RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression

The RECODE database is a compilation of ‘programmed’ translational recoding events taken from the scientific literature and personal communications. The database deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. The entries for each event include the sequences of the corresponding genes, their encoded proteins for both the normal and alternate decoding, the types of the recoding events involved, trans-factors and cis-elements that influence recoding. The database is freely available at http://recode.genetics.utah.edu/.

Evolution of RNA editing in trypanosome mitochondria

Two different RNA editing systems have been described in the kinetoplast-mitochondrion of trypanosomatid protists. The first involves the precise insertion and deletion of U residues mostly within the coding regions of maxicircle-encoded mRNAs to produce open reading frames. This editing is mediated by short overlapping complementary guide RNAs encoded in both the maxicircle and the minicircle molecules and involves a series of enzymatic cleavage-ligation steps. The second editing system is a C34 to U34 modification in the anticodon of the imported tRNATrp, thereby permitting the decoding of the UGA stop codon as tryptophan. U-insertion editing probably originated in an ancestor of the kinetoplastid lineage and appears to have evolved in some cases by the replacement of the original pan-edited cryptogene with a partially edited cDNA. The driving force for the evolutionary fixation of these retroposition events was postulated to be the stochastic loss of entire minicircle sequence classes and their encoded guide RNAs upon segregation of the single kinetoplast DNA network into daughter cells at cell division. A large plasticity in the relative abundance of minicircle sequence classes has been observed during cell culture in the laboratory. Computer simulations provide theoretical evidence for this plasticity if a random distribution and segregation model of minicircles is assumed. The possible evolutionary relationship of the C to U and U-insertion editing systems is discussed.

Protein synthesis editing by a DNA aptamer.

Potential errors in decoding genetic information are corrected by tRNA-dependent amino acid recognition processes manifested through editing reactions. One example is the rejection of difficult-to-discriminate misactivated amino acids by tRNA synthetases through hydrolytic reactions. Although several crystal structures of tRNA synthetases and synthetase-tRNA complexes exist, none of them have provided insight into the editing reactions. Other work suggested that editing required active amino acid acceptor hydroxyl groups at the 3' end of a tRNA effector. We describe here the isolation of a DNA aptamer that specifically induced hydrolysis of a misactivated amino acid bound to a tRNA synthetase. The aptamer had no effect on the stability of the correctly activated amino acid and was almost as efficient as the tRNA for inducing editing activity. The aptamer has no sequence similarity to that of the tRNA effector and cannot be folded into a tRNA-like structure. These and additional data show that active acceptor hydroxyl groups in a tRNA effector and a tRNA-like structure are not essential for editing. Thus, specific bases in a nucleic acid effector trigger the editing response.

The translational function of nucleotide C1054 in the small subunit rRNA is conserved throughout evolution: genetic evidence in yeast.

Mutations at position C1054 of 16S rRNA have previously been shown to cause translational suppression in Escherichia coli. To examine the effects of similar mutations in a eukaryote, all three possible base substitutions and a base deletion were generated at the position of Saccharomyces cerevisiae 18S rRNA corresponding to E. coli C1054. In yeast, as in E. coli, both C1054A (rdn-1A) and C1054G (rdn-1G) caused dominant nonsense suppression. Yeast C1054U (rdn-1T) was a recessive antisuppressor, while yeast C1054-delta (rdn-1delta) led to recessive lethality. Both C1054U and two previously described yeast 18S rRNA antisuppressor mutations, G517A (rdn-2) and U912C (rdn-4), inhibited codon-nonspecific suppression caused by mutations in eukaryotic release factors, sup45 and sup35. However, among these only C1054U inhibited UAA-specific suppressions caused by a UAA-decoding mutant tRNA-Gln (SLT3). Our data implicate eukaryotic C1054 in translational termination, thus suggesting that its function is conserved throughout evolution despite the divergence of nearby nucleotide sequences.

UGA suppression by a mutant RNA of the large ribosomal subunit.

A role for rRNA in peptide chain termination was indicated several years ago by isolation of a 168 rRNA (small subunit) mutant of Escherichia coli that suppressed UGA mutations. In this paper, we describe another interesting rRNA mutant, selected as a translational suppressor of the chain-terminating mutant trpA (UGA211) of E. coli. The finding that it suppresses UGA at two positions in trpA and does not suppress the other two termination codons, UAA and UAG, at the same codon positions (or several missense mutations, including UGG, available at one of the two positions) suggests a defect in UGA-specific termination. The suppressor mutation was mapped by plasmid fragment exchanges and in vivo suppression to domain II of the 23S rRNA gene of the rrnB operon. Sequence analysis revealed a single base change of G to A at residue 1093, an almost universally conserved base in a highly conserved region known to have specific interactions with ribosomal proteins, elongation factor G, tRNA in the A-site, and the peptidyltransferase region of 23S rRNA. Several avenues of action of the suppressor mutation are suggested, including altered interactions with release factors, ribosomal protein L11, or 16S rRNA. Regardless of the mechanism, the results indicate that a particular residue in 23S rRNA affects peptide chain termination, specifically in decoding of the UGA termination codon.

Saberes dos professores da educação profissional técnica de nível médio em enfermagem

A docência na educação profissional técnica de nível médio em enfermagem é uma das dimensões importantes a ser considerada na qualificação da formação de trabalhadores técnicos, no Brasil. Apesar disso, ela é marcada por fragilidade nos processos formativos, adversas condições de trabalho, incluindo, a precariedade. O objetivo deste estudo é descrever e analisar os saberes dos professores de uma escola privada de educação profissional em enfermagem, no município de Ribeirão Preto, considerando suas vivências na prática pedagógica, a partir de referencial de Tardif (2012). Estudo descritivo-exploratório, qualitativo. A técnica de coleta de dados utilizada foi entrevista semiestruturada com 13 professores, realizadas de novembro de 2014 a fevereiro de 2015. As entrevistas foram analisadas, sendo delineadas categorias de decodificação, a saber: Saberes pessoais dos professores; Saberes provenientes da formação escolar anterior; Saberes provenientes da formação profissional para o magistério, subdivididos em Saberes provenientes da formação profissional para o magistério construídos em cursos de Bacharelado e Licenciatura em Enfermagem e Saberes profissionais para o magistério, construídos nos cursos de especialização latu sensu e programas de capacitação docente; Saberes provenientes dos programas e livros didáticos usados no trabalho dos professores; Saberes provenientes de sua própria experiência na profissão envolvendo atuação nos serviços de saúde e na docência. Esses saberes, no exercício cotidiano do trabalho docente, são articulados e reconstruídos. Eles mostram significativamente as suas relações com a diversidade nas possibilidades de formação, dada a fragilidades das políticas de formação docente, bem como suas relações com as condições concretas de trabalho na educação profissional, sendo ainda significativa a concomitância da docência nessa modalidade de ensino com a prática profissional em serviços de saúde, o que também traz implicações para a conformação dos saberes da docência

Relação espacial dos óbitos e internações por tuberculose com indicadores sociais em Ribeirão Preto (SP)

Objetivo: Propôs-se analisar a relação espacial dos óbitos e internações evitáveis por TB com indicadores sociais em Ribeirão Preto/SP. Métodos: Trata-se de um estudo ecológico em que foram considerados os casos de óbitos e internações, tendo como causa básica do óbito e motivo principal da internação, a tuberculose (CID A15.0 a A19.9), ocorridos na zona urbana de Ribeirão Preto e registrados respectivamente no Sistema de Informação sobre Mortalidade e no Sistema de Internação Hospitalar do Sistema Único de Saúde no período de 2006 a 2012. Foi realizada a análise univariada das variáveis sociodemográficas e operacionais dos casos investigados. Para construção dos indicadores sociais utilizou-se a análise de componentes principais, sendo selecionados dados das áreas de abrangência do município, considerando os dados do Censo Demográfico de 2010. A geocodificação dos casos foi processada no TerraView versão 4.2.2. Recorreu-se à regressão linear múltipla, pelo método dos mínimos quadrados e à regressão espacial para análise da relação de dependência espacial entre os indicadores sociais e as taxas de mortalidade e de internações por TB. A autocorrelação nos resíduos da regressão linear múltipla foi testada por meio do Teste Global de Moran, as análises foram realizadas considerando os softwares Arcgis-versão 10.1, Statistica versão 12.0, OpenGeoDa versão 1.0 e R versão 3.2.3. Para o diagnóstico do melhor modelo de regressão espacial, utilizou-se o teste Multiplicador de Lagrange. Em todos os testes, foi fixado o nivel de significancia de alfa em 5% (p< 0,05). Resultados: Foram registrados 50 casos de óbitos e 196 casos de internações por TB. A maioria dos casos registrados em ambos os sistemas se deu em pessoas do sexo masculino (n=41; 82%/n=146; 74,5%) e com a forma clínica pulmonar (n=44; 80,0%/n=138; 67,9%). Na construção dos indicadores sociais, três novas variáveis surgiram, apresentando respectivamente variância total de 46,2%, 18,7% e 14,6% sendo denominadas como indicadores de renda, desigualdade social e equidade social. Na modelagem para verificar relação espacial entre os óbitos e os indicadores sociais observou-se que a equidade social foi indicador estatisticamente significativo (p=0,0013) com relação negativa a mortalidade, sendo o Modelo da Defasagem Espacial o melhor método para testar a dependência espacial, com valor de ? (rho) estimado em 0,53 e altamente significativo (p=0,0014). Já na modelagem da relação espacial entre as internações por tuberculose e os indicadores sociais, o indicador de renda apresentou-se estatisticamente significativo (p=0,015) com relação negativa a internação e o melhor método para testar a dependência espacial também foi o Modelo da Defasagem Espacial com valor de ? (rho) estimado em 0,80 e altamente significativo (p<0,0001). Conclusão: O estudo contribuiu no avanço do conhecimento de que a mortalidade e as internações por tuberculose são eventos socialmente determinados, o que sugere investimento por parte da gestão

Comparison of Reading Development Across Socioeconomic Status in the United States

It is well known that higher parental socioeconomic status (SES) predicts better child reading outcomes, but little work has been done to unpack this finding. The main overall question addressed by this project was whether cognitive models of the two main reading outcomes, single word reading (SWR) and reading comprehension (RC), performed similarly across levels of parental SES. The current study predicted a differential relation between parental SES and both predictors and outcomes because of the known large relation between parental SES and child oral language development. Three questions examined the mediating effects of cognitive predictors on the relation between parental SES and reading outcomes, the moderating effects of SES on the developmental trajectories of reading outcomes, and the strength of the relationship between SES and the two reading outcomes. Participants were part of two large and comprehensive datasets: the cross-sectional Colorado Learning Disability Research Center (CLDRC; n=1554) sample, and the International Longitudinal Twin Study (ILTS; n=463 twin pairs) sample. In terms of cognitive predictors, the relation between SES and SWR was disproportionately mediated by two language skills, vocabulary (VOC) and phonological awareness (PA). For the RC models, both SWR and oral listening comprehension (OLC) did not disproportionally mediate the relation between RC and SES; however, full mediation was not exhibited. With regard to the trajectory of reading outcomes, SES moderated the starting values of SWR and RC, and the slopes of SWR development. When performance on the control measures of early reading skills (e.g., print knowledge, vocabulary, and decoding skills) was included the models, the moderating effects of SES were completely accounted for by these measures. In terms of outcomes, SES had a stronger relation to RC than to SWR, especially at later ages. These findings have implications for interventions aimed at improving reading outcomes in children from lower SES families.

Del síndrome al sinthome

Currently, the concept of symptom is based on the notion of singularity (from a base perspective, underlined by Freud, regarding the persistence of symptomatic residue). This indicates that the demise of the symptom will never be complete, since the demand drive will always persist and will not cease to search for satisfaction.Let us then, insist on this matter, on the existence of an incurable residue in the symptom (which entails a particular relationship between the subject and its own pleasure), resisting sense and interpretation. The following paper has been elaborated following a diachronic trajectory of psychoanalytic theory, which allows establishing pauses, outlining the most important shifts produced in Freudian and Lacanian elaborations, respectively. Starting from Freud‘s productions, as main fulcrum, the Lacanian approach of the symptom will be introduced to link to the proposal of the sinthome proposed by Lacan. Freud will explain symptoms through the theory of trauma; those will find themselves hinged on mnemic traces, which will make the analysis of the patient‘s produced associations a crucial activity, to comprehend the etiology of the symptoms and the development of the cure. The clinical practice of this period may be summarized as ―the unconscious is susceptible to become conscious‖, aiming to the discovery and/or decoding of the symptoms, as long as they carry meaning. All of this at the same time, will be the base of future elaborations...

O ensino contábil para empreendimentos econômicos solidários: um estudo na Incubadora Social da Universidade Federal de Goiás

A pesquisa permeia a contabilidade e autogestão existentes nos empreendimentos econômicos solidários, em que o modelo de gestão é democrático e participativo e requer ferramentas contábeis compatíveis com suas características. O objetivo é verificar se a aplicação de técnica de ensino-aprendizagem contábil baseada nas rotinas gerenciais e demandas dos usuários contribui com a decodificação da informação contábil, colaborando com o controle gerencial dos empreendimentos. Assim, foi feito experimento em que no pré-teste foi analisado o entendimento contábil no que tange ao conteúdo informacional, sua utilidade e domínio. No pós-teste foi feita análise dos efeitos da aplicação da técnica sobre esses entendimentos. O estudo foi realizado com 16 cooperativas pertencentes à Incubadora Social da Universidade Federal de Goiás e a coleta de dados foi realizada por meio de entrevistas estruturadas, observações e análise de registros. Estas foram transcritas e analisadas pelo método de análise de conteúdo, que consistiu em organizar categorias conceituais representantes do entendimento contábil testado, designada pela ocorrência ou expressão nos dados transcritos. A análise dos resultados foi feita pelo teste não-paramétrico, Postos Sinalizados de Wilcoxon. Os resultados apresentados não demonstraram diferenças significativas com relação ao entendimento contábil dos diretores e não diretores antes e depois da intervenção. Limitações como amostra e a rotatividade de pessoas na cooperativa denotam a necessidade de haver formações recorrentes para os cooperados. Para futuras pesquisas fica o tempo de curso ser prolongado permitindo a participação recorrente e de mais cooperados. Como implicações práticas têm-se a percepção dos cooperados na necessidade de ter e entender as ferramentas e controles para administrar à cooperativa.

The Role of Passage Topic Knowledge in Typical and Poor Comprehenders' Recall

This dissertation examines the role of topic knowledge (TK) in comprehension among typical readers and those with Specifically Poor Comprehension (SPC), i.e., those who demonstrate deficits in understanding what they read despite adequate decoding. Previous studies of poor comprehension have focused on weaknesses in specific skills, such as word decoding and inferencing ability, but this dissertation examined a different factor: whether deficits in availability and use of TK underlie poor comprehension. It is well known that TK tends to facilitate comprehension among typical readers, but its interaction with working memory and word decoding is unclear, particularly among participants with deficits in these skills. Across several passages, we found that SPCs do in fact have less TK to assist their interpretation of a text. However, we found no evidence that deficits in working memory or word decoding ability make it difficult for children to benefit from their TK when they have it. Instead, children across the skill spectrum are able to draw upon TK to assist their interpretation of a passage. Because TK is difficult to assess and studies vary in methodology, another goal of this dissertation was to compare two methods for measuring it. Both approaches score responses to a concept question to assess TK, but in the first, a human rater assigns a score whereas in the second, a computer algorithm, Latent Semantic Analysis (LSA; Landauer & Dumais, 1997) assigns a score. We found similar results across both methods of assessing TK, suggesting that a continuous measure is not appreciably more sensitive to variations in knowledge than discrete human ratings. This study contributes to our understanding of how best to measure TK, the factors that moderate its relationship with recall, and its role in poor comprehension. The findings suggest that teaching practices that focus on expanding TK are likely to improve comprehension across readers with a variety of abilities.

Decodificando mediante microfósiles la Crisis de Salinidad del Mediterráneo como recurso didáctico en Ciencias de la Tierra

El estudio de las disciplinas científicas resulta más atractivo si se acompaña de actividades de carácter práctico. En este trabajo se propone un taller cuya finalidad es introducir al alumnado en el estudio de los microfósiles y de las reconstrucciones paleoambientales aplicándolo a uno de los eventos más significativos ocurridos en el área Mediterránea, que conllevó la desecación y posterior reinundación de toda la cuenca hace aproximadamente unos cinco millones de años. El taller consta de tres sesiones: una teórica, de introducción de los contenidos necesarios para el desarrollo de la actividad, una práctica, de obtención de datos, y una final, de interpretación de los cambios ambientales y presentación de los resultados en forma de artículo científico y posterior debate en el aula. Todos los datos necesarios para el desarrollo de la actividad se proporcionan en el presente artículo. Además, se proponen una serie de recursos bibliográficos y audiovisuales de fácil acceso para la introducción de los conceptos teóricos.

Introduction to Coding Theory for Flow Equations of Complex Systems Models

The modeling of complex dynamic systems depends on the solution of a differential equations system. Some problems appear because we do not know the mathematical expressions of the said equations. Enough numerical data of the system variables are known. The authors, think that it is very important to establish a code between the different languages to let them codify and decodify information. Coding permits us to reduce the study of some objects to others. Mathematical expressions are used to model certain variables of the system are complex, so it is convenient to define an alphabet code determining the correspondence between these equations and words in the alphabet. In this paper the authors begin with the introduction to the coding and decoding of complex structural systems modeling.

Methods of Visualization and Analysis of Cardiac Depolarization in the Three Dimensional Space

Research analysis of electrocardiograms (ECG) today is carried out mostly using time depending signals of different leads shown in the graphs. Definition of ECG parameters is performed by qualified personnel, and requiring particular skills. To support decoding the cardiac depolarization phase of ECG there are methods to analyze space-time convolution charts in three dimensions where the heartbeat is described by the trajectory of its electrical vector. Based on this, it can be assumed that all available options of the classical ECG analysis of this time segment can be obtained using this technique. Investigated ECG visualization techniques in three dimensions combined with quantitative methods giving additional features of cardiac depolarization and allow a better exploitation of the information content of the given ECG signals.

Age model and stable isotopes of sediment cores from north-central Chile and south-central Chile

Terrigenous sediment supply, marine transport, and depositional processes along tectonically active margins are key to decoding turbidite successions as potential archives of climatic and seismic forcings. Sequence stratigraphic models predict coarse-grained sediment delivery to deep-marine sites mainly during sea-level fall and lowstand. Marine siliciclastic deposition during transgressions and highstands has been attributed to sustained connectivity between terrigenous sources and marine sinks facilitated by narrow shelves. To decipher the controls on Holocene highstand turbidite deposition, we analyzed 12 sediment cores from spatially discrete, coeval turbidite systems along the Chile margin (29° - 40°S) with changing climatic and geomorphic characteristics but uniform changes in sea level. Sediment cores from intraslope basins in north-central Chile (29° - 33°S) offshore a narrow to absent shelf record a shut-off of turbidite deposition during the Holocene due to postglacial aridification. In contrast, core sites in south-central Chile (36° - 40°S) offshore a wide shelf record frequent turbidite deposition during highstand conditions. Two core sites are linked to the Biobío river-canyon system and receive sediment directly from the river mouth. However, intraslope basins are not connected via canyons to fluvial systems but yield even higher turbidite frequencies. High sediment supply combined with a wide shelf and an undercurrent moving sediment toward the shelf edge appear to control Holocene turbidite sedimentation and distribution. Shelf undercurrents may play an important role in lateral sediment transport and supply to the deep sea and need to be accounted for in sediment-mass balances.