CSSP (Consensus Secondary Structure Prediction): a web-based server for structural biologists

Sequence-structure correlation studies are important in deciphering the relationships between various structural aspects, which may shed light on the protein-folding problem. The first step of this process is the prediction of secondary structure for a protein sequence of unknown three-dimensional structure. To this end, a web server has been created to predict the consensus secondary structure using well known algorithms from the literature. Furthermore, the server allows users to see the occurrence of predicted secondary structural elements in other structure and sequence databases and to visualize predicted helices as a helical wheel plot. The web server is accessible at http://bioserver1.physics.iisc.ernet.in/cssp/.

Stability of Dimeric Interface in Banana Lectin: Insight from Molecular Dynamics Simulations

Banana lectin (Banlec) is a homodimeric non-glycosylated protein. It exhibits the b-prism I structure. High-temperature molecular dynamics simulations have been utilized to monitor and understand early stages of thermally induced unfolding of Banlec. The present study elucidates the behavior of the dimeric protein at four different temperatures and compares the structural and conformational changes to that of the minimized crystal structure. The process of unfolding was monitored by following the radius of gyration, the rms deviation of each residue, change in relative solvent accessibility and the pattern of inter- and intra-subunit interactions. The overall study demonstrates that the Banlec dimer is a highly stable structure, and the stability is mostly contributed by interfacial interactions. It maintains its overall conformation during high-temperature (400–500 K) simulations, with only the unstructured loop regions acquiring greater momentum under such condition. Nevertheless, at still higher temperatures (600 K) the tertiary structure is gradually lost which later extends to loss of secondary structural elements. The pattern of hydrogen bonding within the subunit and at the interface across different stages has been analyzed and has provided rationale for its intrinsic high stability.

Enforceable undertakings: Perceptions of organisational justice

In this thesis the use of enforceable undertakings is examined as a sanction for a breach in work, health and safety legislation through the lens of organisational justice. A framework of justice types - distributive, procedural and interactional - is developed and the perceptions of the three parties to the process - the regulator, the business entity and the worker as the affected third party - are explored. It is argued that the three parties perceive the sanction to be distributively unfair, but procedurally and interactionally just.

Characterization of the molecular components and function of BARE-1, Hin-Mu and Mu transposition machineries

Transposable elements, transposons, are discrete DNA segments that are able to move or copy themselves from one locus to another within or between their host genome(s) without a requirement for DNA homology. They are abundant residents in virtually all the genomes studied, for instance, the genomic portion of TEs is approximately 3% in Saccharomyces cerevisiae, 45% in humans, and apparently more than 70% in some plant genomes such as maize and barley. Transposons plays essential role in genome evolution, in lateral transfer of antibiotic resistance genes among bacteria and in life cycle of certain viruses such as HIV-1 and bacteriophage Mu. Despite the diversity of transposable elements they all use a fundamentally similar mechanism called transpositional DNA recombination (transposition) for the movement within and between the genomes of their host organisms. The DNA breakage and joining reactions that underlie their transposition are chemically similar in virtually all known transposition systems. The similarity of the reactions is also reflected in the structure and function of the catalyzing enzymes, transposases and integrases. The transposition reactions take place within the context of a transposition machinery, which can be particularly complex, as in the case of the VLP (virus like particle) machinery of retroelements, which in vivo contains RNA or cDNA and a number of element encoded structural and catalytic proteins. Yet, the minimal core machinery required for transposition comprises a multimer of transposase or integrase proteins and their binding sites at the element DNA ends only. Although the chemistry of DNA transposition is fairly well characterized, the components and function of the transposition machinery have been investigated in detail for only a small group of elements. This work focuses on the identification, characterization, and functional studies of the molecular components of the transposition machineries of BARE-1, Hin-Mu and Mu. For BARE-1 and Hin-Mu transpositional activity has not been shown previously, whereas bacteriophage Mu is a general model of transposition. For BARE-1, which is a retroelement of barley (Hordeum vulgare), the protein and DNA components of the functional VLP machinery were identified from cell extracts. In the case of Hin-Mu, which is a Mu-like prophage in Haemophilus influenzae Rd genome, the components of the core machinery (transposase and its binding sites) were characterized and their functionality was studied by using an in vitro methodology developed for Mu. The function of Mu core machinery was studied for its ability to use various DNA substrates: Hin-Mu end specific DNA substrates and Mu end specific hairpin substrates. The hairpin processing reaction by MuA was characterized in detail. New information was gained of all three machineries. The components or their activity required for functional BARE-1 VLP machinery and retrotransposon life cycle were present in vivo and VLP-like structures could be detected. The Hin-Mu core machinery components were identified and shown to be functional. The components of the Mu and Hin-Mu core machineries were partially interchangeable, reflecting both evolutionary conservation and flexibility within the core machineries. The Mu core machinery displayed surprising flexibility in substrate usage, as it was able to utilize Hin-Mu end specific DNA substrates and to process Mu end DNA hairpin substrates. This flexibility may be evolutionarily and mechanistically important.

Polymers containing disulfide, tetrasulfide, diselenide and ditelluride linkages in the main chain

The present review articulates the syntheses and properties of industrially important disulfide and tetrasulfide polymers. The diselenide and ditelluride polymers have also been reviewed, for the first time, so that a comprehensive view on the polymers containing group VIA elements can be obtained. The latter two polymers are gaining considerable current attention due to their semi-conducting properties. The emphasis has been made to sift through the developments in the last ten years or so to get the latest flavour in these rapidly developing polymers. We have also attempted to bring to the fore several contradicting results, like, for example, the crystallinity of ditelluride polymers, to clear the mist in such reports. We hope that this review will help those working in the field to assess the progress achieved in this area and that it may also provide useful orientation for those who wish to become involved.

A review of recent developments in parametric based acoustic emission techniques applied to concrete structures

This article presents a review of recent developments in parametric based acoustic emission (AE) techniques applied to concrete structures. It recapitulates the significant milestones achieved by previous researchers including various methods and models developed in AE testing of concrete structures. The aim is to provide an overview of the specific features of parametric based AE techniques of concrete structures carried out over the years. Emphasis is given to traditional parameter-based AE techniques applied to concrete structures. A significant amount of research on AE techniques applied to concrete structures has already been published and considerable attention has been given to those publications. Some recent studies such as AE energy analysis and b-value analysis used to assess damage of concrete bridge beams have also been discussed. The formation of fracture process zone and the AE energy released during the fracture process in concrete beam specimens have been summarised. A large body of experimental data on AE characteristics of concrete has accumulated over the last three decades. This review of parametric based AE techniques applied to concrete structures may be helpful to the concerned researchers and engineers to better understand the failure mechanism of concrete and evolve more useful methods and approaches for diagnostic inspection of structural elements and failure prediction/prevention of concrete structures.

New structural forms of a mycobacterial adenylyl cyclase Rv1625c

Rv1625c is one of 16 adenylyl cyclases encoded in the genome of Mycobacterium tuberculosis. In solution Rv1625c exists predominantly as a monomer, with a small amount of dimer. It has been shown previously that the monomer is active and the dimeric fraction is inactive. Both fractions of wild-type Rv1625c crystallized as head-to-head inactive domain-swapped dimers as opposed to the head-to-tail dimer seen in other functional adenylyl cyclases. About half of the molecule is involved in extensive domain swapping. The strain created by a serine residue located on a hinge loop and the crystallization condition might have led to this unusual domain swapping. The inactivity of the dimeric form of Rv1625c could be explained by the absence of the required catalytic site in the swapped dimer. A single mutant of the enzyme was also generated by changing a phenylalanine predicted to occur at the functional dimer interface to an arginine. This single mutant exists as a dimer in solution but crystallized as a monomer. Analysis of the structure showed that a salt bridge formed between a glutamate residue in the N-terminal segment and the mutated arginine residue hinders dimer formation by pulling the N-terminal region towards the dimer interface. Both structures reported here show a change in the dimerization-arm region which is involved in formation of the functional dimer. It is concluded that the dimerization arm along with other structural elements such as the N-terminal region and certain loops are vital for determining the oligomeric nature of the enzyme, which in turn dictates its activity.

Stochastic Structural Model of Rock and Soil Aggregates by Continuum-Based Discrete Element Method

This paper first presents a stochastic structural model to describe the random geometrical features of rock and soil aggregates. The stochastic structural model uses mixture ratio, rock size and rock shape to construct the microstructures of aggregates,and introduces two types of structural elements (block element and jointed element) and three types of material elements (rock element, soil element, and weaker jointed element)for this microstructure. Then, continuum-based discrete element method is used to study the deformation and failure mechanism of rock and soil aggregate through a series of loading tests. It is found that the stress-strain curve of rock and soil aggregates is nonlinear, and the failure is usually initialized from weaker jointed elements. Finally, some factors such as mixture ratio, rock size and rock shape are studied in detail. The numerical results are in good agreement with in situ test. Therefore, current model is effective for simulating the mechanical behaviors of rock and soil aggregates.

Das paradies in der politik ein kapitel negativer kosmologie

Abstract: The idea of a “paradise in politics” is an answer to the cosmogonic- anthropogonic problem that, through their bodies, the life of human beings has been shaped politically from the very beginning: all creation is a creation of bodies and bodies are power. All creation, furthermore, means separation, it emerges through a multiplicity of things and beings only. The conventional solution for the problem, in the realm of human beings, consists in forming societies out of a multiplicity of indivuals that remains as such. The solution of a “paradise in politics”, however, envisions a “healing” of creation through a bodily transmutation by which a world of bodies emerges that is freed from the problem of bodies: separation, power. The article discusses the negative cosmology with which all tales on a paradise in politics start. It shows the essential role of phantasy in the constitution of these tales, and elucidates the principal structural elements through which visions of a paradise in politics are built. A special attention is given to the parallelism between these visions and known religious thought, as in the case of the concepts of apokatastasis or perichoresis, for instance. Methodically, the article achieves a demonstration of its subject by an extensive presentation and analysis of two case studies: Rousseau’s vision of a “terrestrial paradise” and the attempt at “bodily redemption” put on the stage in 1968-69 by the “Living Theatre” Group with its performance “Paradise Now”.

Estudo da aderência de barras de aço coladas ao concreto com resina Epóxi.

Assim como em outras áreas do conhecimento a construção civil vem evoluindo ao longo dos anos. Grandes investimentos e elevadas taxas de demandas por novos projetos requerem uma maior velocidade na consolidação de obras. Neste cenário, ficam precários os estudos e pesquisas que avaliam a capacidade de novas tecnologias. Na área do concreto e estruturas de concreto armado, depara-se a associação de técnicas consolidadas à métodos inovadores. A utilização de polímeros como material de construção, como é o caso dos aditivos para concreto, dos tubos e conexões, das esquadrias e como adesivos, utilizados em ligações de aduelas de pontes, associados a fibras de vidro ou carbono para reforços estruturais e para fixação de armaduras ou conectores no caso de reparação de estruturas, oferecendo uma solidarização eficiente entre elementos estruturais. O presente trabalho visa avaliar uma pequena parcela de aplicação de materiais poliméricos, principalmente quanto a sua característica de aderência e colagem de barras de aço ao concreto. O desenvolvimento do estudo ocorreu sobre uma perspectiva de ensaios laboratoriais de arrancamento de barras coladas com resina epóxi em blocos de concreto, sendo estes resultados comparados com barras de aço concretadas em blocos de concreto. Desse modo o principal fator de comparação seria a tensão de aderência desenvolvida na área de contato da barra com o substrato. Alguns parâmetros foram inseridos para uma abordagem de maior amplitude, tais como variação do diâmetro da barra (φ = 10,0mm; φ = 12,5mm e φ = 16,0mm), do comprimento de ancoragem (múltiplos do diâmetro, sendo 5φ e 7,5φ) e da espessura da resina (1mm, 2mm e 3mm). De forma complementar procedeu-se ao ensaio de vigas bi-apoiadas submetidas à flexão visando representar o comportamento de uma recuperação/reforço estrutural aplicado em escala. Para avaliar o comportamento destas vigas, foram ensaiados dois espécimes, uma viga padrão concretada de uma única vez e outra submetida a um reparo estrutural, onde possuía a armadura inferior inserida posteriormente à concretagem inicial, colada com resina epóxi nas extremidades da viga.

Reparación y reconocimiento a víctimas del terrorismo: prácticas restaurativas desde el punto de vista de las víctimas de ETA

[ES]En este trabajo sobre las víctimas del terrorismo de ETA se abordarán temas relacionados con su recuperación emocional y su reconocimiento, particularmente, distinguiendo entre las víctimas que han tenido experiencias de encuentro con un ex miembro de ETA, y las que no lo han tenido. En ocasiones, las instituciones públicas facilitan la oportunidad a las víctimas de participar en programas o prácticas de justicia restaurativas frente a ex victimarios, mientras que otras víctimas prefieren no participar en estas experiencias, o simplemente no tienen acceso a ellas. Partiendo del derecho que tienen las víctimas de ser reconocidas tanto en una circunstancia como en la otra, este trabajo explora si éstas cuentan con los suficientes recursos y mecanismos para hacer frente a su recuperación emocional y reconocimiento. La primera parte del trabajo está dedicada a la contextualización y conceptualización de las víctimas, sus derechos y sistema normativo, y los mecanismos de justicia restaurativa. En la segunda parte, se analizan brevemente algunas experiencias internacionales de justicia restaurativa con víctimas del terrorismo. A continuación, exploraremos el caso vasco estudiando diferentes casos de recuperación y reconocimiento en víctimas de Euskadi. Y finalmente, se muestran los resultados del trabajo de campo sobre las tres entrevistas realizadas donde víctimas y victimarios valoran experiencias de justicia restaurativa y su potencial reparador.

Coisas de família: análise antropológica de processos de transmissão familiar

A transmissão inter-geracional diz respeito à passagem de um patrimônio familiar que se constitui de modo complexo,visto envolver elementos de distintas ordens, agregando valor material e simbólico. Os bens materiais, compreendidos no espaço doméstico, prestam-se particularmente bem a expressar a forma como os integrantes do grupo familiar se relacionam, permitindo perceber seus sentimentos e interesses, conflitos e alianças. Todavia, as coisas de família também dizem respeito à dimensão não material, relacionando valores e padrões de ordenamento de mundo. Herda-se. Não uma única herança; não um único e simultâneo movimento de dar e receber. A herança a ser transmitida de uma geração a outra diz respeito a conjunto de elementos que reúnem desde o patrimônio genético até conhecimento nem sempre revelado, direta e explicitamente, constituindo a esfera do segredo e do indizível. As fotografias de família estão aqui sendo trabalhadas no sentido de buscar formas de alcançar tal universo de elementos fragmentados, relacionando memória e identidade familiar.

mRNA 很可能携带三维遗传信息

The forming mechanism of the three - dimensional structures of proteins，i.e.the mechanism of protein folding，is a basic problem in molecular biology which is still unsolved unitl now. In which a core problem is whether there is the three – dimensional genetic information that decide the three - dimensional structures of proteins. However, the research on this field has mot yet been reported. Recently，we made a comparative study on the folded structures of more than 70 mature messeneger RNAs (mRNAs) and the three - dimensional structures of the proteins encoded by them，it has been found that there exist marked correspondences between their featured structures in the following aspects: 1.The number of the structural units. An RNA molecule can form a secondary structure(stem and loop structure) by the folding and the base pairing of itself. The elementary structural unit of an RNA secondary structure is hairpin(or compound hair pin).The regular structural unit in the secondary structure of a protein is # alpha # - helix or #beta# - sheet . We have found that the hairpin number in the secondary structure of each mature mRNA is equal or approximately equal to the number of the regular secondary structural unis of the encoded protein. 2 .Turning region. Turn is a main structrual element in the secondary structure of a protein, which decides the backbone orientation of a protein molecule to some extent .Our analysis shows that the nucleotide sequence segments in an mRNA which encode the turns of the corresponding protein are overall situated in the turning regions of the mRNA secondary structure such as haipin，bulge loop or multibaranch loops. 3 .The arrangement of structural elements in space. In order to understand the backbone orientation of an RNA molecule and the arangement of its structural elements in space，we have modeled the three一dimensional structure of the mRNA molecule on SGI workstation based on its secondary structure.The result shows that the spatial arrangement of most of the nucleotide sequence segments encoding the structural elements of a protein is consistent with that of these stretural exements in the protein. For instance，the nucleotide sequences corresponding to each pleated sheet of a # beta # - sheet structure are close to each other in the mRNA secondary stucture and in the three - dimensional structure，although some of the nucleotide segments are far apart from each other in the one - dimensional sequence. For another instance，the two triplet codons of cysteines which form a disulphide bridge geneal1y are very close to each other in the mRNA folded structure. In addition，we also analyzed the locations of the codons proline - coding and the distrbution of the nucleotide sequences #alpha# - helix - coding in the folded structures of mRNAs . Some distribution laws have been found. All of these results suggest that the transfer of the genetic information from mRNA to protein not only is one – dimensional but also is three - dime ns ional. That is，there exists the genetic information that decide the three - dimensional structures of proteins. To a certain extent，we could say that the mRNA folding detemines the protein folding. Based on these results，it would be possible to predict the three - dimensional structures of proteins from the primary，secondary and tertiary structures of the m RNAs at a higher accuracy.And more important is that a new clue has been provided to uncover the“spatial coding" of the genetic information.

Centrifuge and discrete element modelling of tunnelling effects on pipelines

The paper presents centrifuge test data of the problem of tunnelling effects on buried pipelines and compares them to predictions made using DEM simulations. The paper focuses on the examination of pipeline bending moments, their distribution along the pipe, and their development with tunnel volume loss. Centrifuge results are obtained by PIV analysis and compared to results obtained using the DEM model. The DEM model was built to replicate the centrifuge model as closely as possible and included numerical features formulated specially for this task, such as structural elements to replicate the tunnel and pipeline. Results are extremely encouraging, with deviations between DEM and centrifuge test bending moment results being very small. © 2010 Taylor & Francis Group, London.

A comparison of two models for the vibration response of piled foundations to inertial and underground-railway-induced loadings

The vibration response of piled foundations due to ground-borne vibration produced by an underground railway is a largely-neglected area in the field of structural dynamics. However, this continues to be an important aspect of research as it is expected that the presence of piled foundations can have a significant influence on the propagation and transmission of the wavefield produced by the underground railway. This paper presents a comparison of two methods that can be employed in calculating the vibration response of a piled foundation: an efficient semi-analytical model, and a Boundary Element model. The semi-analytical model uses a column or an Euler beam to model the pile, and the soil is modelled as a linear, elastic continuum that has the geometry of a thick-walled cylinder with an infinite outer radius and an inner radius equal to the radius of the pile. The boundary element model uses a constant-element BEM formulation for the halfspace, and a rectangular discretisation of the circular pile-soil interface. The piles are modelled as Timoshenko beams. Pile-soil-pile interactions are inherently accounted for in the BEM equations, whereas in the semi-analytical model these are quantified using the superposition of interaction factors. Both models use the method of joining subsystems to incorporate the incident wavefield generated by the underground railway into the pile model. Results are computed for a single pile subject to an inertial loading, pile-soil-pile interactions, and a pile group subjected to excitation from an underground railway. The two models are compared in terms of accuracy, computation time, versatility and applicability, and guidelines for future vibration prediction models involving piled foundations are proposed.