form of the molecular chaperone Hsp70. We first develop a data analysis platform to extract information on the microscopic mechanisms of viral capsid self-assembly from experimental data, synthesising the results from several different systems to draw general evolutionary conclusions about the assembly mechanism. Finally, we model the oligomerisation of Hsp70 thermodynamically and kinetically, showing that its self-assembly is a highly cooperative reaction that is under strong structural constraints.

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No. of bitstreams: 1 filgueiras_r_me_bot.pdf: 10047606 bytes, checksum: b710d7378ca5bb6b915801acc7bece8d (MD5) Previous issue date: 2016-02-19 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Devido ao fato da morfologia do terreno influenciar nas medidas radiométricas obtidas por sensores orbitais, o presente estudo teve por objetivo geral, analisar a dinâmica espaçotemporal do saldo de radiação (Rn), na Fazenda Experimental Edgárdia (FEE) pertencente a Faculdade de Ciências Agronômicas/ Universidade Estadual Paulista “Júlio de Mesquita Filho” FCA/UNESP, Botucatu-SP, levando-se em consideração a topografia da mesma, a qual apresenta relevo heterogêneo. Para essa análise foram processados dois métodos de correção topográfica, um que considera a superfície como um reflector lambertiano e outro não lambertiano. Para a estimativa do saldo de radiação, por meio das imagens orbitais, foi utilizada a metodologia do algoritmo SEBAL (Surface Energy Balance Algorithm for Land). Com intuito de avaliar a influência da topografia no cômputo do saldo de radiação, foram aplicadas três metodologias: sem correção topográfica (RnSem); correção cosseno (RnCos) e correção C (RnC). Essas metodologias foram aplicadas em 21 imagens da plataforma orbital Landsat-5/TM, durante os anos de 1985 a 2010. Após a correção das imagens, notou-se que as cenas correspondentes ao RnCos apresentaram sobrecorreção dos parâmetros para algumas porções das imagens, devido a essas regiões apresentarem ângulos de iluminação ( , em relação a normal da superfície, superiores a 69,62°, alcançando ângulos de até 76,11°, isto é, condições de pouca luminosidade. Devido à complexidade do relevo da FEE, a correção cosseno não foi eficaz na atenuação da influência topográfica. Já, para os valores de RnC, foi constatada uma redução média do desvio padrão de 5,97% das imagens sem correção, para as corrigidas pela correção C. Esse resultado foi atribuído como um indício da efetiva correção das cenas. Observou-se nas imagens RnSem da FEE que ocorreu uma tendência à valores elevados de saldo de radiação, de noroeste a sudeste dos mapas dos RnSem, região que encontrava-se sombreada. Essa tendenciosidade foi notoriamente reduzida nas imagens RnC, a qual foi uma comprovação qualitativa de que a correção C foi eficaz para atenuar os efeitos relativos a topografia da FEE para as imagens de saldo de radiação. Com o propósito de validar as estimações, os valores de saldo de radiação obtidos nas diferentes datas foram comparados, utilizando duas estações meteorológicas automáticas, os quais não apresentaram erros relativos maiores que 13,73%. Tais resultados evidenciam a importância da consideração do relevo, para atingir maiores precisões nas estimativas de parâmetros biofísicos com imagens orbitais e reiteram o potencial do SEBAL na estimativa de parâmetros relativos ao balanço de energia. / The measurements obtained by remote sensing are influenced by issues related to relief. Based on that, this study aim to analyze the spatial-temporal dynamic of net radiation (Rn), considering the influence of topographic parameters on it, for the experimental farm Edgárdia (FEE), belonging the FCA/UNESP, Botucatu-SP, Brazil. For this analysis it was processed two methodologies, one based in the Lambertian behavior, and the other in non- Lambertian behavior. For estimate the net radiation, by orbital images, it was utilized the metodology based on the SEBAL (Surface Energy Balance Algorithm for Land) algorithm. In order to assess the topographic influence on the compute of net radiation, was applied three methodologies: without topographic correction (RnSem); cosine correction (RnCos) and C correction (RnC). These methodologies were applied on 21 images of the orbital platform Landsat-5/TM, during the years of 1985, until 2010. After the corrections of the images, it noticed that the scenes corresponding to the RnCos showed overcorrection of the parameters, in some areas of the FEE. This happened because these portions showed illumination angles, in relation to the normal of surface, bigger than 69.62°, reaching angles of 76.11°, ie, conditions of low illumination. Due to complex relief of the FEE, the cosine correction did not show effectiveness on the attenuation of topographic influence for the values of RnC, were noticed an average reduction of 5.97% for the standard deviation for the values of RnC, of the images that had been corrected by the C-correction. This result was assigned as indicative of the scenes correction. It was observed on the images of RnSem of FEE that, occurred a tendency of elevated values of net radiation, located of northwest until southeast of the maps of RnSem, shaded regions. This bias was attenuated on the images of RnC, which qualitatively proved the effectiveness of the Ccorrection, for the effects relief of FEE, on the net radiation images. With the purpose of validated these estimation, the net radiation values, obtained on the dates analyzed, were compared, utilizing two automatic meteorological stations. The results showed standard mean errors no bigger than 13.73%. These results show the importance of considering relief, to achieve higher accuracies on estimates of biophysical parameters with orbital images and confirm the potential of SEBAL in estimating parameters relating to energy balance.

abstract: The transmembrane subunit (gp41) of the envelope glycoprotein of HIV-1 associates noncovalently with the surface subunit (gp120) and together they play essential roles in viral mucosal transmission and infection of target cells. The membrane proximal region (MPR, residues 649-683) of gp41 is highly conserved and contains epitopes of broadly neutralizing antibodies. The transmembrane (TM) domain (residues 684-705) of gp41 not only anchors the envelope glycoprotein complex in the viral membrane but also dynamically affects the interactions of the MPR with the membrane. While high-resolution X-ray structures of some segments of the MPR were solved in the past, they represent the pre-fusion and post-fusion conformations, most of which could not react with the broadly neutralizing antibodies 2F5 and 4E10. Structural information on the TM domain of gp41 is scant and at low resolution. This thesis describes the structural studies of MPR-TM (residues 649-705) of HIV-1 gp41 by X-ray crystallography. MPR-TM was fused with different fusion proteins to improve the membrane protein overexpression. The expression level of MPR-TM was improved by fusion to the C-terminus of the Mistic protein, yielding &#8764;1 mg of pure MPR-TM protein per liter cell culture. The fusion partner Mistic was removed for final crystallization. The isolated MPR-TM protein was biophysically characterized and is a monodisperse candidate for crystallization. However, no crystal with diffraction quality was obtained even after extensive crystallization screens. A novel construct was designed to overexpress MPR-TM as a maltose binding protein (MBP) fusion. About 60 mg of MBP/MPR-TM recombinant protein was obtained from 1 liter of cell culture. Crystals of MBP/MPR-TM recombinant protein could not be obtained when MBP and MPR-TM were separated by a 42 amino acid (aa)-long linker but were obtained after changing the linker to three alanine residues. The crystals diffracted to 2.5 Å after crystallization optimization. Further analysis of the diffraction data indicated that the crystals are twinned. The final structure demonstrated that MBP crystallized as a dimer of trimers, but the electron density did not extend beyond the linker region. We determined by SDS-PAGE and MALDI-TOF MS that the crystals contained MBP only. The MPR-TM of gp41 might be cleaved during or after the process of crystallization. Comparison of the MBP trimer reported here with published trimeric MBP fusion structures indicated that MBP might form such a trimeric conformation under the effect of MPR-TM. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2014

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The ecodynamics analysis of coastal dunes of Sergipe determined the role and the interactive effect of the anthropic action and of the natural dynamics in the occured fast ambient changes in two sample units of the Northern and Southern Coastline from Sergipe. The present research searched the detailing of the existing ambient dynamics in the fields of the dunes of Pirambu (Northern portion) and Estância (Southern portion) by means of the structural and functional aspects with prominence to the conditioning expressive of dunar vulnerability. The knowledge of the conditions of balance of the systems of the dunes based on the Tricart s Ecodynamics principle demanded the deepening of the relations between geomorphological, fitogeographics, climatological and anthropical the components of the systems of dunes. The use of this integrator perspective found for the Northern Coastline (Biolological Reserve of Santa Isabel) a scenery with dune stability predominance explained by the low threat of system degradation, lack of obstacles to the transgression of the frontal dunes and low human interference. However, the current situation of stable environment may suffer anthropogenic derivations generating a growing tendency to ecodynamical intergrade, covering a longer cycle of environmental changes in levels of vulnerability assessed. The dunes of the Southern Coast include such features with predominance of the morphogenesis upon the pedogenesis. In terms of its ecodynamical assessment, they appear as unstable environments and environments intergrade, but with tendency to a progressive instability. Such dune situation in degradation is explained by the increasing process of disordered occupation, for the expansion of the land divisions and touristic enterprises, beyond the nonexistent of measures of protection that glimpse the containment of processes as illegally carried through dune dismountings. / A análise ecodinâmica das dunas costeiras de Sergipe partiu da verificação do papel e dos efeitos interativos da ação antrópica e da dinâmica costeira nas mudanças ambientais rápidas ocorridas em duas unidades amostrais do Litoral Norte e do Litoral Sul sergipano. A presente pesquisa buscou o detalhamento da dinâmica ambiental existente nos campos dunares de Pirambu (porção Norte) e Estância (porção Sul) mediante os aspectos estrutural e funcional com destaque aos condicionantes mais expressivos de vulnerabilidade dunar. O conhecimento das condições de equilíbrio dos sistemas dunares baseado no princípio ecodinâmico de Tricart demandou o aprofundamento das relações entre as componentes geomorfológicas, fitogeográficas, climáticas e antrópicas dos sistemas dunares. A utilização da perspectiva integradora da paisagem encontrou para o Litoral Norte (Reserva Biológica de Santa Isabel) um cenário com predominância da estabilidade dunar explicado pela pouca ameaça de degradação ao sistema, inexistência de obstáculos à transgressão das dunas frontais e baixa interferência antrópica. Todavia, a atual situação de meio estável pode sofrer derivações antropogênicas geradoras de uma crescente tendência ecodinâmica ao intergrade, abrangendo um ciclo mais longo de mudanças ambientais nos patamares de vulnerabilidade aferidos. Nas dunas do Litoral Sul predomina a morfogênese sobre a pedogênese. Em termos de sua avaliação ecodinâmica, apresentam-se como meios instáveis e meios em intergrade, mas com tendência a uma progressiva instabilidade. Tal situação de dunas em arrasamento é explicada pelo crescente processo de ocupação desordenada, pela expansão dos loteamentos e empreendimentos turísticos, além da inexistência de medidas de proteção que vislumbrem a contenção de processos como desmontes de dunas realizados ilegalmente.