Strand Analysis, a free online program for the computational identification of the best RNA interference (RNAi) targets based on Gibbs free energy

The RNA interference (RNAi) technique is a recent technology that uses double-stranded RNA molecules to promote potent and specific gene silencing. The application of this technique to molecular biology has increased considerably, from gene function identification to disease treatment. However, not all small interfering RNAs (siRNAs) are equally efficient, making target selection an essential procedure. Here we present Strand Analysis (SA), a free online software tool able to identify and classify the best RNAi targets based on Gibbs free energy (deltaG). Furthermore, particular features of the software, such as the free energy landscape and deltaG gradient, may be used to shed light on RNA-induced silencing complex (RISC) activity and RNAi mechanisms, which makes the SA software a distinct and innovative tool.

Desenvolvimento da relação de cooperação mediada por computador em ambiente de educação a distância / Increase of cooperation permitted by computers in a distance education environment

O artigo contempla parte dos resultados de uma pesquisa-ação desenvolvida junto aos agentes de saúde dos bairros São Marcos e Santa Mônica, em Campinas-SP. Trata-se de pesquisa longitudinal, com duração de um ano e meio, envolvendo três fases: presencial, semipresencial e a distância. Aqui tratamos apenas das atividades ocorridas na fase presencial, nas quais os agentes começaram a aprender a utilizar o computador, e do TelEduc. Para tanto, optamos por uma observação qualitativa, já que o objetivo principal foi aferir os estágios de desenvolvimento de Piaget com a capacidade dos agentes em dominar as entidades tangíveis e intangíveis da informática (compreendem-se as entidades tangíveis como os elementos de hardware; e as entidades intangíveis, como os de software). Essa relação foi possível quando eles, de maneira presencial, começaram a interagir com os elementos básicos do computador e com o TelEduc. Após superarem a anomia e terem dominado as ferramentas que favoreceram posturas heterônomas, os agentes manipularam recursos que permitiram o começo de uma relação de cooperação.

This article analyzes part of the results of a social research program developed along with neighborhood health agents of São Marcos and Santa Mônica in Campinas, state of São Paulo. It was a longitudinal study carried out over a period of a year and a half carried out throughout three phases: face-to-face, intermediary stage and pure distance work. In this article we solely discuss the activities during the face-to-face phase, whereby agents learnt how to use the computer and the TelEduc system. We opted to apply qualitative observation given that the main objective of this research was to identify Piaget's developmental stages within the context of the agents' capacity to understand tangible and intangible aspects of the technological universe. This relationship was possible when the subjects began to interact with basic elements of the computer and with TelEduc. After overcoming a state of anomia and understanding the tools that allowed a heteronomous attitude, agents used resources allowing them to enter a relationship of cooperation.

Este artículo contempla parte de los resultados de una investigación-acción desarrollada juntamente con los agentes de salud de los barrios Sao Marcos y Santa Mônica, Campinas/ Sao Paulo. Fue una investigación longitudinal, con duración de un año y medio, que constó de tres fases: Presencial, semipresencial y a distancia. En este artículo tratamos solamente de las actividades ocurridas en la fase presencial, en la cual los agentes comenzaron a aprender a utilizar el ordenador y TelEduc. Optamos por una observación cualitativa, ya que el objetivo principal fue asociar las tres fases de desarrollo piagetianas -anomia, heteronomia y cooperación - con la capacidad de los agentes de dominar las propiedades tangibles e intangibles de la informática. Esta asociación fue posible cuando ellos empezaron a interactuar con los elementos básicos del ordenador y del TelEduc. Después de superar la anomia y de dominar las herramientas qué favorecieran actitudes heterónomas, los agentes manipularon recursos que permitieron el comienzo de una relación de cooperación.

In silico evaluation of the Eucalyptus transcriptome

The expressed sequence tags (ESTs) produced in the Forests project provide an invaluable opportunity to assess the Eucalyptus transcriptome. Besides providing information on the different proteins produced by this plant, it is possible to infer gene expression profiles because non-normalized cDNA libraries were used. The EST frequency from any gene is correlated to the transcript levels in the tissues from which the cDNA libraries were constructed. The goal of this work was to identify Eucalyptus genes that showed either differential expression pattern or were ubiquitously expressed in the tissues sampled in the Forests project. Six robust statistical tests and very restrictive rules were applied to gain confidence in the in silico data aiming to avoid false positives. Several genes with interesting expression profiles were identified and some of them were validated by RT-PCR

Eucalyptus ESTs involved in the production of 9-cis epoxycarotenoid dioxygenase, a regulatory enzyme of abscisic acid production

Abscisic acid (ABA) regulates stress responses in plants, and genomic tools can help us to understand the mechanisms involved in that process. FAPESP, a Brazilian research foundation, in association with four private forestry companies, has established the FORESTs database (https://forests.esalq.usp.br). A search was carried out in the Eucalyptus expressed sequence tag database to find ESTs involved with 9-cis epoxycarotenoid dioxygenase (NCED), the regulatory enzyme for ABA biosynthesis, using the basic local BLAST alignment tool. We found four clusters (EGEZLV2206B11.g, EGJMWD2252H08.g, EGBFRT3107F10.g, and EGEQFB1200H10.g), which represent similar sequences of the gene that produces NCED. Data showed that the EGBFRT3107F10.g cluster was similar to the maize (Zea mays) NCED enzyme, while EGEZLV2206B11.g and EGJMWD2252H08.g clusters were similar to the avocado (Persea americana) NCED enzyme. All Eucalyptus clusters were expressed in several tissues, especially in flower buds, where ABA has a special participation during the floral development process

Boron transport in Eucalyptus. 2. Identification in silico of a putative boron transporter for xylem loading in eucalypt

Boron (B) is a low mobility plant micronutrient whose molecular mechanisms of absorption and translocation are still controversial. Many factors are involved in tolerance to Boron excess or deficiency. Recently, the first protein linked to boron transport in biological systems, BOR1, was characterized in Arabidopsis thaliana. This protein is involved in boron xylem loading and is similar to bicarbonate transporters found in animals. There are indications that BOR1 is a member of a conserved protein family in plants. In this work, FORESTS database was used to identify sequences similar to this protein family, looking for a probable BOR1 homolog in eucalypt. We found five consensus sequences similar to BOR1; three of them were then used in multiple alignment analysis. Based on amino acid similarity and in silico expression patterns, a consensus sequence was identified as a candidate BOR1 homolog, helping deeper experimental assays that could identify the function of this protein family in Eucalyptus

Eucalyptus ESTs associated with resistance to herbicide inhibitors of aromatic and branched-chain amino acid synthesis

Herbicides inhibit enzymatic systems of plants. Acetolactate synthase (ALS, EC = 4.1.3.18) and 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS, EC 2.5.1.19) are key enzymes for herbicide action. Hundreds of compounds inhibit ALS. This enzyme is highly variable, enabling the selective control of weeds in a number of crops. Glyphosate, the only commercial herbicide inhibiting EPSPS is widely used for non-selective control of weeds in many crops. Recently, transgenic crops resistant to glyphosate were developed and have been used by farmers. The aim of this study was the data mining of eucalypt expressed sequence tags (ESTs) in the FORESTs Genome Project database (https://forests.esalq.usp.br) related to these enzymes. Representative amino acid sequences from the NCBI database associated with ALS and EPSPS were blasted with ESTs from the FORESTs database using the tBLASTx option of the blast tool. The best blasting reads and clusters from FORESTs, represented as nucleotide sequences, were blasted back with the NCBI database to evaluate the level of similarity with available sequences from different species. One and seven clusters were identified as showing high similarity with EPSPS and ALS sequences from the literature, respectively. The alignment of EPSPS sequences allowed the identification of conserved regions that can be used to design specific primers for additional sequencings

Eucalyptus ESTs corresponding to the enzyme glutamine synthetase and the protein D1, sites of action of herbicides that cause oxidative stress

This work was aimed at locating Eucalyptus ESTs corresponding to the GS enzyme (Glutamine Synthetase, EC = 6.3.1.2) and to the D1 protein, which are directly related to resistance to herbicides that promote oxidative stress. Glutamine Synthetase corresponds to the site of action of the herbicide glufosinate. Herbicides that belong to groups such as ureas, uracils, triazines and triazinones act on the D1-Qb complex (receptor of electrons from the Photosystem II) by inactivating it. The clusters EGEQRT3302E01.g, EGEQRT3001F12.b; EGEZLV1203B04.g; EGBGFB1211H06.g and EGEZLV1205F09.g enclosed complete sequences (with 356 amino acids) of the Glutamine Synthetase enzyme. The cluster EGEQSL1054G06.g is a consensus of four reads and enclosed a complete sequence of D1 Protein (with 353 amino acids). The comparison of the sequences of Protein D1 from different species showed that the substitutions of serine (S) by glycine (G) or serine (S) by threonine (T) at the position 264 could produce plants resistant to herbicides that act on electron flow on Photosystem II. The sequence of amino acids corresponding to the cluster EGEQSL1054G06.g had a serine in position 264 indicating sensitivity of the Eucalyptus plants to herbicides that act on this site

Eucalyptus ESTs corresponding to the protoporphyrinogen IX oxidase enzyme related to the synthesis of heme, chlorophyll, and to the action of herbicides

This work was aimed at locating Eucalyptus ESTs corresponding to the PROTOX or PPO enzyme (Protoporphyrinogen IX oxidase, E.C. 1.3.3.4) directly related to resistance to herbicides that promote oxidative stress, changing the functionality of this enzyme. PROTOX, which is the site of action of diphenyl-ether (oxyfluorfen, lactofen, fomesafen), oxadiazole (oxadiazon and oxadiargyl), and aryl triazolinone (sulfentrazone and carfentrazone) herbicides, acts on the synthesis route of porphyrins which is associated with the production of chlorophyll a, catalases, and peroxidases. One cluster and one single read were located, with e-values better than e-70, associated to PROTOX. The alignment results between amino acid sequences indicated that this enzyme is adequately represented in the ESTs database of the FORESTs project

The post-transcriptional gene silencing pathway in Eucalyptus

Post-transcriptional gene silencing (PTGS) is a conserved surveillance mechanism that identifies and cleaves double-stranded RNA molecules and their cellular cognate transcripts. The RNA silencing response is actually used as a powerful technique (named RNA interference) for potent and specific inhibition of gene expression in several organisms. To identify gene products in Eucalyptus sharing similarities with enzymes involved in the PTGS pathway, we queried the expressed sequence tag database of the Brazilian Eucalyptus Genome Sequence Project Consortium (FORESTs) with the amino acid sequences of known PTGS-related proteins. Among twenty-six prospected genes, our search detected fifteen assembled sequences encoding products presenting high level of similarity (E value < 10-40) to proteins involved in PTGS in plants and other organisms. We conclude that most of the genes known to be involved in the PTGS pathway are represented in the FORESTs database

N-glycosylation in sugarcane

A N-glicosilaçäo é uma das principais modificações pós-tradicionais, sendo responsável por alterações na conformaçäo, estabilidade e conseqüentemente na funcionalidade de proteínas em eucariotos. Com a finalidade de melhor compreender a via de N-glicosilaçäo em plantas foi realizada uma prospecçäo no banco de seqüências expressas do projeto genoma da cana de açúcar (SUCEST). Foram identificadas noventa seqüências cujos produtos gênicos apresentam alto grau de similaridade com enzimas envolvidas na biossíntese e processamento de N-glicanos. Dos vinte e três genes da via de N-glicosilaçäo previamente descritos em diferentes espécies, vinte e um foram detectados em cana de açúcar.

Cardiomiopatia arritimogênica do ventrículo direito. Valor preditivo da dispersäo do intervalo QT para avaliaçäo de risco arritmogênico e de morte súbita / Arrhythmogenic cardiomyopathy of the right ventricle. Predictive value of QT interval dispersion to assess arrhythmogenic risk and sudden death

OBJECTIVE: To determine in arrhythmogenic right ventricular cardiomyopathy the value of QT interval dispersion for identifying the induction of sustained ventricular tachycardia in the electrophysiological study or the risk of sudden cardiac death. METHODS: We assessed QT interval dispersion in the 12-lead electrocardiogram of 26 patients with arrhythmogenic right ventricular cardiomyopathy. We analyzed its association with sustained ventricular tachycardia and sudden cardiac death, and in 16 controls similar in age and sex. RESULTS: (mean +/- SD). QT interval dispersion: patients = 53.8+/-14.1ms; control group = 35.0+/-10.6ms, p=0.001. Patients with induction of ventricular tachycardia: 52.5+/-13.8ms; without induction of ventricular tachycardia: 57.5+/-12.8ms, p=0.420. In a mean follow-up period of 41+/-11 months, five sudden cardiac deaths occurred. QT interval dispersion in this group was 62.0+/-17.8, and in the others it was 51.9+/-12.8ms, p=0.852. Using a cutoff > or = 60ms to define an increase in the degree of the QT interval dispersion, we were able to identify patients at risk of sudden cardiac death with a sensitivity of 60 percent, a specificity of 57 percent, and positive and negative predictive values of 25 percent and 85 percent, respectively. CONCLUSION: Patients with arrhythmogenic right ventricular cardiomyopathy have a significant increase in the degree of QT interval dispersion when compared with the healthy population. However it, did not identify patients with induction of ventricular tachycardia in the electrophysiological study, showing a very low predictive value for defining the risk of sudden cardiac death in the population studied.

Síndrome de Brugada: observaçöes sobre a evoluçä de um caso / The Brugada syndrome: outcome of one case

The Brugada syndrome is a rare condition, and due to its mutating manner of presentation it may be difficult to diagnose. We report one case and discuss the diagnostic aspects and the clinical outcome of one patient with characteristic findings of this syndrome. These findings are especially defined by J-ST elevation in the right leads of serial electrocardiographic records, wide oscillations of J points and ST segments during 24-hour Holter monitoring, and nocturnal sudden death. We stress the importance of the Holter monitor findings for diagnostic complementation. Through this method it is possible to establish a correlation between vigil activities and sleep and the variability of the degree of impairment in ventricular repolarization.

O estado atual do emprego de antiagregantes plaquetários e anticoagulantes para prevençäo de eventos tromboembólicos na fibrilaçäo atrial / The role of antiplatelets and anticoagulants in prevention of thromboembolic events in atrial fibrilation

A fibrilaçäo atrial é uma condiçäo clínica comum com alto potencial para eventos tromboembolíticos. Com as recentes publicaçöes dos grandes ensaios randomizados na prevençäo primária e secundária dos fenômenos tromboembolíticos, tem sido possível caracterizar subgrupos de alto e baixo risco para estes eventos. Também, apesar de algumas diferenças nos resultados é possível atualmente planejarmos uma terapia anticoagulantes mais substanciada. As metanálises destes estudos mostram que o warfarin pode reduzir em até 70 'por cento' o risco de tromboembolismo, mas, em somente 30 'por cento' com a aspirina. Em praticamente todos os pacientes a melhor opçäo terapêutica é a antiacoagulaçäo plena com warfarin, reservando a aspirina para os de baixo risco ou os com contra-indicaçäo para o anticoagulante.

Bradarritmias na sala de emergência / Bradyarrhythmias in the emergency room

Tem sido reconhecido, há muito tempo, que o ritmo cardíaco extremamente lento é capaz de produzir sintomas severos. As bradiarritmias sintomáticas implicam em distúrbios da função sinusal, da condução AV, ou de ambos. As causas dessas anormalidades podem ser classificadas, de uma maneira ampla em: 1) distúrbios intrínsecos, 2) distúrbios extrínsecos, ou 3) distúrbios funcionais reflexos mediados neuralmente. A disfunção do nódulo sinusal (ou doença do nódulo sinusal) compreende um espectro de arritmia do nódulo sinusal e/ou atriais, que resultam em períodos intermitentes ou persistentes de batimentos cardíacos inapropriados, lentos ou rápidos. Distúrbios da condução AV abrangem desde alentecimento da condução AV, à falta intermitente da transmissão do impulso, até completa falha da condução. Na maioria dos casos, a estimulação cardíaca artificial substituiu a terapia farmacológica no tratamento de pacientes com bradiarritmia sintomática. A disfunção dos MP, em pacientes dependentes do mesmo, representa também uma importante causa de períodos intermitentes de ritmo cardíaco lento sintomático

Síncope: Avaliação diagnóstica e conduta / Syncope: Diagnostic assessment and procedure

Este artigo tem como finalidade oferecer aos clínicos uma atualização sobre síncope, suas causas, mecanismos fisiopatológicos envolvidos bem como as condutas terapêuticas atuais. Consideraçöes especiais serão dirigidas à síncope cardio-neurogênica, sua importância clínica e as diversas opçöes atuais de tratamento. Discutiremos as indicaçöes e metodologias utilizadas no teste de inclinação, bem como a sua utilidade para a definição das diversas formas de apresentação da síncope cardio-neurogênica.

Avaliação das arritmias ventriculares na cardiopatia isquêmica / Assessment of ventricular arrhytthmias in ischemic cardiopathy

As arritmias cardíacas nas fases iniciais do infarto do miocárdio estão relacionadas principalmente ao processo de base (isquemia). Existe uma significativa variabilidade na ocorrência e frequência de taquicardia ventricular não sustentada pós-IAM. Os efeitos da isquemia nas propriedades eletrofisiológicas do músculo cardíaco são inúmeras e complexas. A identificação de pacientes com risco para alta mortalidade e morbidade pós-infarto permite uma base racional para se individualizar estratégias diagnósticas e terapêuticas. A estratificação de risco pode oferecer valiosas informaçöes sobre os mecanismos de risco e, desse modo, aumentar o nosso entendimento dos processos patológicos envolvidos. O uso de testes não invasivos para predizer eventos arrítmicos pós-IAM cresceu significativamente.