The X-ray crystallographic structure of Escherichia coli branching enzyme

Branching enzyme catalyzes the formation of alpha-1,6 branch points in either glycogen or starch. We report the 2.3-Angstrom crystal structure of glycogen branching enzyme from Escherichia coli. The enzyme consists of three major domains, an NH2-terminal seven-stranded beta-sandwich domain, a COOH-terminal domain, and a central alpha/beta-barrel domain containing the enzyme active site. While the central domain is similar to that of all the other amylase family enzymes, branching enzyme shares the structure of all three domains only with isoamylase. Oligosaccharide binding was modeled or branching enzyme using the enzyme-oligosaccharide complex structures of various alpha-amylases and cyclodextrin glucanotransferase and residues were implicated in oligosaccharide binding. While most of the oligosaccharides modeled well in the branching enzyme structure, an approximate 50degrees rotation between two of the glucose units was required to avoid steric clashes with Trp(298) of branching enzyme. A similar rotation was observed in the mammalian alpha-amylase structure caused by an equivalent tryptophan residue in this structure. It appears that there are two binding modes for oligosaccharides in these structures depending on the identity and location of this aromatic residue.

Search for anomalous production of multilepton events in pp collisions at root s=7 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Dominação e contrapoder: o candomblé no fogo cruzado entre construções e desconstruções de diferença e significado

Este ensaio debate a questão da dominação e do contrapoder com base no exemplo de alguns momentos específicos da história do candomblé. Partindo de uma reflexão sobre perspectivas teóricas antropológicas e pós-coloniais recentes sobre cultura, identidade e poder, procura-se mostrar que o candomblé se apresenta como um campo disputado, não apenas internamente, mas, inclusive, no que diz respeito à sua delimitação externa. Argumenta-se que uma aproximação entre olhares antropológicos e preocupações pós-coloniais pode ajudar a entender melhor como os agentes sociais tecem, por meio da articulação de signos e significados, relações de poder ao mesmo tempo em que promovem atos de identificação e de delimitação; e, como este processo contribui para a construção e desconstrução dos cenários de dominação e de contrapoder.

EFFECT OF FENCAMFAMINE ON AVOIDANCE PERFORMANCES OF RATS

The effects of fencamfamine (1.0 and 5.0 mg/kg, ip, single dose) on an inhibitory task were studied in rats (N = 15 per group). Post-training treatment with fencamfamine (1.0 mg/kg) significantly increased avoidance latency from 23 +/- 3 to 146 +/- 28 and 170 +/- 33 s for training day 1 and day 7, respectively, indicating an enhancement of retention. However, retention was significantly reduced with a high dose of fencamfamine (5.0 mg/kg). These results demonstrate that fencamfamine caused a reproducible dose-related increase and reduction in avoidance latency.

Food-web composition affects cross-ecosystem interactions and subsidies

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

Molecular modeling databases: A new way in the search of protein targets for drug development

DBMODELING is a relational database of annotated comparative protein structure models and their metabolic, pathway characterization. It is focused on enzymes identified in the genomes of Mycobacterium tuberculosis and Xylella fastidiosa. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. However, since the accuracy of structural models is highly dependent on sequence identity between template and target, it is necessary to make clear to the user that only models which show high structural quality should be used in such efforts. Molecular modeling of these genomes generated a database, in which all structural models were built using alignments presenting more than 30% of sequence identity, generating models with medium and high accuracy. All models in the database are publicly accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools. DBMODELING user interface provides users friendly menus, so that all information can be printed in one stop from any web browser. Furthermore, DBMODELING also provides a docking interface, which allows the user to carry out geometric docking simulation, against the molecular models available in the database. There are three other important homology model databases: MODBASE, SWISSMODEL, and GTOP. The main applications of these databases are described in the present article. © 2007 Bentham Science Publishers Ltd.

A contribuição da psicologia no estudo da relação trabalho bancário-saúde

Pós-graduação em Serviço Social - FCHS

Literatura e debate pós-colonial em A história do bando de Kelly, de Peter Carey

Pós-graduação em Letras - IBILCE

Linguagem e identidade: a construção discursiva das identidades sociais em interações com menores infratores

Este trabalho analisa a construção discursiva das identidades sociais em três interações com menores infratores sob o regime semiliberdade. O objetivo desta investigação é correlacionar língua e identidades. Para isto, o estudo começa por problematizar as idéias sobre o sujeito e sua identificação com diferentes centros sociais numa sociedade moderna e plural. Destaca, também, a influência das instituições na formação identitária do indivíduo, especialmente das instituições reguladoras para menores infratores e do Estatuto da Criança e do Adolescente (ECA). Assim, relaciona o estigma, socialmente construído, às contingências identitárias com os quais os menores se deparam nas interações verbais. Deste modo, recorre a abordagens teóricas que consideram a língua em seu contexto social, como a Sociolingüística Interacional e as teorias da Enunciação, como também a outras áreas do conhecimento, como os Estudos Culturais e a Psicologia Social. É uma investigação de cunho interpretativista e etnográfico que analisa a construção das identidades sociais por meio de diferentes alinhamentos e enquadres no discurso, e estuda a relação do discurso dos adolescentes com os discursos que circulam na unidade onde estão e na sociedade. Para tanto, entrevistas com funcionários e pessoas que visitam o referido local foram realizadas, assim como notas de campo sobre a situação social dos participantes foram tomadas. O trabalho observa as identidades emergentes mais relevantes no discurso dos menores, tais como a identidade estigmatizada, a identidade religiosa, as familiares e a identidade da transformação, sempre formadas na sua necessária relação com o outro. A análise revela o conflito entre a identidade do infrator e as identidades, consideradas socialmente como normais, o que demonstra a complexidade das identidades sociais e suscita novas problematizações a serem consideradas em pesquisas futuras.

Telenomus remus (Hymenoptera: Platygastridae) parasitism on eggs of Anticarsia gemmatalis (Lepidoptera: Eribidae) compared with its natural host Spodoptera frugiperda (Lepidoptera: Noctuidae)

The capacity of Telenomus remus to parasitize eggs of Anticarsia gemmatalis, compared with its natural host, Spodoptera frugiperda, was evaluated under different temperatures. The parasitoid T. remus was reared at 25 +/- 1 degrees C for a single generation on both hosts. After reaching the adult stage, they were allowed to parasitize both hosts to study parasitoid biology and parasitism capacity at temperatures between 19 degrees C and 37 +/- 1 degrees C. Egg-to-adult developmental time was similar on both hosts. The number of A. gemmatalis eggs parasitized was lower than that of S. frugiperda eggs at all temperatures. Parental female longevity of parasitoids was greater on A. gemmatalis eggs. This indicated a smaller metabolic expense during parasitism, a common feature observed on nonpreferable hosts. In general, sex ratio was little affected by temperature or hosts. When parental T. remus were reared on A. gemmatalis before the experiment, base temperature (Tb) and the thermal constant (K) were 9.53 degrees C and 209.57 DD on eggs of A. gemmatalis and 9.68 degrees C and 197.79 DD on eggs of S. frugiperda, respectively. When parental T. remus were reared on S. frugiperda eggs, Tb and K were 10.12 degrees C and 188.46 DD and 9.69 degrees C and 190.24 DD for the evaluated host eggs of A. gemmatalis and S. frugiperda, respectively. Therefore, T. remus develops in eggs of A. gemmatalis. This can be beneficial for its use in field crops where outbreaks of both Spodoptera spp. and A. gemmatalis occur. However, A. gemmatalis is a less favorable host for the parasitoid development.

Brands Analysis Using Informational Ergonomics Concepts: A Proposal

Currently, a lot of visual information present in all media is form vehemently, for example, in print media and interfaces used for publicity in conjunction with informational design. This visual information has great influence in the life of human beings, since the vision of these individuals is the most used sense. Studies on visual identity have not explored this issue in a satisfactory manner, favoring thus the subject of this small development projects in the area. It is noted the need for analyzes to enable implementation principles of project, making them accessible to the comprehension of most individuals. This study aimed to propose an evaluation of visual identities, which were analyzed by means of visual concepts of usability, design methodologies and Gestalt. We contacted design firms specialized in visual identity projects, places where interviews were conducted to collect the brands allowed for analysis. The results point to a frequent demand for the employment of visual usability principles, design methodologies and Gestalt design in visual identities.

Diretrizes para análise e desenvolvimento de identidade visual: contribuições para o design ergonômico

Currently, too much visual information present in all media is form vehemently, for example, in print media and interfaces used for publicity in conjunction with informational design. This visual information has great influence in the lives of human beings, since the vision of these individuals is the sense most used. Studies on visual identity have not explored this issue in a satisfactory manner, favoring thus the subject of this little development projects in the area. Note the need for analyzes to enable implementation principles of projective, making them accessible to the understanding of most individuals. This study aimed to propose an evaluation of visual identities, which were analyzed by means of visual concepts of usability, design methodologies and Gestalt. We contacted design firms specializing in visual identity projects, places where interviews were conducted to collect the marks allowed for analysis. The results point to a frequent demand the employment of visual usability principles, design methodologies and design in Gestalt visual identities.

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Design and Performance Evaluation of Network-on-Chip Communication Protocols and Architectures

The scale down of transistor technology allows microelectronics manufacturers such as Intel and IBM to build always more sophisticated systems on a single microchip. The classical interconnection solutions based on shared buses or direct connections between the modules of the chip are becoming obsolete as they struggle to sustain the increasing tight bandwidth and latency constraints that these systems demand. The most promising solution for the future chip interconnects are the Networks on Chip (NoC). NoCs are network composed by routers and channels used to inter- connect the different components installed on the single microchip. Examples of advanced processors based on NoC interconnects are the IBM Cell processor, composed by eight CPUs that is installed on the Sony Playstation III and the Intel Teraflops pro ject composed by 80 independent (simple) microprocessors. On chip integration is becoming popular not only in the Chip Multi Processor (CMP) research area but also in the wider and more heterogeneous world of Systems on Chip (SoC). SoC comprehend all the electronic devices that surround us such as cell-phones, smart-phones, house embedded systems, automotive systems, set-top boxes etc... SoC manufacturers such as ST Microelectronics , Samsung, Philips and also Universities such as Bologna University, M.I.T., Berkeley and more are all proposing proprietary frameworks based on NoC interconnects. These frameworks help engineers in the switch of design methodology and speed up the development of new NoC-based systems on chip. In this Thesis we propose an introduction of CMP and SoC interconnection networks. Then focusing on SoC systems we propose: • a detailed analysis based on simulation of the Spidergon NoC, a ST Microelectronics solution for SoC interconnects. The Spidergon NoC differs from many classical solutions inherited from the parallel computing world. Here we propose a detailed analysis of this NoC topology and routing algorithms. Furthermore we propose aEqualized a new routing algorithm designed to optimize the use of the resources of the network while also increasing its performance; • a methodology flow based on modified publicly available tools that combined can be used to design, model and analyze any kind of System on Chip; • a detailed analysis of a ST Microelectronics-proprietary transport-level protocol that the author of this Thesis helped developing; • a simulation-based comprehensive comparison of different network interface designs proposed by the author and the researchers at AST lab, in order to integrate shared-memory and message-passing based components on a single System on Chip; • a powerful and flexible solution to address the time closure exception issue in the design of synchronous Networks on Chip. Our solution is based on relay stations repeaters and allows to reduce the power and area demands of NoC interconnects while also reducing its buffer needs; • a solution to simplify the design of the NoC by also increasing their performance and reducing their power and area consumption. We propose to replace complex and slow virtual channel-based routers with multiple and flexible small Multi Plane ones. This solution allows us to reduce the area and power dissipation of any NoC while also increasing its performance especially when the resources are reduced. This Thesis has been written in collaboration with the Advanced System Technology laboratory in Grenoble France, and the Computer Science Department at Columbia University in the city of New York.

The social construction of cooperation: exchange, identification and collective intentions within the organization

My aim is to develop a theory of cooperation within the organization and empirically test it. Drawing upon social exchange theory, social identity theory, the idea of collective intentions, and social constructivism, the main assumption of my work implies that both cooperation and the organization itself are continually shaped and restructured by actions, judgments, and symbolic interpretations of the parties involved. Therefore, I propose that the decision to cooperate, expressed say as an intention to cooperate, reflects and depends on a three step social process shaped by the interpretations of the actors involved. The first step entails an instrumental evaluation of cooperation in terms of social exchange. In the second step, this “social calculus” is translated into cognitive, emotional and evaluative reactions directed toward the organization. Finally, once the identification process is completed and membership awareness is established, I propose that individuals will start to think largely in terms of “We” instead of “I”. Self-goals are redefined at the collective level, and the outcomes for self, others, and the organization become practically interchangeable. I decided to apply my theory to an important cooperative problem in management research: knowledge exchange within organizations. Hence, I conducted a quantitative survey among the members of the virtual community, “www.borse.it” (n=108). Within this community, members freely decide to exchange their knowledge about the stock market among themselves. Because of the confirmatory requirements and the structural complexity of the theory proposed (i.e., the proposal that instrumental evaluations will induce social identity and this in turn will causes collective intentions), I use Structural Equation Modeling to test all hypotheses in this dissertation. The empirical survey-based study found support for the theory of cooperation proposed in this dissertation. The findings suggest that an appropriate conceptualization of the decision to exchange knowledge is one where collective intentions depend proximally on social identity (i.e., cognitive identification, affective commitment, and evaluative engagement) with the organization, and this identity depends on instrumental evaluations of cooperators (i.e., perceived value of the knowledge received, assessment of past reciprocity, expected reciprocity, and expected social outcomes of the exchange). Furthermore, I find that social identity fully mediates the effects of instrumental motives on collective intentions.