112,735 research outputs found
Mobility of the SecA 2-helix-finger is not essential for polypeptide translocation via the SecYEG complex
No full textThe bacterial ATPase SecA and protein channel complex SecYEG form the core of an essential protein translocation machinery. The nature of the conformational changes induced by each stage of the hydrolytic cycle of ATP and how they are coupled to protein translocation are not well understood. The structure of the SecA-SecYEG complex revealed a 2-helix-finger (2HF) of SecA in an ideal position to contact the substrate protein and push it through the membrane. Surprisingly, immobilization of this finger at the edge of the protein channel had no effect on translocation, whereas its imposition inside the channel blocked transport. This analysis resolves the stoichiometry of the active complex, demonstrating that after the initiation process translocation requires only one copy each of SecA and SecYEG. The results also have important implications on the mechanism of energy transduction and the power stroke driving transport. Evidently, the 2HF is not a highly mobile transducing element of polypeptide translocation
The dynamic action of SecA during the initiation of protein translocation
No full textBiotechnology and Biological Sciences Research Council (BBSRC) [a doctoral training grant Ph.D. studentship to S.W. and project grant number BB/I008675/1] and the Wellcome Trust [project grant number 084452]
Reversible solid oxide fuel cells as energy conversion and storage devices
No full textA reversible solid oxide fuel cell (RSOFC) system could buffer intermittent electrical generation, e.g. wind, wave power by storing electrical energy as hydrogen and heat. RSOFC were fabricated by thermoplastic extrusion of (La₀.₈Sr₀.₂)₀.₉₅MnO[subscript(3−δ)] (LSM) ceramic support tubes, which were microstructurally stable with 55% porosity at 1350°C. A composite oxygen electrode of LSM-YSZ was applied, providing a homogeneous substrate for a 20 μm - 30 μm thick YSZ electrolyte. A dip-coated 8YSZ slurry, and a painted commercial 3YSZ ink gave sintered densities of 90% and nearly 100% at 1350°C, respectively. A porous NiO/YSZ fuel electrode was also painted on. A Ag/Cu reactive air braze was unsuccessful at forming a void-free joint between the RSOFC and a 316 stainless steel gas delivery tube, as the braze did not penetrate the oxidation layer on the steel. Two alumina-based ceramic cements failed to fully seal the cell to an alumina gas delivery tube, due to thermal expansion coefficient mismatches and porosity after curing. Therefore, the maximum open circuit voltage (OCV) obtained during RSOFC testing was 0.8 V at 440°C. LSM-YSZ symmetrical cell performance measurements with oxygen pressure showed a diffusion polarisation, which was assigned to dissociative adsorption and surface diffusion of oxygen species. A collaborative RSOFC system software model showed ohmic and activation losses dominated the RSOFC, and diffusion losses were insignificant. Pressurisation from 1 to 70 bar increased the RSOFC Nernst voltage by 11% at 900°C, and reduced the entropy of the gases, reducing heat production and increasing electrical efficiency. A 500 kg Sn/Cu phase change heat store prevented the system overheating. Over a 16 h discharge-charge RSOFC cycle in the range 5 mol.% - 95 mol.% hydrogen in steam, at 20.4 A per cell or 3250 A m⁻², the electrical energy storage efficiency was 64.4%
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Studien zur Proteintranslokation in Escherichia coli : Untersuchung der Membranproteine SecYEG und YidC unter Verwendung biochemischer und kristallographischer Methoden
No full textTransport of proteins into or across cellular membranes is mediated by the conserved and ubiquitous Sec-machinery. The Sec-homologue in the inner membrane of Escherichia coli is SecYEG. Sec-mediated insertion of numerous membrane proteins is aided by YidC, another protein integral to the inner membrane of Escherichia coli. YidC fulfils in addition the integration of a variety of membrane proteins Sec-independently. It belongs to a conserved but structurally uncharacterised family of proteins important for membrane protein biogenesis and comprises homologues in mitochondria and chloroplasts. By modification of a former crystallisation protocol two-dimensional crystals of SecYEG were grown in presence of the signal sequence peptide of LamB. Recording of structural data by electron cryo-microscopy and calculation of a difference structure comparing a former SecYEG projection structure with the one of SecYEG crystallised in presence of the substrate revealed several new and vacant densities. These hint to signal peptide binding close to the translocation pore and to significant rearrangements in proximity to the lateral exit site for transmembrane domains in SecYEG. The difference structure suggests that dimeric SecYEG is an asymmetric molecule consisting of one active and one inactive SecYEG monomer. Detergent removal from a mixture of purified YidC and lipids produced two-dimensional crystals that were highly dependent on the ionic strength and lipid composition for their growth. Electron cryo-microscopy on the frozen-hydrated crystals and image processing visualised structural details at about 10 Å resolution. Averaging two alternative projection structures in p2 and p121_a symmetry, respectively, yielded essentially the same features. Four YidC monomers form one unit cell (dimensions 82 x 71 Å, included angle 85 ° and 90 °, respectively) and seem to be arranged as two sets of dimers integrated in an anti-parallel fashion into the membrane. An area of low density in the centre of each YidC monomer resembles possibly a constriction of the membrane, which could have particular relevance for the integration of substrate proteins into the lipid bilayer.Der Transport von Proteinen in zelluläre Membranen hinein oder durch diese hindurch wird durch die konservierte und überall anzutreffende Sec-Maschinerie vermittelt. Das Sec-Homolog in der inneren Membran von Escherichia coli ist SecYEG. Der Sec-vermittelte Einbau von vielen Membranproteinen wird unterstützt von YidC, einem weiteren Protein in der inneren Membran von Escherichia coli. YidC führt zusätzlich den Einbau einiger Proteine Sec-unabhängig durch. YidC gehört zu einer konservierten aber strukturell uncharakterisierten Familie von Proteinen, die wichtig für die Biogenese von Membranproteinen sind und hat Homologe in Mitochondrien und Chloroplasten. Durch Modifikation eines früheren Kristallisations-Protokolles wurde zweidimensionale Kristalle von SecYEG in Gegenwart des Signalsequenz-Peptides von LamB gezüchtet. Das Aufnehmen von Strukturdaten mittels Elektronen-Kryomikroskopie und die Berechnung einer Differenzstruktur, welche eine frühere SecYEG-Projektionsstruktur mit der von SecYEG kristallisiert in Gegenwart von Substrat vergleicht, demonstrierte eine Reihe neuer bzw. fehlender Dichten. Diese deuten auf das Binden von Signalpeptid in räumlicher Nähe zur Translokationspore sowie auf signifikante Umlagerungen in der Nähe des lateralen Austrittsortes für Transmembrandomänen in SecYEG hin. Die Differenzstruktur legt nahe, dass dimeres SecYEG ein asymmetrisches Molekül ist, bestehend aus einem aktiven und einem inaktiven SecYEG-Monomer. Detergenzentfernung aus einem Gemisch von gereinigtem YidC und Lipiden brachte zweidimensionale Kristalle hervor, welche bezüglich ihrer Bildung sehr abhängig von Ionenstärke und Lipidkomposition waren. Eine elektronen-kryomikroskopische Untersuchung der in hydratisiertem Zustand gefrorenen Kristalle und Bildverarbeitung machten strukturelle Details mit einer Auflösung von etwa 10 Å sichtbar. Mitteln von Einzelbildern zu zwei alternativen Projektionsstrukturen in p2 bzw. p121_a Symmetrie brachte grundsätzlich gleiche strukturelle Merkmale hervor. Vier YidC-Monomere bilden eine Einheitszelle (Dimensionen 82 x 71 Å, eingeschlossener Winkel 85 ° bzw. 90 °) und scheinen als zwei Dimere vorzuliegen, welche in gegensätzlicher Orientierung in die Membran eingebettet sind. Ein Bereich geringer Dichte im Zentrum eines jeden YidC-Monomers stellt möglicherweise eine Einstülpung der Membran dar, die besondere Bedeutung für den Einbau von Substratproteinen in die Lipid-Doppelschicht haben könnte
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Chinese medicine functional diagnosis: An integrative insight to understand rheumatoid arthritis of the hand
No full textIntroduction: Chinese medicine (CM), may provide insights into understanding the neuro-immunological mechanisms involved in Rheumatoid Arthritis (RA). The objective of this study was to ascertain if objective assessment strategies could help to determine CM functional diagnosis and if the complicated issues surrounding the symptoms of RA of the hand could be more easily understood by using the Shang Han Lun. Methods: First, 190 RA patients were stratified into two groups: (1) “hand pain worsened by handgrip” or (2) “hand pain worsened by thumb resistance”. Second, a CM diagnosis of patients with “hand pain worsened by handgrip” was performed, obtained through inspection, auscultation, interrogation and palpation. Third, clinical features based on data from tongue-diagnosis were assessed by two CM doctors. Results: (1) 79.5% of the participants showed worsening hand pain by handgrip; (2) all these patients showed concomitant presence of imbalances and intermingled symptoms; (3) clinical findings of the invasion of the pathogen agent algor/“cold” were: cold hands (62.9%), tearing and localized pain with gradual onset (82.9%), worse pain upon cold exposure (82.9%), pain relief by applying warmth to the affected area (62.9%), tongue exhibiting a hyaline (85.7%) and white coating (52.4%). Conclusions: This study provides new options for assessing the CM diagnosis, which may improve RA treatment strategies. Identification of joint non-related symptoms and pathogenic external factors such as algor/“cold” may help understanding activation of specific immunological mechanisms, changes of capillary endothelium and the microcirculation disturbances. Overactivation of the functional defence mechanisms by algor/“cold” seem to be of utmost importance for RA symptoms
Enriquecimento da cana-de-açucar com fontes de nitrogênio em agroecossistemas do norte e noroeste do Paraná
No full textDissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Programa de Pós-Graduação em Agroecossistemas, Florianópolis, 2010A busca por volumosos em épocas de escassez de forragens que sejam economicamente viáveis faz da cana-de-açúcar uma forrageira em potencial, pois é de fácil cultivo e tradicionalmente utilizada por produtores em boa parte do território nacional, principalmente para alimentação de ruminantes. Entretanto, a cana-de-açúcar apresenta um teor de proteína bruta limitante para ser usado como única fonte de alimento para animais. Esta pesquisa teve como objetivo avaliar formas de enriquecimento da cana-de-açúcar com fontes de nitrogênio protéico e não protéico na tentativa de melhorar o valor nutricional dos nutrientes da cana-de-açúcar, assim como incentivar o uso de alimentos existentes nas regiões norte e noroeste do Paraná, como alternativa ao uso da uréia como forma de enriquecimento da cana-de-açúcar. Foram realizados dois experimentos, um no assentamento Dorcelina Folador, em Arapongas e o outro no assentamento Oziel Alves, em Santa Cruz de Monte Castelo, norte e noroeste do Estado do Paraná, respectivamente. As análises bromatológicas foram realizadas nos laboratórios de análise de alimentos e nutrição animal da Universidade Estadual de Maringá - UEM e no laboratório de bromatologia e nutrição animal da Embrapa Clima Temperado - Pelotas - RS, segundo metodologia proposta por Silva e Queiroz (2009). No primeiro experimento os tratamentos foram: Testemunha (T) - cana-de-açúcar; Tratamento Uréia (TU) - cana-de-açúcar + uréia + suplemento mineral; Tratamento Farelo de Soja (TFS) - cana-de-açúcar + farelo de soja + suplemento mineral e Tratamento Leucena (TL) - cana-de-açúcar + leucena + suplemento mineral. Os teores de matéria seca (MS) obtidos 59,85; 72,85; 68,75 e 51,77% para os tratamentos T, TFS, TL e TU respectivamente. Resultados estes abaixo do esperado, que seriade 86%. Para a proteína bruta (PB), obteve-se teores de 2,92; 17,68; 13,29 e 15,35% para os tratamentos T, TFS, TL e TU respectivamente. Concluiu-se que o TU, também denominado de sacharina é uma alternativa viável de enriquecimento nutricional da cana-de-açúcar para ser utilizada nos períodos de escassez de forragens. A leucena e o farelo de soja podem substituir a uréia na produção da sacharina. A leucena pode ser uma alternativa para locais em fase de transição e certificação agroecológica. Considerando as restrições do uso da uréia em processos agroecológicos, no segundo experimento procurou-se avaliar alternativas de suplementação da cana-de-açúcar somente com fontes de nitrogênio protéico disponíveis na região. Os tratamentos foram: cana-de-açúcar + farelo de soja + suplemento mineral - CFS; cana-de-açúcar + guandu + suplemento mineral - CG; cana-de-açúcar + leucena + suplemento mineral - CL. Independente da fonte protéica utilizada sua inclusão proporcionou aumentos significativos nos valores de Proteína Bruta dos compostos. A presença das leguminosas nos compostos com leucena (CL) e com guandu (CG) determinou teores de fibra em detergente neutro (FDN) e fibra em detergente ácido (FDA) superiores ao composto com farelo de soja. A digestibilidade do Farelo de Soja no composto a base de cana-de-açúcar + farelo de soja (CFS) foi determinante para o teor mais elevado de nutrientes digestíveis totais (NDT) neste composto (64,94%) quando comparado aos demais tratamentos, que obtiveram teores de 51,83 e 53,34% para os tratamentos CG e CL respectivamente. Os resultados obtidos nestes dois experimentos indicam a viabilidade de enriquecimento da cana-de-açúcar utilizando fontes de nitrogênio de leguminosas de fácil obtenção e menores custos em pequenas propriedades rurais localizadas no norte e noroeste do estado do Paraná.A produção avícola intensiva é uma atividade de grande importância para o Brasil e para Santa Catarina, onde está concentrada em algumas regiões. Este sistema de produção gera uma significativa quantidade de resíduos, onde se destaca a cama de aviário. Com a tendência de aumento desta atividade, aumentará ainda mais a produção deste resíduo. A alta concentração de cama de aviário em algumas regiões, onde o solo e a extração dos nutrientes pelas culturas não estão sendo mais suficientes para reciclá-lo, está causando a contaminação por nutrientes, microorganismos patogênicos e resíduos de produtos químicos, com repercussões econômicas na saúde pública e no ambiente. Para minimizar estes impactos, os agricultores têm sido estimulados a fazer a decomposição da cama de aviário antes de sua aplicação como fertilizante. Existem ainda muitas dúvidas sobre a eficiência deste tratamento na diminuição do potencial poluidor deste resíduo. O objetivo deste trabalho foi estudar os principais aspectos inerentes à produção, processamento e uso da cama de aviário. Foi realizado também um experimento para comparar tipos de decomposição deste resíduo. Os três processos (tratamentos) usados foram: Tratamento CSC (cama de aviário com camadas de solo e coberto com capim) CP (cama de aviário coberta com polietileno) e CCC (cama de aviário com camadas de capim e coberto com capim). Amostras foram coletadas semanalmente no primeiro mês e mensalmente até o final do experimento aos 180 dias. Acompanhou-se a evolução da temperatura das pilhas, umidade, pH, teor de carbono, nitrogênio, nível de Escherichia coli, Salmonella, oocistos de eimérias e concentrações do antibiótico salinomicina. Os resultados mostram que, dependendo do tipo de tratamento de decomposição adotado, pode-se interferir no potencial de contaminação ambiental da cama de aviário. O uso do processo de decomposição usualmente adotado pelos agricultores (tratamento CP) apresenta menores perdas de carbono e nitrogênio, entretanto é menos eficiente na degradação do antibiótico salinomicina. A adição do capim e o seu uso como cobertura mantém uma temperatura mais elevada durante a decomposição e, com o passar do tempo, permite uma maior infiltração de água que acarreta perdas posteriores de carbono. A decomposição da cama de aviário, independente dos tratamentos, é eficiente no controle de Escherichia coli, porém os tipos de decomposição não interferem na redução do número de oocistos de eimérias. A adaptação da técnica de cromatografia líquida de alta eficiência (CLAE) para a determinação de salinomicina em cama de aviário se apresentou de simples execução, foi suficientemente sensível, específica e reprodutível. Apesar do processo de decomposição diminuir o potencial contaminante da cama de aviário, é uma medida isolada e insuficiente. A produção da cama de aviário está ligada ao processo produtivo como um todo, e este deve passar por um planejamento de acordo com a capacidade de cada ecossistema em reciclar os resíduos destas atividades
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Dropping Out and Other Fates of Transmembrane Segments Inserted by the SecA ATPase
No full textType II single-span membrane proteins, such as CadC or RodZ, lacking a signal sequence and having a far-downstream hydrophobic segment, require the SecA secretion motor for insertion into the inner membrane of Escherichia coli. Using two chimeric single-span proteins containing a designed hydrophobic segment H, we have determined the requirements for SecA-mediated secretion, the molecular distinction between TM domains and signal peptides, and the propensity for hydrophobic H-segments to remain embedded within the bilayer after targeting. By means of engineered H-segments and a strategically placed SPase I cleavage site, we determined how targeting and stability of the chimeric proteins are affected by the length and hydrophobicity of the H-segment. Very hydrophobic segments (e.g., 16 Leu) are stably incorporated into the inner membrane, resulting in a C-terminal anchored membrane protein, while a 24L construct was not targeted to the membrane by SecA and remained in the cytoplasm. However, a construct carrying preMalE at the N-terminus led to SecA targeting to SecYEG via the native signal sequence and stable insertion of the downstream 24L H-segment. We show that the RseP intramembrane protease degrades weakly stable H-segments and is a useful tool for investigating the borderline between stable and unstable TM segments. Using RseP- cells, we find that moderately hydrophobic sequences (e.g., 5Leu + 11Ala) are targeted to SecYEG by SecA and inserted, but subsequently drop out of the membrane into the cytoplasm. Therefore, the free energy of transfer from translocon to bilayer is different from the transfer free energy from membrane to water
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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