A structural census of the current population of protein sequences

We examine the occurrence of the ≈300 known protein folds in different groups of organisms. To do this, we characterize a large fraction of the currently known protein sequences (≈140,000) in structural terms, by matching them to known structures via sequence comparison (or by secondary-structure class prediction for those without structural homologues). Overall, we find that an appreciable fraction of the known folds are present in each of the major groups of organisms (e.g., bacteria and eukaryotes share 156 of 275 folds), and most of the common folds are associated with many families of nonhomologous sequences (i.e., >10 sequence families for each common fold). However, different groups of organisms have characteristically distinct distributions of folds. So, for instance, some of the most common folds in vertebrates, such as globins or zinc fingers, are rare or absent in bacteria. Many of these differences in fold usage are biologically reasonable, such as the folds of metabolic enzymes being common in bacteria and those associated with extracellular transport and communication being common in animals. They also have important implications for database-based methods for fold recognition, suggesting that an unknown sequence from a plant is more likely to have a certain fold (e.g., a TIM barrel) than an unknown sequence from an animal.

DNA polymerase active site is highly mutable: Evolutionary consequences

DNA polymerases contain active sites that are structurally superimposable and highly conserved in sequence. To assess the significance of this preservation and to determine the mutational burden that active sites can tolerate, we randomly mutated a stretch of 13 amino acids within the polymerase catalytic site (motif A) of Thermus aquaticus DNA polymerase I. After selection, by using genetic complementation, we obtained a library of approximately 8,000 active mutant DNA polymerases, of which 350 were sequenced and analyzed. This is the largest collection of physiologically active polymerase mutants. We find that all residues of motif A, except one (Asp-610), are mutable while preserving wild-type activity. A wide variety of amino acid substitutions were obtained at sites that are evolutionarily maintained, and conservative substitutions predominate at regions that stabilize tertiary structures. Several mutants exhibit unique properties, including DNA polymerase activity higher than the wild-type enzyme or the ability to incorporate ribonucleotide analogs. Bacteria dependent on these mutated polymerases for survival are fit to replicate repetitively. The high mutability of the polymerase active site in vivo and the ability to evolve altered enzymes may be required for survival in environments that demand increased mutagenesis. The inherent substitutability of the polymerase active site must be addressed relative to the constancy of nucleotide sequence found in nature.

A comprehensive BAC resource

The Human Genome Project has generated extensive map and sequence data for a large number of Bacterial Artificial Chromosome (BAC) clones. In order to maximize the efficient use of the data and to minimize the redundant work for the research community, The Institute for Genomic Research (TIGR) comprehensive BAC resource (cBACr) (http://www.tigr.org/tdb/BacResource/BAC_resource_intro.html) was built as an expansion of the TIGR human BAC ends database. This resource collects, integrates and reports the information on library, maps, sequence, annotation and functions for each human and mouse BAC. The current database contains 635 016 human BACs and 265 617 mouse BACs that were characterized by various approaches, among which 22 705 human clones and 1000 mouse clones have sequence and annotation data.

Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase.

Recent studies on proteins whose N and C termini are in close proximity have demonstrated that folding of polypeptide chains and assembly of oligomers can be accomplished with circularly permuted chains. As yet no methodical study has been conducted to determine how extensively new termini can be introduced and where such termini cannot be tolerated. We have devised a procedure to generate random circular permutations of the catalytic chains of Escherichia coli aspartate transcarbamoylase (ATCase; EC 2.1.3.2) and to select clones that produce active or stable holoenzyme containing permuted chains. A tandem gene construct was made, based on the desired linkage between amino acid residues in the C- and N-terminal regions of the polypeptide chain, and this DNA was treated with a suitable restriction enzyme to yield a fragment containing the rearranged coding sequence for the chain. Circularization achieved with DNA ligase, followed by linearization at random with DNase I, and incorporation of the linearized, repaired, blunt-ended, rearranged genes into a suitable plasmid permitted the expression of randomly permuted polypeptide chains. The plasmid with appropriate stop codons also contained pyrI, the gene encoding the regulatory chain of ATCase. Colonies expressing detectable amounts of ATCase-like molecules containing permuted catalytic chains were identified by an immunoblot technique or by their ability to grow in the absence of pyrimidines in the growth medium. Sequencing of positive clones revealed a variety of novel circular permutations. Some had N and C termini within helices of the wild-type enzyme as well as deletions and insertions. Permutations were concentrated in the C-terminal domain and only few were detected in the N-terminal domain. The technique, which is adaptable generally to proteins whose N and C termini are near each other, can be of value in relating in vivo folding of nascent, growing polypeptide chains to in vitro renaturation of complete chains and determining the role of protein sequence in folding kinetics.

A functional Rev-erb alpha responsive element located in the human Rev-erb alpha promoter mediates a repressing activity.

Rev-erb alpha belongs to the nuclear receptor superfamily, which contains receptors for steroids, thyroid hormones, retinoic acid, and vitamin D, as well as "orphan" receptors. No ligand has been found for Rev-erb alpha to date, making it one of these orphan receptors. Similar to some other orphan receptors, Rev-erb alpha has been shown to bind DNA as a monomer on a specific sequence called a Rev-erb alpah responsive element (RevRE), but its transcriptional activity remains unclear. In this paper, we characterize a functional RevRE located in the human Rev-erb alpha promoter itself. We also present evidence that (i) Rev-erb alpha mediates transcriptional repression of its own promoter in vitro, (ii) this repressing effect strictly depends on the binding of Rev-erb alpha to its responsive element and is transferable to a heterologous promoter; and (iii) Rev-erb alpha binds to this responsive sequence as a homodimer.

Nonclathrin coat protein gamma, a subunit of coatomer, binds to the cytoplasmic dilysine motif of membrane proteins of the early secretory pathway.

Coatomer, a cytosolic heterooligomeric protein complex that consists of seven subunits [alpha-, beta-, beta'-, gamma-, delta-, epsilon-, and zeta-COP (nonclathrin coat protein)], has been shown to interact with dilysine motifs typically found in the cytoplasmic domains of various endoplasmic-reticulum-resident membrane proteins [Cosson, P. & Letourneur, F. (1994) Science 263, 1629-1631]. We have used a photo-cross-linking approach to identify the site of coatomer that is involved in binding to the dilysine motifs. An octapeptide corresponding to the C-terminal tail of Wbp1p, a component of the yeast N-oligosaccharyltransferase complex, has been synthesized with a photoreactive phenylalanine at position -5 and was radioactively labeled with [125I]iodine at a tyrosine residue introduced at the N terminus of the peptide. Photolysis of isolated coatomer in the presence of this peptide and immunoprecipitation of coatomer from photo-cross-linked cell lysates reveal that gamma-COP is the predominantly labeled protein. From these results, we conclude that coatomer is able to bind to the cytoplasmic dilysine motifs of membrane proteins of the early secretory pathway via its gamma-COP subunit, whose complete cDNA-derived amino acid sequence is also presented.

Percepção de professores sobre a influência genética e ambiental em comportamentos relevantes no processo educacional

Como as pessoas percebem as outras é relevante no processo de ensino aprendizagem e nas interações sociais como um todo. Essas percepções definem a maneira com que as pessoas reagem umas às outras. Em particular, a avaliação da percepção de professores colabora na compreensão das atitudes do professor diante dos comportamentos de seus alunos. O objetivo do presente estudo foi avaliar a percepção de professores sobre a influência genética e ambiental em comportamentos relevantes no processo educacional: personalidade, inteligência, dificuldades de aprendizagem, problemas de comportamento e doenças mentais. Para tanto, o questionário The NatureNurture Question:Teachers perceptions of how genes and the environment influence educationally relevant behavior foi adaptado à língua portuguesa do Brasil e aplicado para 501 professores de todos os níveis de ensino, do estado de São Paulo. Os resultados demonstraram que os professores atribuíram influências genéticas e ambientais em proporções aproximadamente iguais considerando todos os domínios, personalidade e dificuldades e aprendizagem. Atribuíram maior influência genética à inteligência e doenças mentais, bem como maior influência ambiental aos problemas de comportamento. Metade dos participantes afirmou ter estudado aspectos da genética em sua formação para professor. A maioria dos professores declarou que ter um aluno com dificuldade de aprendizagem geneticamente influenciada afetaria seu método de instruí-lo. Os professores percebem que genes e ambiente criação são imprescindíveis nos comportamentos de seus alunos, reconhecendo, inclusive, a interatividade dos dois fatores, informações importantes para o delineamento de ações na formação dos mesmos possíveis intervenções no âmbito educacional.

Da tradução ou não de pronomes e partículas pronominais do Italiano ao Português: algumas escolhas feitas por dois tradutores

Este estudo é movido pela curiosidade quanto a como se resolvem, nas traduções do italiano para o português, questões de colocação pronominal. Encontramos, normal e frequentemente, na língua italiana, principalmente na língua falada, pronomes cujos equivalentes em português existem em gramáticas normativas da língua portuguesa, mas que, na prática, não são utilizados pelos falantes e escritores brasileiros. Encontramos, também, na língua italiana, um significativo número de verbos pronominais (como esserci, volerci, averne etc.) e um considerável número de verbos pronominais múltiplos (como andarsene, farcela, fregarsene etc.) que, juntamente com esses pronomes, constituem, para os professores brasileiros de italiano língua estrangeira (LE), elementos difíceis de trabalhar na sala de aula. Além disso, tais elementos também podem dificultar o trabalho dos tradutores, que devem fazer determinadas escolhas ao traduzi-los para o português. Como são traduzidos os pronomes combinados do italiano nas versões brasileiras? Será que os portugueses, que possuem, por exemplo, tais pronomes utilizam-nos em todos os casos em que os encontramos nos textos de partida? E as partículas pronominais são simplesmente eliminadas no texto de chegada ou são substituídas? Tais aspectos, se observados e organizados, podem levar a uma melhor compreensão das duas línguas em contato e dar subsídios a estudantes, professores e tradutores. Pensando nessa dificuldade, esta pesquisa buscou e listou alguns autores e obras disponíveis para consulta e analisou um corpus com cento e sessenta e três ocorrências de pronomes no italiano, mais sete acréscimos de pronomes no português brasileiro (PB) e/ou português europeu (PE), partindo do romance Uno, nessuno e centomila de Luigi Pirandello e suas respectivas traduções em PB e PE. Nosso objetivo consiste em encontrar respostas úteis à diminuição do estranhamento, por parte de um italiano, que escuta, de um brasileiro, frases sem pronomes (ainda que o italiano as entenda) e/ou a sensação de inadequação e, até mesmo, de desconforto, por parte de um brasileiro, ao produzir frases com todos os pronomes. No corpus analisado, temos uma amostra das escolhas e respectivas traduções propostas pelos tradutores para casos de pronomes reflexivos, de pronomes pessoais do caso reto, de pronomes pessoais do caso oblíquo, de pronomes combinados e de partículas pronominais ne, ci e vi, com manutenções, omissões, trocas por outros pronomes (possessivos, retos, oblíquos, demonstrativos) e, até mesmo, uma espécie de compensação numérica com a inclusão de palavra inexistente no texto de partida.

ATTOS: Análisis de Tendencias y Temáticas a través de Opiniones y Sentimientos

El proyecto ATTOS centra su actividad en el estudio y desarrollo de técnicas de análisis de opiniones, enfocado a proporcionar toda la información necesaria para que una empresa o una institución pueda tomar decisiones estratégicas en función a la imagen que la sociedad tiene sobre esa empresa, producto o servicio. El objetivo último del proyecto es la interpretación automática de estas opiniones, posibilitando así su posterior explotación. Para ello se estudian parámetros tales como la intensidad de la opinión, ubicación geográfica y perfil de usuario, entre otros factores, para facilitar la toma de decisiones. El objetivo general del proyecto se centra en el estudio, desarrollo y experimentación de técnicas, recursos y sistemas basados en Tecnologías del Lenguaje Humano (TLH), para conformar una plataforma de monitorización de la Web 2.0 que genere información sobre tendencias de opinión relacionadas con un tema.

Evaluation of the Implementation of CLIL (Content and Language Integrated Learning) Methodology in the Didactics of the English Language in Preschool Education Course Taught in the Preschool Education Teacher Undergraduate Program at the University of Alicante

Although it is known that the Spanish current Educative System promotes using the Communicate Approach to teach foreign languages in schools, other recently designed approaches are also used to help students improve their skills when communicating in a foreign language. One of these approaches is Content and Language Integrated Learning, also known as CLIL, which is used to teach content courses using the English language as the language of instruction. This approach improves the students’ skills in English as the same time as they learn content from other areas. The goal of this thesis is to present a research project carried out at the University of Alicante during the academic year 2011-2012. With this research we obtained results that provide quantitative and qualitative data which explains how the use of the CLIL methodology affects the English level of students in the “Didactics of the English Language in Preschool Education” course in Preschool Education Teacher Undergraduate Program as students acquire the contents of the course.

Análise fenomenológica de fenómenos corporais anómalos na esquizofrenia

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

A expressão e educação dramática : uma área transversal no pré-escolar e no 1º ciclo do ensino básico

Relatório final apresentado para a obtenção do grau de mestre em Educação pré-escolar e 1º ciclo do ensino básico.

Apostilas aos dicionários portugueses ...

Mode of access: Internet.

Colèção de estudos e documentos a favor da refórma da ortografia em sentido sónico /

Mode of access: Internet.

Questões de philologia; resposta aos criticos da "Grammatica expositiva."

Mode of access: Internet.