Re-annotation of the genome sequence of Helicobacter pylori 26695

Helicobacter pylori is a pathogenic bacterium that colonizes the human epithelia, causing duodenal and gastriculcers, and gastric cancer. The genome of H. pylori 26695 has been previously sequenced and annotated. In addition, two genome-scale metabolic models have been developed. In order to maintain accurate and relevant information on coding sequences (CDS) and to retrieve new information, the assignment of new functions to Helicobacter pylori 26695s genes was performed in this work. The use of software tools, on-line databases and an annotation pipeline for inspecting each gene allowed the attribution of validated EC numbers and TC numbers to metabolic genes encoding enzymes and transport proteins, respectively. 1212 genes encoding proteins were identified in this annotation, being 712 metabolic genes and 500 non-metabolic, while 191 new functions were assignment to the CDS of this bacterium. This information provides relevant biological information for the scientific community dealing with this organism and can be used as the basis for a new metabolic model reconstruction.This work was supported by the project FCOMP-01-0124-FEDER-009707, entitled HeliSysBio molecular Systems Biology in Helicobacter pylori (Ref.: FCT PTDC/EBB-EBI/104235/2008). Daniela Correia is grateful for financial support from the FCT (PhD grant: SFRH/BD/47596/2008)

Using strucutral information for predicting NAD(P)(H) cofactor specificity, while unveiling the responsible molecular determinants, in enzymes with unknown structure

Systems biology foundations broadly rely upon well performed gene homology annotations. As metabolic model reconstructions become a relevant tool for performing fundamental studies and bioprocess design, the impact of accurate enzymatic function assignments becomes evident. Uncertainty on the usage of NADP(H) or NAD(H) as co-factors has a major impact in metabolic engineering applications, severely affecting both predictions and strain design results. In this work, we unveil the molecular determinants for cofactor specificity, using enzyme structural information. To do so, we have created a representative dataset of enzymes present in Protein DataBase with NAD(P)(H) as cofactors and retrieved information on every interaction between aminoacid residues and cofactor atoms, storing numerous data on binding site properties. The ensuing data analysis culminated on the identification of aminoacid residues with a significantly higher amount of binding contacts with specific cofactor atoms. These findings where successfully applied to enzymes not structurally characterized, by using protein modelling and machine learning algorithms. To enable high throughput cofactor preference prediction, a method was developed to automatically attribute cofactor specificity preference, when given the aminoacid sequence only, whilst returning the modelled structure of the query sequence. We believe these results represent an important contribution for metabolic engineering, with the enhancement of the sensitivity and reliability of metabolic models, through the lower input of erroneous or redundant reactions, improving the overall performance of metabolic simulation

Assignment of novel functions to Helicobacter pylori 26695’s genome

Helicobacter pylori is a pathogenic bacterium that colonizes the human epithelia, causing duodenal and gastric ulcers as well as gastric cancer. The genome of H. pylori 26695 has been sequenced and annotated. In addition, two genome-scale metabolic models have been developed. In order to maintain accurate and relevant information on coding sequences (CDS) and to retrieve new information, the assignment of new functions to Helicobacter pylori 26695’s genes was performed. The use of software tools, on-line databases and an annotation pipeline for inspecting each gene allowed the attribution of validated E.C. numbers to metabolic genes, and the assignment of 177 new functions to the CDS of this bacterium. This information provides relevant biological information for the scientific community dealing with this organism and can be used as the basis for a new metabolic model reconstruction.(undefined

Assignment of novel functions to Helicobacter pylori 26695’s genome and reconstruction of a genome-scale metabolic model

Helicobacter pylori is a pathogenic organism associated with human gastric diseases. The development of mathematical models of metabolism is now considered a fundamental part of the study of the cell. For the particular case of microorganisms associated with human diseases, information on metabolic and regulatory networks can be used to understand the molecular factors of the microorganism that are likely to interact with the host and cause diseases. The availability of the genome sequence of H. pylori 26695 and its annotation has allowed in the past the construction of a metabolic model for this organism. The first genome-scale metabolic model for H. pylori 26695 was published in 2002 (iCS291) and a corrected reconstruction was published in 2005 (iIT341 GSM/GPR). The main goal of the present work was to update H. pylori’s genome-scale metabolic model based on the new information made available. For that purposes, using new annotation methodologies and data available in databases, an assignment of novel functions to H. pylori 26695’s genome was performed. For a total of 510 “hypothetical proteins” (almost 1/3 of the genes) identified in the last re-annotation, 137 new functions were attributed. A total of 581 E.C. numbers were assigned to CDS, being 528 complete E.C. numbers. This new information was used as the basis of the model reconstruction. In addition, transport reactions in the model were updated. The biomass equation was reviewed and H. pylori biomass coefficients and composition were adjusted. The obtained model successfully predicted the nutritional requirements and amino acids essentialities, which were experimentally validated. As a result, the present work presents a new H. pylori 26695 genome-scale metabolic model with more accurate and reliable predictions and can be used to identify potential targets for designing more effective drugs for H. pylori inactivation

Measurement of peroxisomal enzyme activities in the liver of brown trout (Salmo trutta), using spectrophotometric methods

BACKGROUND: This study was aimed primarily at testing in the liver of brown trout (Salmo trutta) spectrophotometric methods previously used to measure the activities of catalase and hydrogen peroxide producing oxidases in mammals. To evaluate the influence of temperature on the activities of those peroxisomal enzymes was the second objective. A third goal of this work was the study of enzyme distribution in crude cell fractions of brown trout liver. RESULTS: The assays revealed a linear increase in the activity of all peroxisomal enzymes as the temperature rose from 10° to 37°C. However, while the activities of hydrogen peroxide producing oxidases were strongly influenced by temperature, catalase activity was only slightly affected. A crude fraction enriched with peroxisomes was obtained by differential centrifugation of liver homogenates, and the contamination by other organelles was evaluated by the activities of marker enzymes for mitochondria (succinate dehydrogenase), lysosomes (aryl sulphatase) and microsomes (NADPH cytochrome c reductase). For peroxisomal enzymes, the activities per mg of protein (specific activity) in liver homogenates were strongly correlated with the activities per g of liver and with the total activities per liver. These correlations were not obtained with crude peroxisomal fractions. CONCLUSIONS: The spectrophotometric protocols originally used to quantify the activity of mammalian peroxisomal enzymes can be successfully applied to the study of those enzymes in brown trout. Because the activity of all studied peroxisomal enzymes rose in a linear mode with temperature, their activities can be correctly measured between 10° and 37°C. Probably due to contamination by other organelles and losses of soluble matrix enzymes during homogenisation, enzyme activities in crude peroxisomal fractions do not correlate with the activities in liver homogenates. Thus, total homogenates will be used in future seasonal and toxicological studies of brown trout peroxisomes

A crise dos refugiados venezuelanos sob a ótica dos Direitos Humanos e da Segurança Internacional

II Semana Acadêmica de Relações Internacionais foi realizada de 05 a 09 denovembro de 2017, na Universidade Federal da Integração Latino-Americana (UNILA)Desde 2015 a Venezuela se encontra em grave crise econômica. Uma das principais consequências dessa crise é a geração de um grande número de refugiados e migrantes. O Brasil é um dos principais destinos para os refugiados e migrantes venezuelanos que deixam seu país em busca de melhores condições de vida. De acordo com a Agência da ONU para Refugiados (ACNUR, 2018), 85 mil refugiados e migrantes entraram no Brasil, desde o início da crise no país vizinho. Este trabalho procura analisar a forma que os refugiados e migrantes venezuelanos são tratados quando chegam no Brasil. Para tanto, procura-se analisar se o tratamento brasileiro dado aos refugiados e migrantes venezuelanos corresponde a uma abordagem dos Direitos Humanos (DH) que respeita os direitos básicos de cada indivíduo, como garantia à liberdade, segurança e bem-estar (HUNT, 2007). Ou, se o tratamento dado a estes refugiados e migrantes está mais relacionado a uma abordagem da Segurança Internacional com foco somente na segurança e no pleno funcionamento dos Estados nacionais que, por muitas vezes, adota práticas que, no plano doméstico, ferem os DH como, por exemplo, perseguições e restrições às liberdades individuais. O argumento central desta pesquisa é que – apesar da existência dos Regimes Internacionais como a Carta das Nações Unidas (1948) e a Convenção de Genebra Relativa aos Refugiados (1949) que possuem grande influência no Sistema Internacional – o Brasil, na maioria das vezes, utiliza a lógica da Segurança Internacional para o tratamento dos refugiados venezuelanos. A metodologia empregada será a qualitativa com pesquisa bibliográfica e documenta

Análise de uma suspensão para um veículo de Fórmula SAE via elementos finitos

Monografia (graduação)—Universidade de Brasília, Faculdade UnB Gama, Curso de Engenharia Automotiva, 2016.Este trabalho mostra uma análise de um sistema de suspensão para um veículo elétrico da Fórmula SAE, com base em efeitos respectivos à dinâmica de veículos e uma análise via elementos finitos. O trabalho traz definições e conceitos importantes para a elaboração de uma boa análise da suspensão com base em fatores dinâmicos. O trabalho permite o entendimento de diversos elementos geométricos da suspensão, como: câmber, cáster, convergência, centro de rolagem, angulação e tamanho dos braços, com seus conceitos definidos e analisados durante este estudo. Logo, cálculos como a taxa de variação de câmber, efeitos anti dive, anti squat e transferências de cargas laterais e longitudinais foram realizados. E, a partir da definição da angulação do sistema push rod, foi possível verificar qual a porcentagem da carga proveniente das transferências de carga que será transmitida ao conjunto rocker arm e amortecedor-mola do veículo. Portanto, a partir dos valores das transferências de cargas no veículo, foi possível definir condições de contorno para posterior simulação estrutural do conjunto de suspensão via método dos elementos finitos, por meio do software Ansys. Já através do conceito de Pugh se define materiais para o sistema. Parte-se então às simulações estruturais no Ansys iniciando-se pela estática por meio de análises de tensões, deformações e coeficientes de segurança. Nesta etapa verifica-se que os componentes em análise sofrem esforços que geram tensões menores do que as de escoamento dos materiais. Os coeficientes de segurança mostram quais componentes carecem de ajustes e quais estão bem dimensionados. Nas etapas de análises dinâmicas inicia-se com a modal definindo as seis primeiras frequências naturais e seus respectivos modos de vibração. Prosseguindo a análise realiza-se em seguida as análises harmônicas da manga de eixo, push rod e bandeja superior, verificando as frequências encontradas na etapa modal e validando o sistema por frequências de tais magnitudes dificilmente atingidas em condições reais. Na análise transiente utiliza-se uma função harmônica com frequência próxima as de excitação de pistas. Utiliza-se também do ruído branco para conseguir simular condições próximas as reais.This work shows an analysis of a suspension system for an electric vehicle of Formula SAE based on their effect on the vehicle dynamics and through finite element analysis. The work brings definitions and important concepts for the development of a good analysis of the suspension based on dynamic factors. The work allows the understanding of various geometric elements of the suspension, such as camber, caster, convergence, roll center, angle and size of the arms, with its defined concepts and analyzed during this study. Thus, calculations such as camber variation rate, effects anti dive, anti-squat and lateral and longitudinal load transfers were performed. And, from the definition of the angulation of the push rod system, it was possible to determine the percentage of load from load transfers to be transmitted to the rocker arm assembly and vehicle bumper-spring. Therefore, from the values of the transfer of cargo in the vehicle, it was possible to set boundary conditions for further structural simulation of suspension set with the finite element method by Ansys software. Through the Pugh’s concept the materials of analysis are defined to the system. In this step the structural simulations in Ansys started with the static case through analysis of stresses, strains and safety factors. At this stage it appears that the components undergo analysis efforts generating lower stress than the yield strength of materials. Safety coefficients show which components require adjustments and which are well-sized. The dynamic analysis starts with setting the first six natural frequencies and the respective vibration modes. Pursuing the analysis is carried out then the harmonic analysis of the steering knuckle, push rod and upper arm, checking the frequencies found in the modal stage and validating the system frequency of such magnitudes rarely achieved in real conditions. In transient analysis is used a harmonic function with frequency close to the road excitation. It is also used white noise to get simulate conditions close to reality

HISTÓRIA E FICÇÃO: MIMÉSIS COMO JOGO DE ESPELHOS NAS AULAS DE LITERATURA

Observando o cenário da educação atual e da, ainda precária, ausência de posicionamento crítico da maioria dos alunos, este artigo discute que a perspectiva metodológica no ensino de literatura deve ter relação intima com o discurso histórico. Do diálogo existente entre o texto históriográfico e o texto literário, é necessário analisar a importância da língua enquanto meio de comunicação e relacionamento entre os grupos sociais, bem como enquanto reflexos na constituição da linguagem. Dessa forma, a reflexão sobre a existência de “fronteiras” entre história e literatura abre a possibilidade de se trazer ao debate o pensamento bakhtiniano. Além disso, o conceito teorizado por Luiz Costa Lima sobre a noção de memorialismo e mimésis é defendido aqui como proposta adequada para o ensino da literatura

AO LEITOR, AS ADVERTÊNCIAS

IN THIS ARTICLE WE INTEND TO ANALYZE THE PREFACES WRITTEN BY MACHADO DE ASSIS FOR HIS NOVELS. IN ORDER TO DO SO, WE SHALL COMPARE THEM WITH THE NARRATIVE FIGURATIONS OF THE READER.NESTE ARTIGO PRETENDE-SE ANALISAR OS PREFÁCIOS ESCRITOS POR MACHADO DE ASSIS PARA SEUS ROMANCES MEDIANTE A COMPARAÇÃO COM AS FIGURAÇÕES NARRATIVAS DO LEITOR