DNA-mediated charge transport signaling within the cell

DNA possesses the curious ability to conduct charge longitudinally through the π-stacked base pairs that reside within the interior of the double helix. The rate of charge transport (CT) through DNA has a shallow distance dependence. DNA CT can occur over at least 34 nm, a very long molecular distance. Lastly, DNA CT is exquisitely sensitive to disruptions, such as DNA damage, that affect the dynamics of base-pair stacking. Many DNA repair and DNA-processing enzymes are being found to contain 4Fe-4S clusters. These co-factors have been found in glycosylases, helicases, helicase-nucleases, and even enzymes such as DNA polymerase, RNA polymerase, and primase across the phylogeny. The role of these clusters in these enzymes has remained elusive. Generally, iron-sulfur clusters serve redox roles in nature since, formally, the cluster can exist in multiple oxidation states that can be accessed within a biological context. Taken together, these facts were used as a foundation for the hypothesis that DNA-binding proteins with 4Fe-4S clusters utilize DNA-mediated CT as a means to signal one another to scan the genome as a first step in locating the subtle damage that occurs within a sea of undamaged bases within cells.

Herein we describe a role for 4Fe-4S clusters in DNA-mediated charge transport signaling among EndoIII, MutY, and DinG, which are from distinct repair pathways in E. coli. The DinG helicase is an ATP-dependent helicase that contains a 4Fe-4S cluster. To study the DNA-bound redox properties of DinG, DNA-modified electrochemistry was used to show that the 4Fe-4S cluster of DNA-bound DinG is redox-active at cellular potentials, and shares the 80 mV vs. NHE redox potential of EndoIII and MutY. ATP hydrolysis by DinG increases the DNA-mediated redox signal observed electrochemically, likely reflecting better coupling of the 4Fe-4S cluster to DNA while DinG unwinds DNA, which could have interesting biological implications. Atomic force microscopy experiments demonstrate that DinG and EndoIII cooperate at long range using DNA charge transport to redistribute to regions of DNA damage. Genetics experiments, moreover, reveal that this DNA-mediated signaling among proteins also occurs within the cell and, remarkably, is required for cellular viability under conditions of stress. Knocking out DinG in CC104 cells leads to a decrease in MutY activity that is rescued by EndoIII D138A, but not EndoIII Y82A. DinG, thus, appears to help MutY find its substrate using DNA-mediated CT, but do MutY or EndoIII aid DinG in a similar way? The InvA strain of bacteria was used to observe DinG activity, since DinG activity is required within InvA to maintain normal growth. Silencing the gene encoding EndoIII in InvA results in a significant growth defect that is rescued by the overexpression of RNAseH, a protein that dismantles the substrate of DinG, R-loops. This establishes signaling between DinG and EndoIII. Furthermore, rescue of this growth defect by the expression of EndoIII D138A, the catalytically inactive but CT-proficient mutant of EndoIII, is also observed, but expression of EndoIII Y82A, which is CT-deficient but enzymatically active, does not rescue growth. These results provide strong evidence that DinG and EndoIII utilize DNA-mediated signaling to process DNA damage. This work thus expands the scope of DNA-mediated signaling within the cell, as it indicates that DNA-mediated signaling facilitates the activities of DNA repair enzymes across the genome, even for proteins from distinct repair pathways.

In separate work presented here, it is shown that the UvrC protein from E. coli contains a hitherto undiscovered 4Fe-4S cluster. A broad shoulder at 410 nm, characteristic of 4Fe-4S clusters, is observed in the UV-visible absorbance spectrum of UvrC. Electron paramagnetic resonance spectroscopy of UvrC incubated with sodium dithionite, reveals a spectrum with the signature features of a reduced, [4Fe-4S]+1, cluster. DNA-modified electrodes were used to show that UvrC has the same DNA-bound redox potential, of ~80 mV vs. NHE, as EndoIII, DinG, and MutY. Again, this means that these proteins are capable of performing inter-protein electron transfer reactions. Does UvrC use DNA-mediated signaling to facilitate the repair of its substrates?

UvrC is part of the nucleotide excision repair (NER) pathway in E. coli and is the protein within the pathway that performs the chemistry required to repair bulky DNA lesions, such as cyclopyrimidine dimers, that form as a product of UV irradiation. We tested if UvrC utilizes DNA-mediated signaling to facilitate the efficient repair of UV-induced DNA damage products by helping UvrC locate DNA damage. The UV sensitivity of E. coli cells lacking DinG, a putative signaling partner of UvrC, was examined. Knocking out DinG in E. coli leads to a sensitivity of the cells to UV irradiation. A 5-10 fold reduction in the amount of cells that survive after irradiation with 90 J/m2 of UV light is observed. This is consistent with the hypothesis that UvrC and DinG are signaling partners, but is this signaling due to DNA-mediated CT? Complementing the knockout cells with EndoIII D138A, which can also serve as a DNA CT signaling partner, rescues cells lacking DinG from UV irradiation, while complementing the cells with EndoIII Y82A shows no rescue of viability. These results indicate that there is cross-talk between the NER pathway and DinG via DNA-mediated signaling. Perhaps more importantly, this work also establishes that DinG, EndoIII, MutY, and UvrC comprise a signaling network that seems to be unified by the ability of these proteins to perform long range DNA-mediated CT signaling via their 4Fe-4S clusters.

Polaron hopping in olivine phosphates studied by nuclear resonant scattering

Valence fluctuations of Fe²⁺ and Fe³⁺ were studied in a solid solution of Li_xFePO₄ by nuclear resonant forward scattering of synchrotron x rays while the sample was heated in a diamond-anvil pressure cell. The spectra acquired at different temperatures and pressures were analyzed for the frequencies of valence changes using the Blume-Tjon model of a system with a fluctuating Hamil- tonian. These frequencies were analyzed to obtain activation energies and an activation volume for polaron hopping. There was a large suppression of hopping frequency with pressure, giving an anomalously large activation volume. This large, positive value is typical of ion diffusion, which indicates correlated motions of polarons, and Li⁺ ions that alter the dynamics of both.

In a parallel study of Na_xFePO₄, the interplay between sodium ordering and electron mobility was investigated using a combination of synchrotron x-ray diffraction and nuclear resonant scattering. Conventional Mossbauer spectra were collected while the sample was heated in a resistive furnace. An analysis of the temperature evolution of the spectral shapes was used to identify the onset of fast electron hopping and determine the polaron hopping rate. Synchrotron x-ray diffraction measurements were carried out in the same temperature range. Reitveld analysis of the diffraction patterns was used to determine the temperature of sodium redistribution on the lattice. The diffraction analysis also provides new information about the phase stability of the system. The temperature evolution of the iron site occupancies from the Mossbauer measurements, combined with the synchrotron diffraction results give strong evidence for a relationship between the onset of fast electron dynamics and the redistribution of sodium in the lattice.

Measurements of activation barriers for polaron hopping gave fundamental insights about the correlation between electronic carriers and mobile ions. This work established that polaron-ion interactions can alter the local dynamics of electron and ion transport. These types of coupled processes may be common in many materials used for battery electrodes, and new details concerning the influence of polaron-ion interactions on the charge dynamics are relevant to optimizing their electrochemical performance.

Tratamento de efluentes líquidos na Estação Antártica Comandante Ferraz (EACF): avaliação da aplicabilidade do processo eletrolítico.

Esta pesquisa enfoca o uso do processo eletrolítico, como alternativa para tratamento de efluentes líquidos na Estação Antártica Comandante Ferraz (EACF), considerando as limitações ambientais locais e aspectos de consumo de energia. Este processo, classificado como não convencional, vem sendo estudado pela comunidade científica nacional e internacional para tratamento de diversos efluentes, inclusive esgotos domésticos, apresentando várias vantagens que estimularam a verificação de sua aplicabilidade para as condições peculiares da EACF. Foram realizados ensaios, em escala de laboratório, com esgotos domésticos coletados em um condomínio no Rio de Janeiro, usando reatores eletrolíticos com capacidade de 4 L, com eletrodos de desgaste de alumínio (Al) e de ferro (Fe), distância entre as placas de 0,9 cm e 1,8 cm, temperaturas na faixa de 7C a 22C, e ensaios para verificação da sua eficiência, por meio de parâmetros como DQO, DBO5, SST, turbidez e volume de lodo gerado. Sob temperatura de 15C e condições de condutividade da ordem de 900 S/cm, estimada para os esgotos da EACF, aplicando densidade de corrente de 22,9 A/m2, 4,5 V, tempo de retenção de 25 min, os resultados apresentaram valores de DQO no efluente tratado de 65 mg/L(redução de 89%), DBO de 56 mg/L (redução de 64 %), SST de 8 mg/L, com turbidez de 11,3 uT e, após filtração, turbidez de 3,2 uT, consumo de energia de 0,8 Wh/L. O aspecto é límpido e a qualidade final obtida é compatível para ser submetida a tratamento de desinfecção. A partir dos dados obtidos, foram avaliadas por meio de pré-projeto: a viabilidade de sua implantação em container, a estimativa de consumo de energia e de lodo gerado, requisitos de manutenção, operação, além da sugestão de monitoramentos e de medidas de mitigação de impactos ambientais associados à respectiva instalação.

Photoelectrochemistry of GaAs and Si liquid junctions

A quantitative study has been performed on the stability of GaAs surfaces in a 0.10 M K₂Se-0.01 M K₂Se₂ aqueous solution. In this electrolyte, n-type GaAs electrodes displayed significant photocorrosion in competition with faradaic charge transfer to Se^2-. Chemisorption of group VIIIB metal ions onto the GaAs surfaces yielded improved current-voltage behavior of the GaAs photoanodes, and also resulted in a significant reduction in photocorrosion. This behavior implies that the chemisorbed metal ions act to increase the rate of hole transfer to the Se^2- species. Related experiments on n-GaAs, pGaAs, and Sn-doped In₂O₃ electrodes in Te^2-/- aqueous solutions have also been performed.

The majority carrier (electrons) transfer rate constant at a highly doped n⁺-Si/Co(Cp)₂Cl-methanol junction has been measured directly using the chronoamperometry electrochemical technique. The reduction reaction rate of Co(Cp)₂+ was 0.03 cm-s^-1 at the Si electrode, and was more than 100 times slower than at a hanging mercury electrode. The slower rate was attributed to the smaller optical and static dielectric constants, and the lower density of electrons of the semiconductor. The experimental results were compared to the Marcus theory of charge transfer.

The unique properties of high purity Si/liquid junctions have been investigated under illumination conditions in which the photogenerated carrier concentration exceeds the dopant concentration. Under these high injection conditions, negligible electric fields exist at the semiconductor/liquid interface, and carrier motion is driven by diffusion. Studies of the current-voltage properties of the Si in methanol solutions containing various redox couples suggested that high efficiency photoelectrochemical cells could be established through selective collection of carriers at the semiconductor/liquid junction. The quasi-Fermi levels of electrons and holes were measured directly against the solution potential. Steady-state and transient photovoltage measurements, and theoretical modeliug of the carrier transport, generation, and recombination dynamics indicated that the quasi-Fermi levels were flat across the semiconductor sample. The recombination velocities at the Si/liquid junctions have also been measured, and were shown to vary with the solution potential following the Shockley-Read-Hall theory on recombination.

Experimental and theoretical studies of the electrothermal instability in a nonequilibrium plasma

Experimental and theoretical studies have been made of the electrothermal waves occurring in a nonequilibrium MHD plasma. These waves are caused by an instability that occurs when a plasma having a dependence of conductivity on current density is subjected to crossed electric and magnetic fields. Theoretically, these waves were studied by developing and solving the equations of a steady, one-dimensional nonuniformity in electron density. From these nonlinear equations, predictions of the maximum amplitude and of the half width of steady waves could be obtained. Experimentally, the waves were studied in a nonequilibrium discharge produced in a potassium-seeded argon plasma at 2000°K and 1 atm. pressure. The behavior of such a discharge with four different configurations of electrodes was determined from photographs, photomultiplier measurements, and voltage probes. These four configurations were chosen to produce steady waves, to check the stability of steady waves, and to observe the manifestation of the waves in a MHD generator or accelerator configuration.

Steady, one-dimensional waves were found to exist in a number of situations, and where they existed, their characteristics agreed with the predictions of the steady theory. Some extensions of this theory were necessary, however, to describe the transient phenomena occurring in the inlet region of a discharge transverse to the gas flow. It was also found that in a discharge away from the stabilizing effect of the electrodes, steady waves became unstable for large Hall parameters. Methods of prediction of the effective electrical conductivity and Hall parameter of a plasma with nonuniformities caused by the electrothermal waves were also studied. Using these methods and the values of amplitude predicted by the steady theory, it was found that the measured decrease in transverse conductivity of a MHD device, 50 per cent at a Hall parameter of 5, could be accounted for in terms of the electrothermal instability.

有限尺寸平行电极的边缘电场效应

电场分布是影响集成电光器件特性的主要因素。本丈研究了有限尺寸平行电极的电场分布，得到了其电荷分布密度、电容、电场强度的数学解析式，并分析了边缘电场效应，在此基础上得到了在集成电光器件中相邻光通道互不干扰所需的平行电极对的间隔距离。最后以单晶1×4光开关为例给出了当电极板长度为5mm、宽度为2mm、电极板间距为2mm时，离开电极板边缘3mm处的电场强度就已经降到电极板中心处的5％左右，引起的信道串扰约为0．25％，可忽略不计。

基于电光材料的光学相控阵技术研究进展

综述了基于电光材料的光学相控阵(OPA)的研究进展。介绍了光学相控阵技术的基本原理以及不同电光材料(铌酸锂电光晶体,AlGaAs光波导,液晶和掺镧锆钛酸铅(PLZT)电光陶瓷)光学相控阵技术的基本构想和涉及的关键技术;着重介绍近年来基于PLZT电光陶瓷材料光学相控阵技术的发展情况以及在这方面的最新研究成果,包括单级相控阵、级联相控阵、不同电极结构(表面电极和上下电极结构)相控阵技术等;最后简要介绍了光学相控阵技术在激光雷达等军事领域中的应用。

Chemical and electrochemical investigations of cobalt cyanide and ruthenium ammine complexes

Part I.

The stoichiometry and kinetics of the reaction between Co(CN₅H^3- and HgX₂ (X = CN, OH) have been investigated. The products of the reaction are two new complexes, [(NC)₅Co-HgX]^3- and [(NC)₅Co-Hg-Co(CN)₅]^6-, whose spectra are reported. The kinetic measurements produced a value for the forward rate constant of the reaction Co(CN)₅H^3- + OH^- k₁/k_-1 Co(CN)₅^4- +H₂O, k1 = (9.7 ± 0.8) x 10^-2 M^-1 sec^-1 at 24°C, and an equilibrium constant for the reaction K = 10^-6 M^-1.

Part II.

Unusually large and sharp "adsorption waves" appear in cyclic voltammograms of Co(CN)₅^3- and several cobalt(III) pentacyano complexes at stationary mercury electrodes. The nature of the adsorbed species and the reasons for the absence of the adsorption waves in polarograms taken with a d.m.e. have been examined. The data are compatible with the adsorption, in all cases, of a coordinatively unsaturated cobalt(II) complex, Co(CN)₄^2-, by means of a cobalt-mercury bond. When the resulting adsorbed complex is reduced, a series of subsequent chemical and electrode reactions is initiated in which three faradays of charge are consumed for each mole of adsorbed complex. The adsorption of the anionic complex strongly retards the reduction of other negatively charged complexes.

Part III.

A number of formal redox potentials for Ru^III (NH₃)₅L + e = Ru^II (NH₃)₅L and Ru^III(NH₃)₄L₂ + e = Ru^II (NH₃)₄L₂ (where L is various ligands) has been measured by cyclic voltammetry, potentiometry, and polarography and are discussed in terms of the properties of the ligands, such as π-accepting capability. Reduction of coordinated pyrazine in the complexes, Ru(NH₃)₅ Pz²⁺, cis- and trans-Ru(NH₃)₄Pz₂²⁺, on a mercury electrode has been observed. The behavior of this reduction in various acidity of the solution as well as the reoxidation of the reduction products are discussed.

Effect of the A cation size disorder and synthesis conditions on the properties of an iron perovskite series

Póster presentado en The Energy and Materials Research Conference - EMR2015 celebrado en Madrid (España) entre el 25-27 de febrero de 2015

Nonlinear response and optical limiting in SrBi2Ta2O9 thin films

SrBi2Ta2O9 (SBT) thin films on quartz substrates were prepared by use of the pulsed-laser deposition technique. The nonlinear refractive indices, n(2), Of the SBT films were measured by use of z-scan techniques with picosecond pulses. Large negative nonlinear refractive indices of 3.84 and 3.58 cm(2)/GW were obtained for the wavelengths 532 nm and 1.064 mum, respectively. The two-photon absorption coefficient was determined to be 7.3 cm/GW for 532 nm. The limiting behavior of SBT thin film on a quartz substrate was investigated in an f/5 defocusing geometry by use of 38-ps-duration, 532-nm, 1.064-mum. laser excitation. (C) 2001 Optical Society of America.

Evaluación del impacto radiológico ambiental de una industria NORM

[ES]El proceso de soldadura más común es la soldadura por arco metálico con electrodos revestidos. A veces ese revestimiento contiene materiales radiactivos de origen natural (NORMs). En España los electrodos más utilizados son los recubiertos de rutilo mezclado con otros materiales. El rutilo contiene algunos radionúclidos naturales detectables, por lo que puede ser considerado como un NORM. Este trabajo principalmente se centra en la aplicación de la metodología expuesta en la Guía de Seguridad 11.3 del Consejo de Seguridad Nuclear (Metodología para la evaluación del impacto radiológico en las industrias NORM), como una herramienta para obtener las dosis en una fábrica que produce este tipo de electrodo y evaluar el impacto radiológico en una instalación específica. Para ello, se aplicaron en dicha instalación los pasos requeridos por la metodología para su cumplimiento. Se analizaron los beneficios inherentes al estudio y se identificaron las zonas de radiación más altas así como la posición de los trabajadores. Habiendo hecho uso de evaluaciones de dosis llevadas a cabo con anterioridad por otros procedimientos, métodos de simulación, se establecieron las pautas de protección radiológica a seguir para el cumplimiento de dicha guía, mediante la colocación de dosímetros personales y monitores de radiación.

Diseño y fabricación de un electrodo para electroerosión por penetración mediante fabricación aditiva.

[ES]Este trabajo pretende dar solución a la fabricación de los electrodos utilizados en el proceso de la electroerosión, los cuales presentan numerosos requisitos a los que los electrodos actuales no dan respuesta. Por ello, se propone utilizar un material de bajo coste como núcleo y recubrirlo con una fina capa de cobre mediante laser cladding. De esta forma, se reduce el coste del electrodo manteniendo sus propiedades y se posibilita la creación de geometrías complejas.

Emprego dos processos de eletrofloculação e osmose inversa no tratamento de águas oleosas

A descarga desenfreada de águas residuais no meio ambiente, ao longo dos últimos anos, vem acelerando o processo de contaminação e degradação dos corpos hídricos no mundo. Tais rejeitos apresentam elevada carga de contaminantes e de concentração de matéria orgânica o que leva a mortandade das espécies pela concorrência ao oxigênio e, em casos extremos, a aceleração dos processos de eutrofização. Pensando nisso, o presente trabalho estudou um sistema híbrido, em batelada, de tratamento de águas oleosas simuladas em laboratório pela adição de um determinado óleo lubrificante em uma solução aquosa de agentes emulsificantes e eletrólito suporte. O sistema de tratamento foi composto de duas etapas, onde na primeira avaliou-se o uso da técnica da eletrofloculação, responsável por quebrar a estabilidade das emulsões óleo/água e de uma segunda que avaliou o uso de processos de separação com membranas visando à remoção do metal adicionado ao efluente na etapa anterior. O sistema de eletrofloculação foi avaliado em relação ao uso de eletrodos de alumínio e ferro com correntes elétricas de 1A, 2A e 3A, nos modos contínuo e alternado. Os resultados apontaram um maior consumo evidente de massa de eletrodos quando do uso da corrente contínua, 4,0337g 0,0132 para o alumínio e 3,8260g 0,0181 para o ferro ao passo que o consumo foi de 2,1400g 0,0099 para o alumínio e 2,4121g 0,0127 para o ferro quando do o uso da corrente alternada. Foram alcançadas remoções máximas de 98 % 0 da DQO, 99,77 % 0,27 de remoção da cor e 100 % 0 de remoção da turbidez para o uso de corrente alternada e eletrodos de alumínio enquanto se alcançaram remoções máximas 96 % 1 da DQO, 99,46 % 0,82 de remoção da cor e também 100 % 0 de remoção da turbidez no uso de eletrodos de ferro. Na segunda etapa do estudo, a osmose inversa, o sistema utilizado atingiu rejeições de 99,53 % 0,12; 99,56 % 0,13 e de 98,87 % 0,36, para pressões respectivas de 10, 20 e 30 bar. Além disso, foram obtidos fluxos crescentes de permeado 10,87 L/h.m2 0,25; 15,67 L/h.m2 0,53; 18,49 L/h.m2 0,74 com o também aumento da pressão. Ao final do estudo alcançou-se um efluente final com baixa carga orgânica e de metais, estando o mesmo apto ao lançamento nos corpos receptores. Entretanto, mecanismos de controle, sobretudo de pH devem ser incluídos no projeto desses sistemas uma vez que esse parâmetro sofre alterações ao longo do processo

Directional algebraic reconstruction technique for electrical impedance tomography

We assume that the resistance matrix can be found in electrical impedance tomography from the assumption of linear dependence between the voltages and the currents and with the help of the resistance matrix and the transfer impedance between the electrodes, a directional algebraic reconstruction technique is proposed. The goal is to reconstruct the resistivity distribution by weighting the matrices that are obtained by calculating the orthogonal distance of the underlying mesh elements from the neighbouring port resistivity lines. These weighting matrices, which only depend on the topology of the underlying mesh, can be calculated offline and result in a computationally efficient online procedure with a reasonable image reconstruction performance. Simulation results are provided to validate this approach.

Controle de um sistema de eletroestimulação funcional.

Esta Dissertação irá apresentar a utilização de técnicas de controle nãolinear, tais como o controle adaptativo e robusto, de modo a controlar um sistema de Eletroestimulação Funcional desenvolvido pelo laboratório de Engenharia Biomédica da COPPE/UFRJ. Basicamente um Eletroestimulador Funcional (Functional Electrical Stimulation FES) se baseia na estimulação dos nervos motores via eletrodos cutâneos de modo a movimentar (contrair ou distender) os músculos, visando o fortalecimento muscular, a ativação de vias nervosas (reinervação), manutenção da amplitude de movimento, controle de espasticidade muscular, retardo de atrofias e manutenção de tonicidade muscular. O sistema utilizado tem por objetivo movimentar os membros superiores através do estímulo elétrico de modo a atingir ângulos-alvo pré-determinados para a articulação do cotovelo. Devido ao fato de não termos conhecimento pleno do funcionamento neuro-motor humano e do mesmo ser variante no tempo, não-linear, com parâmetros incertos, sujeito a perturbações e completamente diferente para cada indivíduo, se faz necessário o uso de técnicas de controle avançadas na tentativa de se estabilizar e controlar esse tipo de sistema. O objetivo principal é verificar experimentalmente a eficácia dessas técnicas de controle não-linear e adaptativo em comparação às técnicas clássicas, de modo a alcançar um controle mais rápido, robusto e que tenha um desempenho satisfatório. Em face disso, espera-se ampliar o campo de utilização de técnicas de controle adaptativo e robusto, além de outras técnicas de sistemas inteligentes, tais como os algoritmos genéticos, provando que sua aplicação pode ser efetiva no campo de sistemas biológicos e biomédicos, auxiliando assim na melhoria do tratamento de pacientes envolvidos nas pesquisas desenvolvidas no Laboratório de Engenharia Biomédica da COPPE/UFRJ.