Engineered discoidin domain from factor VIII binds αvβ3 integrin with antibody-like affinity

Alternative scaffolds are non-antibody proteins that can be engineered to bind new targets. They have found useful niches in the therapeutic space due to their smaller size and the ease with which they can be engineered to be bispecific. We sought a new scaffold that could be used for therapeutic ends and chose the C2 discoidin domain of factor VIII, which is well studied and of human origin. Using yeast surface display, we engineered the C2 domain to bind to αvβ3 integrin with a 16 nM affinity while retaining its thermal stability and monomeric nature. We obtained a crystal structure of the engineered domain at 2.1 Å resolution. We have christened this discoidin domain alternative scaffold the “discobody.”

Biophysics of V(D)J recombination and Genome Packaging: In singulo studies on RAG, HMGB1, and TFAM

The recombination-activating gene products, RAG1 and RAG2, initiate V(D)J recombination during lymphocyte development by cleaving DNA adjacent to conserved recombination signal sequences (RSSs). The reaction involves DNA binding, synapsis, and cleavage at two RSSs located on the same DNA molecule and results in the assembly of antigen receptor genes. Since their discovery full-length, RAG1 and RAG2 have been difficult to purify, and core derivatives are shown to be most active when purified from adherent 293-T cells. However, the protein yield from adherent 293-T cells is limited. Here we develop a human suspension cell purification and change the expression vector to boost RAG production 6-fold. We use these purified RAG proteins to investigate V(D)J recombination on a mechanistic single molecule level. As a result, we are able to measure the binding statistics (dwell times and binding energies) of the initial RAG binding events with or without its co-factor high mobility group box protein 1 (HMGB1), and to characterize synapse formation at the single-molecule level yielding insights into the distribution of dwell times in the paired complex and the propensity for cleavage upon forming the synapse. We then go on to investigate HMGB1 further by measuring it compact single DNA molecules. We observed concentration dependent DNA compaction, differential DNA compaction depending on the divalent cation type, and found that at a particular HMGB1 concentration the percentage of DNA compacted is conserved across DNA lengths. Lastly, we investigate another HMGB protein called TFAM, which is essential for packaging the mitochondrial genome. We present crystal structures of TFAM bound to the heavy strand promoter 1 (HSP1) and to nonspecific DNA. We show TFAM dimerization is dispensable for DNA bending and transcriptional activation, but is required for mtDNA compaction. We propose that TFAM dimerization enhances mtDNA compaction by promoting looping of mtDNA.

Fundamentos da exploração de petróleo e gás natural e análise geoeconômica da matriz energética brasileira atual e projeções futuras

A análise da matriz energética mundial, assim como a brasileira, nos mostra que o gás natural representará em breve um importante insumo energético favorecendo a balança de pagamentos nacional, visto que o gás poderá ser usado tanto para consumo interno, quanto para exportação. O aumento das reservas nacionais de hidrocarbonetos se deve ao desenvolvimento de tecnologias, que favoreceram o conhecimento das bacias brasileiras quanto ao seu potencial produtor de combustíveis fósseis, permitindo a descoberta de novas jazidas. O amadurecimento do mercado nacional quanto ao consumo de gás natural passa pela construção de uma infraestrutura robusta, eficiente e que possibilite a captação, o armazenamento e distribuição do mesmo. O Brasil tem todos os requisitos necessários para adentrar ao seleto grupo de países exportadores de hidrocarbonetos, a descoberta do Pré-sal tende a incrementar a importância do gás natural para o país. Ao final do trabalho são descritos cenários futuros (quanto o consumo de energéticos), onde se vê que o consumo de energia para os próximos anos crescerá a taxas superiores as das duas últimas décadas. Análise destes cenários permite antecipar o interesse de futuros investimentos no desenvolvimento do conhecimento geológico para áreas promissoras.

Avaliação dos métodos para análise da microinfiltração marginal em restaurações de resina composta classe V in vitro

O objetivo deste estudo foi comparar os resultados da microinfiltração marginal obtidos por diferentes meios de aquisição de imagens e métodos de mensuração da penetração de prata em restaurações de resina composta classe V, in vitro. Dezoito pré-molares humanos hígidos, recém extraídos, foram divididos em três grupos, de acordo com o tipo de instrumento para preparação cavitária utilizado. Grupo 1: ponta diamantada número 3100, em alta rotação. Grupo 2: broca carbide número 330, em alta rotação. Grupo 3: ponta CVDentus código 82137, em aparelho de ultrassom. Foram realizados preparos cavitários padronizados (3x4x2mm) classe V nas faces vestibular e lingual de todos os dentes, com margens oclusais em esmalte e cervicais em dentina/cemento. As cavidades foram restauradas com o sistema adesivo Solobond M (VOCO) e resina composta Grandio (VOCO), a qual foi inserida e fotoativada em três incrementos. Os corpos de prova ficaram imersos em água destilada por 24h a 37oC; receberam acabamento e polimento com discos SofLex (3M) e foram novamente armazenados em água destilada, por sete dias. Posteriormente, as superfícies dentárias foram coberta com duas camadas de esmalte para unhas vermelho, exceto as áreas adjacentes às restaurações. Os espécimes ficaram imersos em solução aquosa de nitrato de prata a 50% por 24h e em solução fotorreveladora por 2h e foram seccionados no sentido vestíbulo-lingual, passando pelo centro das restaurações, com disco diamantado em baixa rotação. As amostras foram polidas em politriz horizontal e analisadas por diferentes métodos. À extensão da microinfiltração foi atribuído escores de 0 a 3 através de análises por meio de estereomicroscópio tradicional e com leds e microscópio ótico. As imagens obtidas na lupa com leds e no microscópio ótico tiveram as áreas infiltradas medidas através do software AxioVision. O teste χ2 de McNemar-Bowker revelou concordância estatística entre estereomicroscópio tradicional e o com leds (p=0,809) durante análises semiquantitativas. Porém, houve diferenças significantes entre microscópio ótico e estereomicroscópios (p<0,001). Houve boa correlação entre análises semiquantitativas e quantitativas de acordo com o teste de Spearmann (p<0,001). O teste de Kruskall-Wallis não revelou diferenças estatisticamente significantes (p=0,174) entre os grupos experimentais na análise quantitativa por microscópio ótico, em esmalte. Ao contrário do que se observa com a mesma em lupa (p<0,001). Conclui-se que o método de atribuição de escores comumente aplicado com a lupa nos estudos da microinfiltração marginal é uma opção confiável para análise da microinfiltração.

Phase effects on group velocity propagation in a V-type system with spontaneously generated coherence

The effects of the relative phase between two laser beams on the propagation of a weak electromagnetic pulse are investigated in a V-type system with spontaneously generated coherence (SGC). Due to the relative phase, the subluminal and superluminal group velocity can be unified. Meanwhile, SGC can be regarded as a knob to manipulate light propagation between subluminal and superluminal.

Upper level and phase controlling group velocity in V-type system

With the external field coupling the two upper levels, we investigate the light pulse propagation properties with weak probe field in a V-type system. Due to the external upper level (UL) coupling field, the dispersion of the system has been influenced by the relative phase. It is shown that the UL field and the relative phase can be regarded as switches to manipulate light propagation between subluminal and superluminal. (c) 2007 Elsevier B.V. All rights reserved.

A Aplicação Errônea do Direito Brasileiro pelo Árbitro: Uma Análise à Luz do Direito Comparado

A presente tese versa sobre a aplicação errônea, pelo árbitro, do Direito Brasileiro ao mérito do litígio. Tendo em vista o ineditismo, em nosso País, do estudo das consequências advindas à sentença arbitral prolatada mediante uma aplicação equivocada do Direito que rege o mérito da controvérsia, revelou-se fundamental uma análise de Direito Comparado. Assim, consultou-se o Direito dos Estados Unidos da América, do Reino Unido, da Alemanha, da Itália, da Áustria, da Suíça e da França, a fim de se constatar se é admissível, nos referidos Países, alguma medida judicial contra tal situação. Primeiramente, empreendeu-se um exame das consequências que podem advir, nos 7 (sete) Países citados, a uma sentença arbitral doméstica, assim definida conforme a legislação de cada País. Como a medida habitual para se afastar uma sentença arbitral doméstica é a ação de anulação, buscou-se examinar as hipóteses que ensejam seu ajuizamento em cada País estudado, a fim de se constatar se dentre elas insere-se a aplicação errônea do Direito que rege o fundo da disputa. Ou, em caso negativo, se a violação à ordem pública inclui-se nas hipóteses de anulação. E, por último, se a ofensa à ordem pública compreende a aplicação errônea, pelo árbitro, do Direito de cada País sub examine. Em segundo lugar, examinaram-se as consequências que advêm para uma sentença arbitral estrangeira em que se aplicou erroneamente o Direito que rege o mérito da controvérsia. Como todos os sete Países examinados são Estados-membros da Convenção de Nova Iorque de 10 de junho de 1958 sobre o Reconhecimento e a Execução de Sentenças Arbitrais Estrangeiras, que prevê em seu artigo V, n 2, alínea b, a violação à ordem pública como óbice à homologação da sentença arbitra alienígena, a aplicação do referido dispositivo em cada Estado foi analisado. Tentou-se averiguar se a ofensa à ordem pública consubstanciada na referida Convenção poderia abranger a aplicação errônea do Direito material pelo árbitro. Em seguida, examinou-se a legislação e a doutrina brasileiras tanto no que tange à ação anulatória de laudos arbitrais brasileiros, quanto à homologação dos laudos estrangeiros , a fim de se proporem soluções para esta questão em nosso ordenamento jurídico. Por fim, analisou-se se é possível, no Brasil, homologar uma sentença arbitral estrangeira que tenha sido anulada no País em que foi prolatada com base no argumento da aplicação errônea do Direito do referido Estado ao mérito da arbitragem.

Discovery of viruses lysing blue-green algae in the Dneprovsk reservoirs. [Translation of: Water blooms (ed. A. V. Topachevskii) pp.171-174. Kiev, Naukova Dumka, 1968]

Viruses, which are characterised by a relative simplicity of chemical composition, are involved with all the groups of the animal and plant world. The discovery of viruses of lower organisms has special interest. Along with the already known viruses lysing bacteria and actinomycetes, viruses have been discovered in recent years which lyse algae. During investigations of water from water-bloom patches and of mud taken from zones of massive accumulation of blue-green algae in the Dneprovsk reservoirs, the authors obtained viruses lysing algae. The revealing of viruses producing lysis of blue-green algae, which one could use in the control of water-blooms, has the greatest interest. With this aim, samples of water were collected from various zones of water-bloom patches in the Kremenchug, Dneprovsk and Kukhov reservoirs. For viruses lysing algae we propose the name 'algophages'. Along with the existence of viruses of algae of the phage type, one cannot deny the possibility of the existence of viruses of another type, multiplying in the cells of algae and causing their virus illnesses.

Key to the larvae of the genera of the sub-family Orthocladiinae from Larvae and Pupae of midges of the sub-family Orthocladiinae of the fauna of the USSR. [Translation from: Larvae and pupae of midges of the subfamily Orthocladiinae of the fauna of the USSR (Diptera, Chironomidae = Tendipedidae) (ed. Pankratova V.Ya.), 51-55. Leningrad, Nauka, 1970. ]

A key to the larvae of the genera of the sub-family Orthocladiinae from Larvae and Pupae of midges of the sub-family Orthocladiinae. Parts of the key refer to the rest of the publication which is not included in this partial translation.

Keys to the larvae of the species of the genera Diamesa, Eukiefferiella, Orthocladius, Cricotopus, Psectrocladius and Chaetocladius. [Translation from: Larvae and pupae of midges of the subfamily Orthocladiinae of the fauna of the USSR (Diptera, Chironomidae = Tendipedidae) (ed. V.Y. Pankratova) p76-8,151-152,173-174,188-189. Leningrad, Nauka, 1970. ]

Eudiaptomus vulgaris Schmeil is the most abundant copepod in Lake Maggiore and forms also, in respect to other entomostraca, the most important element, through its average biomass and because it is fairly numerous throughout the year. Plankton samples collected in a systematic and quantitative way, gave the opportunity to study some aspects of the dynamics of the population of this copepod, in safety in view of the uncertainty which in this kind of study can ensue when samples are taken only at a single station - in consequence of the changes in size of population between different water masses. The results of the biometrical observations are of the population of Eudiaptomus vulgaris is presented.

Special carbon requirement of Spirulina platensis culture. [Translation from: Materialy VII Vsesoyuznogo Rabochego Soveshchanii po Voprosu Krugovorota Veshchestv v Zamknutoi Sisteme na Osnove Zhiznedeyatel'nosti Nizshikh Organizmov p55-57. Kiev, Naukova Dumka, 1972.]

By the industrial cultivation of blue-green algae, there very much appears the important question about their carbon nutrition. Spirulina grows within the range of pH value of medium of 8.5 - 11.0. In this range of pH value in the culture medium CO2 is present in the form of bicarbonate and carbonate, which serves as principal source of carbon for the present type of algae. There is little information yet about the influence of the pH of the medium, and the form of carbon components of the medium, on the rate-increase of Spirulina. Investigations were conducted into the influence of some pH values of medium on the rate-increase of the alga Spirulina platensis.

Extent and biomass of the aquatic chariphytes and mosses in Lake Sevan [Translation from: Rasprostranenie i biomassa kharovykh vodoroslei i mkha v os. Sevan, 1951]

This study focusses on the plants in the open parts of the lake - mostly aquatic charophytes and mosses, in what are called in Lake Sevan (Armenia), the ”zones of chara and moss”. Distribution and other ecological conditions are reviewed. Quantity of chara in the littoral zone of lake Sevan is provided

The effect of oxygen concentration in water on the growth and nitrogen metabolism in the fry of rainbow trout [Translation from: Rybnoe Khoziaistvo,V.33, 74-75, 1957]

To ascertain the effect of various concentrations of oxygen in water on the fry of rainbow trout experiments were made with aquaria at various concentrations of oxygen. The food supplied was chironomid larvae (Chironomus plumosus). A surplus of food was supplied to the fry. Indices are given of the reaction of the fry to different temperatures.

Heteroepitaxy of Group IV and Group III-V semiconductor alloys for photovoltaic applications

Photovoltaic energy conversion represents a economically viable technology for realizing collection of the largest energy resource known to the Earth -- the sun. Energy conversion efficiency is the most leveraging factor in the price of energy derived from this process. This thesis focuses on two routes for high efficiency, low cost devices: first, to use Group IV semiconductor alloy wire array bottom cells and epitaxially grown Group III-V compound semiconductor alloy top cells in a tandem configuration, and second, GaP growth on planar Si for heterojunction and tandem cell applications.

Metal catalyzed vapor-liquid-solid grown microwire arrays are an intriguing alternative for wafer-free Si and SiGe materials which can be removed as flexible membranes. Selected area Cu-catalyzed vapor-liquid solid growth of SiGe microwires is achieved using chlorosilane and chlorogermane precursors. The composition can be tuned up to 12% Ge with a simultaneous decrease in the growth rate from 7 to 1 μm/min^-1. Significant changes to the morphology were observed, including tapering and faceting on the sidewalls and along the lengths of the wires. Characterization of axial and radial cross sections with transmission electron microscopy revealed no evidence of defects at facet corners and edges, and the tapering is shown to be due to in-situ removal of catalyst material during growth. X-ray diffraction and transmission electron microscopy reveal a Ge-rich crystal at the tip of the wires, strongly suggesting that the Ge incorporation is limited by the crystallization rate.

Tandem Ga_1-xIn_xP/Si microwire array solar cells are a route towards a high efficiency, low cost, flexible, wafer-free solar technology. Realizing tandem Group III-V compound semiconductor/Si wire array devices requires optimization of materials growth and device performance. GaP and Ga_1-xIn_xP layers were grown heteroepitaxially with metalorganic chemical vapor deposition on Si microwire array substrates. The layer morphology and crystalline quality have been studied with scanning electron microscopy and transmission electron microscopy, and they provide a baseline for the growth and characterization of a full device stack. Ultimately, the complexity of the substrates and the prevalence of defects resulted in material without detectable photoluminescence, unsuitable for optoelectronic applications.

Coupled full-field optical and device physics simulations of a Ga_0.51In_0.49P/Si wire array tandem are used to predict device performance. A 500 nm thick, highly doped "buffer" layer between the bottom cell and tunnel junction is assumed to harbor a high density of lattice mismatch and heteroepitaxial defects. Under simulated AM1.5G illumination, the device structure explored in this work has a simulated efficiency of 23.84% with realistic top cell SRH lifetimes and surface recombination velocities. The relative insensitivity to surface recombination is likely due to optical generation further away from the free surfaces and interfaces of the device structure.

Finally, GaP has been grown free of antiphase domains on Si (112) oriented substrates using metalorganic chemical vapor deposition. Low temperature pulsed nucleation is followed by high temperature continuous growth, yielding smooth, specular thin films. Atomic force microscopy topography mapping showed very smooth surfaces (4-6 Å RMS roughness) with small depressions in the surface. Thin films (~ 50 nm) were pseudomorphic, as confirmed by high resolution x-ray diffraction reciprocal space mapping, and 200 nm thick films showed full relaxation. Transmission electron microscopy showed no evidence of antiphase domain formation, but there is a population of microtwin and stacking fault defects.