Comparative modeling of DNA and RNA polymerases from Moniliophthora perniciosa mitochondrial plasmid

<p>Abstract</p> <p>Background</p> <p>The filamentous fungus <it>Moniliophthora perniciosa </it>(Stahel) Aime & Phillips-Mora is a hemibiotrophic Basidiomycota that causes witches' broom disease of cocoa (<it>Theobroma cacao </it>L.). This disease has resulted in a severe decrease in Brazilian cocoa production, which changed the position of Brazil in the market from the second largest cocoa exporter to a cocoa importer. Fungal mitochondrial plasmids are usually invertrons encoding DNA and RNA polymerases. Plasmid insertions into host mitochondrial genomes are probably associated with modifications in host generation time, which can be involved in fungal aging. This association suggests activity of polymerases, and these can be used as new targets for drugs against mitochondrial activity of fungi, more specifically against witches' broom disease. Sequencing and modeling: DNA and RNA polymerases of <it>M. perniciosa </it>mitochondrial plasmid were completely sequenced and their models were carried out by Comparative Homology approach. The sequences of DNA and RNA polymerase showed 25% of identity to 1XHX and 1ARO (pdb code) using BLASTp, which were used as templates. The models were constructed using Swiss PDB-Viewer and refined with a set of Molecular Mechanics (MM) and Molecular Dynamics (MD) in water carried out with AMBER 8.0, both working under the ff99 force fields, respectively. Ramachandran plots were generated by Procheck 3.0 and exhibited models with 97% and 98% for DNA and RNA polymerases, respectively. MD simulations in water showed models with thermodynamic stability after 2000 ps and 300 K of simulation.</p> <p>Conclusion</p> <p>This work contributes to the development of new alternatives for controlling the fungal agent of witches' broom disease.</p

Knowledge of Patients with Mechanical Valve Prostheses Concerning Chronic Oral Anticoagulant Therapy

Adherence to chronic Oral Anticoagulant Therapy (OAT) is directly related to patients&#39; understanding of the therapy. This study verified the knowledge of patients with mechanical valve prostheses concerning OAT. This is a contemporary cross-sectional study, the sample is composed of patients with mechanical valve prostheses (MVP) in outpatient follow-up. A 10-question instrument was used; answers were ‘know&#39; (1 point), ‘know partially&#39; (half point), or ‘do not know&#39; (zero). Patients were grouped according to the result obtained: &#8804; 4 points was considered insufficient knowledge; > 4 &#8804; 8 equated to moderate knowledge; and > 8 was considered appropriate knowledge. Of the 110 patients, 61.8% presented moderate knowledge, 40.9% were not able to name at least one factor that may alter the INR (International Normalized Ratio) and 37.3% were not able to report their INR target range. The majority of patients presented moderate knowledge concerning the treatment. Strategies to improve knowledge on the topic should be implemented to minimize risks.El objetivo de este estudio fue verificar el conocimiento de pacientes con prótesis valvular sobre la terapia de anticoagulación oral. La adhesión a la terapia de anticoagulación oral crónica está directamente relacionada al entendimiento del paciente sobre esta terapia. Se trata de un estudio transversal contemporáneo, en el cual se incluyeron pacientes de ambulatorio con prótesis valvular mecánica (PVM). Se aplicó un cuestionario con 10 preguntas; las respuestas fueron "sabe" (1 punto), "sabe parcialmente" (medio punto), "no sabe" (cero puntos). Los pacientes fueron agrupados según la puntuación obtenida: &#8804; 4 puntos, conocimiento insuficiente; > 4 &#8804; 8 puntos, conocimiento regular; > 8 puntos, conocimiento adecuado. De los 110 pacientes incluidos, el 61,8% demostró conocimiento regular, 40,9% no supieron citar un factor que altera el REI (razón estandarizada internacional) y 37,3% no supieron informar su REI objetivo. Se concluyó que la mayoría de los pacientes demostró conocimiento regular sobre el tratamiento. Se recomienda implantar estrategias para mejorar el conocimiento y minimizar los riesgos de la terapia.A adesão à terapia com anticoagulação oral crônica está diretamente relacionada ao entendimento dos pacientes sobre essa terapia. O objetivo deste estudo foi verificar o conhecimento dos pacientes, com prótese valvar mecânica, sobre terapia de anticoagulação oral. Como método, usou-se o estudo transversal contemporâneo. Incluem-se pacientes com prótese valvar mecânica (PVM) em acompanhamento ambulatorial. Aplicou-se instrumento com 10 questões. As respostas eram sabe (um ponto), sabe parcialmente (meio ponto), ou não sabe (zero). Os pacientes foram agrupados conforme a pontuação obtida. Considerou-se &#8804;4 pontos conhecimento insuficiente, >4 &#8804;8 conhecimento regular e >8 conhecimento adequado. Os resultados mostram que, dos 110 pacientes, 61,8% apresentaram conhecimento regular, 40,9% não souberam citar ao menos um fator que alterasse a razão normatizada internacional (RNI) e 37,3% não souberam informar o seu RNI alvo. Conclui-se que a maioria dos pacientes apresentou conhecimento regular sobre o tratamento. Estratégias devem ser implementadas para melhorar o conhecimento e, consequentemente, minimizar os riscos dessa terapêutica

Influence of the interaction between nodal fibroblast and breast cancer cells on gene expression

Our aim was to evaluate the interaction between breast cancer cells and nodal fibroblasts, by means of their gene expression profile. Fibroblast primary cultures were established from negative and positive lymph nodes from breast cancer patients and a similar gene expression pattern was identified, following cell culture. Fibroblasts and breast cancer cells (MDA-MB231, MDA-MB435, and MCF7) were cultured alone or co-cultured separated by a porous membrane (which allows passage of soluble factors) for comparison. Each breast cancer lineage exerted a particular effect on fibroblasts viability and transcriptional profile. However, fibroblasts from positive and negative nodes had a parallel transcriptional behavior when co-cultured with a specific breast cancer cell line. The effects of nodal fibroblasts on breast cancer cells were also investigated. MDA MB-231 cells viability and migration were enhanced by the presence of fibroblasts and accordingly, MDA-MB435 and MCF7 cells viability followed a similar pattern. MDA-MB231 gene expression profile, as evaluated by cDNA microarray, was influenced by the fibroblasts presence, and HNMT, COMT, FN3K, and SOD2 were confirmed downregulated in MDA-MB231 co-cultured cells with fibroblasts from both negative and positive nodes, in a new series of RT-PCR assays. In summary, transcriptional changes induced in breast cancer cells by fibroblasts from positive as well as negative nodes are very much alike in a specific lineage. However, fibroblasts effects are distinct in each one of the breast cancer lineages, suggesting that the inter-relationships between stromal and malignant cells are dependent on the intrinsic subtype of the tumor

Detecting Network Communities: An Application to Phylogenetic Analysis

This paper proposes a new method to identify communities in generally weighted complex networks and apply it to phylogenetic analysis. In this case, weights correspond to the similarity indexes among protein sequences, which can be used for network construction so that the network structure can be analyzed to recover phylogenetically useful information from its properties. The analyses discussed here are mainly based on the modular character of protein similarity networks, explored through the Newman-Girvan algorithm, with the help of the neighborhood matrix . The most relevant networks are found when the network topology changes abruptly revealing distinct modules related to the sets of organisms to which the proteins belong. Sound biological information can be retrieved by the computational routines used in the network approach, without using biological assumptions other than those incorporated by BLAST. Usually, all the main bacterial phyla and, in some cases, also some bacterial classes corresponded totally (100%) or to a great extent (>70%) to the modules. We checked for internal consistency in the obtained results, and we scored close to 84% of matches for community pertinence when comparisons between the results were performed. To illustrate how to use the network-based method, we employed data for enzymes involved in the chitin metabolic pathway that are present in more than 100 organisms from an original data set containing 1,695 organisms, downloaded from GenBank on May 19, 2007. A preliminary comparison between the outcomes of the network-based method and the results of methods based on Bayesian, distance, likelihood, and parsimony criteria suggests that the former is as reliable as these commonly used methods. We conclude that the network-based method can be used as a powerful tool for retrieving modularity information from weighted networks, which is useful for phylogenetic analysis