From protein structure to function with bioinformatics

It has long been known that amino acids are the building blocks for proteins and govern their folding into specific three-dimensional structures. However, the details of this process are still unknown and represent one of the main problems in structural bioinformatics, which is a highly active research area with the focus on the prediction of three-dimensional structure and its relationship to protein function. The protein structure prediction procedure encompasses several different steps from searches and analyses of sequences and structures, through sequence alignment to the creation of the structural model. Careful evaluation and analysis ultimately results in a hypothetical structure, which can be used to study biological phenomena in, for example, research at the molecular level, biotechnology and especially in drug discovery and development. In this thesis, the structures of five proteins were modeled with templatebased methods, which use proteins with known structures (templates) to model related or structurally similar proteins. The resulting models were an important asset for the interpretation and explanation of biological phenomena, such as amino acids and interaction networks that are essential for the function and/or ligand specificity of the studied proteins. The five proteins represent different case studies with their own challenges like varying template availability, which resulted in a different structure prediction process. This thesis presents the techniques and considerations, which should be taken into account in the modeling procedure to overcome limitations and produce a hypothetical and reliable three-dimensional structure. As each project shows, the reliability is highly dependent on the extensive incorporation of experimental data or known literature and, although experimental verification of in silico results is always desirable to increase the reliability, the presented projects show that also the experimental studies can greatly benefit from structural models. With the help of in silico studies, the experiments can be targeted and precisely designed, thereby saving both money and time. As the programs used in structural bioinformatics are constantly improved and the range of templates increases through structural genomics efforts, the mutual benefits between in silico and experimental studies become even more prominent. Hence, reliable models for protein three-dimensional structures achieved through careful planning and thoughtful executions are, and will continue to be, valuable and indispensable sources for structural information to be combined with functional data.

Evaluation of suitable spectral intervals for near-IR laboratory detection of water vapour continuum absorption

The water vapour continuum absorption is an important component of molecular absorption of radiation in atmosphere. However, uncertainty in knowledge of the value of the continuum absorption at present can achieve 100% in different spectral regions leading to an error in flux calculation up to 3-5 W/m2 global mean. This work uses line-by-line calculations to reveal the best spectral intervals for experimental verification of the CKD water vapour continuum models in the currently least studied near-infrared spectral region. Possible sources of errors in continuum retrieval taken into account in the simulation include the sensitivity of laboratory spectrometers and uncertainties in the spectral line parameters in HITRAN-2004 and Schwenke-Partridge database. It is shown that a number of micro-windows in near-IR can be used at present for laboratory detection of the water vapour continuum with estimated accuracy from 30 to 5%.

Two methods for modelling the propagation of terahertz radiation in a layered structure

Modelling the interaction of terahertz(THz) radiation with biological tissueposes many interesting problems. THzradiation is neither obviously described byan electric field distribution or anensemble of photons and biological tissueis an inhomogeneous medium with anelectronic permittivity that is bothspatially and frequency dependent making ita complex system to model.A three-layer system of parallel-sidedslabs has been used as the system throughwhich the passage of THz radiation has beensimulated. Two modelling approaches havebeen developed a thin film matrix model anda Monte Carlo model. The source data foreach of these methods, taken at the sametime as the data recorded to experimentallyverify them, was a THz spectrum that hadpassed though air only.Experimental verification of these twomodels was carried out using athree-layered in vitro phantom. Simulatedtransmission spectrum data was compared toexperimental transmission spectrum datafirst to determine and then to compare theaccuracy of the two methods. Goodagreement was found, with typical resultshaving a correlation coefficient of 0.90for the thin film matrix model and 0.78 forthe Monte Carlo model over the full THzspectrum. Further work is underway toimprove the models above 1 THz.

Aplicação do modelo all-or-none em condições de aquisição de associação aos pares

O presente estudo teve por objetivo submeter a nova verificação experimental o modelo "all-or-none" de aprendizagem de pares-associados, em que as associações estímulo resposta são formadas inteiramente em uma única tentativa. Justifica o presente trabalho a necessidade de estudos na área da teoria da aprendizagem, a fim de fornecer subsídios para uma tecnologia educacional. A hipótese testada foi a de que a probabilidade de uma associação se efetuar é constante para qualquer número de treinos anteriores. Foram testados 100 sujeitos de classe de alfabetização, divididos em 5 grupos, com 5 níveis de reforçamentos e 5 grupos de itens. Foi usado um esquema de quadrados latinos, combinando três fatores em cinco níveis cada um: 1 - número de reforçamentos, 2 - grupo de itens e 3 - grupo de sujeitos. A análise dos resultados levou à aceitação da hipótese de que a aprendizagem é, em essência, all-or-none.

O desenvolvimento do conceito de probabilidade em pré-adolescentes e adolescentes

Este trabalho, baseado na teoria de Jean Piaget sobre o desenvolvimento do pensamento adolescente, visa continuar a mesma linha de investigação no que se refere à aquisição do conceito de probabilidade. O conceito de probabilidade na teoria piagetiana representando a intercepção do real e do possível, foi submetido, neste trabalho, a uma análise crítica e a um projeto de verificação experimental. Em termos teóricos, a crítica orientou-se para a relação entre os canais sensoriais receptores de informação e a organização do nível formal que permite elaborar relações de probabilidade. Importante papel foi atribuído ao estudo da manipulação - expressão direta da ação em seus níveis primordiais - como fator determinante de elaboração específica nas relações de probabilidade. Uma segunda vertente sociogênica do problema foi analisada em termos do nível sócio-econômico como fator que influencia o desenvolvimento do pensamento formal e especificamente a aquisição do conceito de probabilidade. Em termos de verificação experimental, constatou se a possibilidade de se definirem diversos estágios de desenvolvimento, chegando-se a classificar, de modo geral, os sujeitos em: aqueles que ainda não possuem habilidade de pensamento para solução de problema de probabilidade, aqueles que já apresentam tal habilidade, porém, são incapazes de generalização, e outros, em menor parte, que têm estabelecidas as estruturas operatórias do período lógico formal. Dentre estes grupos somente o último faz uso sistemático de estratégias corretas e corresponde aos sujeitos adolescentes do sexo masculino. Isto mostra que existe uma diferença nos resultados devido às diferenças sexuais a favor do sexo masculino e que a capacidade de lidar com relações probabilísticas se torna mais organizada e estruturada com o avanço da idade dos sujeitos. As variáveis ambientais exercem influência no rendimento do sujeito, os resultados variam de acordo com o meio socio econômico, favorecendo os de nível superior, isto é, permitindo-lhes um desenvolvimento normal.

Population persistence in weakly-coupled sinks

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Aprender versus ensinar: Charles Sanders Peirce e a universidade americana do final do século XIX

A produção científica e filosófica de Charles Sanders PEIRCE (1839-1914), exigindo como critério para o trabalho intelectual e para a conduta da vida do pensador o absoluto rigor na construção dos conceitos e a estrita verificação experimental, teve por conseqüência desvincular o trabalho científico e filosófico de qualquer função apologética. A afirmação de que todo conhecimento do mundo da experiência e mesmo daquele elaborado pela matemática é intrinsecamente provável e falível se opôs a todo e qualquer dogmatismo e mesmo ao a priori de tradição Kantiana. O interesse pela teoria evolucionista e a coerência inabalável da filosofia e das atitudes de PEIRCE, como professor e pesquisador, encontraram profunda resistência no meio universitário e editorial de seu tempo. Num momento de grave crise na Universidade norte-americana, decorrente das transformações econômicas e políticas ocorridas com a guerra da Secessão (1861-1865), o posicionamento de PEIRCE contribuiu muito provavelmente para sua demissão como professor das Universidades de Harvard e de John Hopkins; para dificultar a publicação de seus escritos e para seu total isolamento nos últimos anos de vida.

The Gerasimov-Drell-Hearn Sum Rule and the Spin Structure of the Proton

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Disappearance of squeezed back-to-back correlations: a new signal of hadron freeze-out from a supercooled quark gluon plasma

We briefly discuss four different possible types of transitions from quark to hadronic matter and their characteristic signatures in terms of correlations. We also highlight the effects arising from mass modification of hadrons in hot and dense hadronic matter, as well as their quantum statistical consequences: the appearance of squeezed quantum states and the associated experimental signatures, i.e., the back-to-back correlations of particle-antiparticle pairs. We briefly review the theoretical results of these squeezed quanta, generated by in-medium modified masses, starting from the first indication of the existence of surprising particle-antiparticle correlations, and ending by considering the effects of chiral dynamics on these correlation patterns. Nevertheless, a prerequisite for such a signature is the experimental verification of its observability. Therefore, the experimental observation of back-to-back correlations in high energy heavy ion reactions would be a unique signature, proving the existence of in-medium mass modification of hadronic states. on the other hand, their disappearance at some threshold centrality or collision energy would indicate that the hadron formation mechanism would have qualitatively changed: asymptotic hadrons above such a threshold are not formed from medium modified hadrons anymore, but rather by new degrees of freedom characterizing the medium. Furthermore, the disappearance of the squeezed BBC could also serve as a signature of a sudden, non-equilibrium hadronization scenario from a supercooled quark-gluon plasma phase.

Fatores que influenciam a produção de biomassa e glicerol quinase pela levedura recombinante Pichia pastoris

Pós-graduação em Alimentos e Nutrição - FCFAR

Estudo de propriedades estruturais e de piezeletricidade nos cristais de ADP e KDP puros e dopados com íons Ni2+ e Mn3+ com DMRX utilizando radiação síncrotron

A difração múltipla de raios-X utilizando radiação Síncrotron foi aplicada para o estudo de cátions de metais de transição Mn³⁺ e Ni²⁺ incorporados a rede cristalina do Fosfato de Amônio Monobásico (ADP) e Fosfato de Potássio Monobásico (KDP). Em todos os diagramas Renninger obtidos para as diferentes amostras e diferentes comprimentos de onda podemos observar que as posições angulares e o número de picos não sofrem alteração. Este fato nos diz que os parâmetros da célula unitária e a simetria do cristal são praticamente os mesmos, independentemente da incorporação de cátíons Mn³⁺ e Ni²⁺. Cálculos precisos dos parâmetros da célula unitária revelam que há expansão dos parâmetros de rede a = b e contração do parâmetro de rede c do cristal de ADP dopado com Ni²⁺ e Mn³⁺. Nas medidas com ambos os comprimentos de onda no ADP:Mn o digrama Renninger apresenta picos com perfis semelhantes aos perfis dos picos nos diagrama Renninger do cristal de ADP puro. Nenhum pico extra aparece no diagrama Renninger do cristal dopado. A partir dos diagramas resultantes das medidas no cristal de ADP:Ni pode-se observar claramente: (i) alguns picos que tinham um perfil assimétrico no diagrama do cristal de ADP puro apresentam perfis quase totalmente simétricos no diagrama do cristal dopado com Ni (nas medidas com comprimento de onda abaixo da borda de absorção do Ni) e, (ii) alguns picos sofrem uma forte inversão em seus perfis (nas medidas com comprimento de onda acima da borda de absorção do Ni), por exemplo, o pico (5-12)/(-112), que representa um caso de quatro feixes. Estes resultados indicam que o diagrama Renninger com radiação Síncrotron é uma sonda de alta resolução a serem utilizados na incorporação de impurezas na rede ADP. Além disso, investigamos os coeficientes piezelétricos dos cristais de ADP:Mn, KDP:Mn e KDP:Ni por difração de raios-X à temperatura ambiente. Os resultados das medidas das reflexões 440 e 066 permitiram a obtenção dos coeficientes d₃₆ e d₂₅. Nós observamos que estes coeficientes aumentaram com a dopagem dos íons Mn³⁺ e Ni²⁺ nos cristais de ADP e KDP.

Evaluation of Human Exposure to Magnetic Fields Generated by Electric Power Systems in Complex Configurations

The international growing concern for the human exposure to magnetic fields generated by electric power lines has unavoidably led to imposing legal limits. Respecting these limits, implies being able to calculate easily and accurately the generated magnetic field also in complex configurations. Twisting of phase conductors is such a case. The consolidated exact and approximated theory regarding a single-circuit twisted three-phase power cable line has been reported along with the proposal of an innovative simplified formula obtained by means of an heuristic procedure. This formula, although being dramatically simpler, is proven to be a good approximation of the analytical formula and at the same time much more accurate than the approximated formula found in literature. The double-circuit twisted three-phase power cable line case has been studied following different approaches of increasing complexity and accuracy. In this framework, the effectiveness of the above-mentioned innovative formula is also examined. The experimental verification of the correctness of the twisted double-circuit theoretical analysis has permitted its extension to multiple-circuit twisted three-phase power cable lines. In addition, appropriate 2D and, in particularly, 3D numerical codes for simulating real existing overhead power lines for the calculation of the magnetic field in their vicinity have been created. Finally, an innovative ‘smart’ measurement and evaluation system of the magnetic field is being proposed, described and validated, which deals with the experimentally-based evaluation of the total magnetic field B generated by multiple sources in complex three-dimensional arrangements, carried out on the basis of the measurement of the three Cartesian field components and their correlation with the field currents via multilinear regression techniques. The ultimate goal is verifying that magnetic induction intensity is within the prescribed limits.

Effects of drilling and stress release on hydraulic properties and porewater chemistry of crystalline rocks

The experimental verification of matrix diffusion in crystalline rocks largely relies on indirect methods performed in the laboratory. Such methods are prone to perturbations of the rock samples by collection and preparation and therefore the laboratory-derived transport properties and fluid composition might not represent in situ conditions. We investigated the effects induced by the drilling process and natural rock stress release by mass balance considerations and sensitivity analysis of analytical out-diffusion data obtained from originally saturated, large-sized drillcore material from two locations drilled using traced drilling fluid. For in situ stress-released drillcores of quartz-monzodiorite composition from the Aspo HRL, Sweden, tracer mass balance considerations and 1D and 2D diffusion modelling consistently indicated a contamination of <1% of the original pore water. This chemically disturbed zone extends to a maximum of 0.1 mm into the drillcore (61.8 mm x 180.1 mm) corresponding to about 0.66% of the total pore volume (0.77 vol.%). In contrast, the combined effects of stress release and the drilling process, which have influenced granodioritic drillcore material from 560 m below surface at Forsmark. Sweden, resulted in a maximum contamination of the derived porewater Cl(-) concentration of about 8%. The mechanically disturbed zone with modified diffusion properties covers the outermost similar to 6 mm of the drillcore (50 mm x 189 mm), whereas the chemically disturbed zone extends to a maximum of 0.3 mm based on mass balance considerations, and to 0.15 mm to 0.2 mm into the drillcore based on fitting the observed tracer data. This corresponds to a maximum of 2.4% of the total pore volume (0.62 vol.%) being affected by the drilling-fluid contamination. The proportion of rock volume affected initially by drilling fluid or subsequently with experiment water during the laboratory diffusion and re-saturation experiments depends on the size of the drillcore material and will become larger the smaller the sample used for the experiment. The results are further in support of matrix diffusion taking place in the undisturbed matrix of crystalline rocks at least in the cm range.

Performance analysis of a miniature turbine generator for intracorporeal energy harvesting

Replacement intervals of implantable medical devices are commonly dictated by battery life. Therefore, intracorporeal energy harvesting has the potential to reduce the number of surgical interventions by extending the life cycle of active devices. Given the accumulated experience with intravascular devices such as stents, heart valves, and cardiac assist devices, the idea to harvest a small fraction of the hydraulic energy available in the cardiovascular circulation is revisited. The aim of this article is to explore the technical feasibility of harvesting 1 mW electric power using a miniature hydrodynamic turbine powered by about 1% of the cardiac output flow in a peripheral artery. To this end, numerical modelling of the fluid mechanics and experimental verification of the overall performance of a 1:1 scale friction turbine are performed in vitro. The numerical flow model is validated for a range of turbine configurations and flow conditions (up to 250 mL/min) in terms of hydromechanic efficiency; up to 15% could be achieved with the nonoptimized configurations of the study. Although this article does not entail the clinical feasibility of intravascular turbines in terms of hemocompatibility and impact on the circulatory system, the numerical model does provide first estimates of the mechanical shear forces relevant to blood trauma and platelet activation. It is concluded that the time-integrated shear stress exposure is significantly lower than in cardiac assist devices due to lower flow velocities and predominantly laminar flow.

Chemical studies of elements with Z ⩾ 104 in gas phase

Chemical investigations of superheavy elements in the gas-phase, i.e. elements with Z≥104Z≥104, allow assessing the influence of relativistic effects on their chemical properties. Furthermore, for some superheavy elements and their compounds quite unique gas-phase chemical properties were predicted. The experimental verification of these properties yields supporting evidence for a firm assignment of the atomic number. Prominent examples are the high volatility observed for HsO4 or the very weak interaction of Cn with gold surfaces. The unique properties of HsO4 were exploited to discover the doubly-magic even–even nucleus 270Hs and the new isotope 271Hs. The combination of kinematic pre-separation and gas-phase chemistry allowed gaining access to a new class of relatively fragile compounds, the carbonyl complexes of elements Sg through Mt. A not yet resolved issue concerns the interaction of Fl with gold surfaces. While competing experiments agree on the fact that Fl is a volatile element, there are discrepancies concerning its adsorption on gold surfaces with respect to its daughter Cn. The elucidation of these and other questions amounts to the fascination that gas-phase chemical investigations exert on current research at the extreme limits of chemistry today.