Predicting cancer involvement of genes from heterogeneous data

Background: Systematic approaches for identifying proteins involved in different types of cancer are needed. Experimental techniques such as microarrays are being used to characterize cancer, but validating their results can be a laborious task. Computational approaches are used to prioritize between genes putatively involved in cancer, usually based on further analyzing experimental data. Results: We implemented a systematic method using the PIANA software that predicts cancer involvement of genes by integrating heterogeneous datasets. Specifically, we produced lists of genes likely to be involved in cancer by relying on: (i) protein-protein interactions; (ii) differential expression data; and (iii) structural and functional properties of cancer genes. The integrative approach that combines multiple sources of data obtained positive predictive values ranging from 23% (on a list of 811 genes) to 73% (on a list of 22 genes), outperforming the use of any of the data sources alone. We analyze a list of 20 cancer gene predictions, finding that most of them have been recently linked to cancer in literature. Conclusion: Our approach to identifying and prioritizing candidate cancer genes can be used to produce lists of genes likely to be involved in cancer. Our results suggest that differential expression studies yielding high numbers of candidate cancer genes can be filtered using protein interaction networks.

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

Background: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results: Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://ibi.imim.es/osirisform.html. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://ibi.imim.es/OSIRISv1.2.html webcite) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion: OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.

Validação de indicadores da classificação dos resultados de enfermagem para pacientes com problemas ortopédicos

Estudo de validação de conteúdo, descritivo, transversal, com abordagem quantitativa, realizado num hospital universitário. Objetivou-se validar os indicadores de quatro resultados de enfermagem da Classificação dos Resultados de Enfermagem - NOC, para o diagnóstico de enfermagem Déficit no autocuidado: banho/higiene, apresentados por pacientes em pós-operatório de cirurgia ortopédica. Construiu-se um instrumento contendo os indicadores dos resultados Autocuidado: Atividades da Vida Diária, Autocuidado: Banho, Autocuidado: Higiene e Autocuidado: Higiene Oral, e uma escala Likert de cinco pontos (1=não relevante; 5=extremamente relevante). Os peritos foram enfermeiros que atendem esses pacientes há pelo menos um ano e utilizam diagnósticos de enfermagem. Para análise dos dados empregou-se estatística descritiva. Dos 34 indicadores pesquisados, 2 (6%) foram considerados indicadores principais provisórios, 22 (65%), secundários provisórios e 10 (29%) foram descartados. Os indicadores principais e secundários provisórios serão utilizados na observação do banho de pacientes em pós-operatório de Artroplastia Total de Quadril e terão suas evoluções monitoradas.

Tumor necrosis factor and transforming growth factor β regulate clock genes by controlling the expression of the cold inducible RNA-binding protein (CIRBP).

The circadian clock drives the rhythmic expression of a broad array of genes that orchestrate metabolism, sleep wake behavior, and the immune response. Clock genes are transcriptional regulators engaged in the generation of circadian rhythms. The cold inducible RNA-binding protein (CIRBP) guarantees high amplitude expression of clock. The cytokines TNF and TGFβ impair the expression of clock genes, namely the period genes and the proline- and acidic amino acid-rich basic leucine zipper (PAR-bZip) clock-controlled genes. Here, we show that TNF and TGFβ impair the expression of Cirbp in fibroblasts and neuronal cells. IL-1β, IL-6, IFNα, and IFNγ do not exert such effects. Depletion of Cirbp is found to increase the susceptibility of cells to the TNF-mediated inhibition of high amplitude expression of clock genes and modulates the TNF-induced cytokine response. Our findings reveal a new mechanism of cytokine-regulated expression of clock genes.

Amamentação: a prática do enfermeiro na perspectiva da Classificação Internacional de Práticas de Enfermagem em Saúde Coletiva

Estudo descritivo exploratório que objetivou descrever os diagnósticos e as intervenções de Enfermagem sob a perspectiva da Classificação Internacional das Práticas de Enfermagem em Saúde Coletiva - CIPESC® na atenção à Saúde da Mulher, subtema Pré-Natal e Puerpério, correlacionando-os com as competências do Enfermeiro no Programa Mãe Curitibana. Os dados utilizados foram os diagnósticos e intervenções gerados nas consultas de Enfermagem nos meses de abril a julho de 2005 e trabalhados em estatística simples. O diagnóstico Amamentação Adequada foi o mais frequente e as intervenções mais acionadas relacionam-se ao fortalecimento da usuária frente ao processo saúde-doença (68,9%). Apesar da atuação do Enfermeiro no puerpério, esta competência não consta do Protocolo do Programa. Concluiu-se que são necessários pequenos ajustes nos diagnósticos analisados e uma revisão do Protocolo para abrigar as competências do Enfermeiro que são desenvolvidas em sua prática nos serviços de saúde, conforme constam nos registros da base CIPESC®.

Sistema de Classificação de Pacientes Pediátricos: construção e validação de categorias de cuidados

A classificação de pacientes é essencial para o gerenciamento de uma unidade. Entretanto, a literatura não dispõe de conceituações de categorias de pacientes pediátricos. Os objetivos deste estudo foram definir e validar categorias de cuidado de pacientes pediátricos, de acordo com o grau de dependência da equipe de enfermagem. Utilizou-se revisão bibliográfica para definição das categorias de cuidado e a validação de conteúdo das categorias propostas foi realizada por um grupo de juízes envolvidos em assistência e gerência de unidades pediátricas e por juízes envolvidos em ensino e pesquisa de pediatria e construção de instrumentos de classificação de pacientes. Foram estabelecidas e validadas cinco categorias de cuidados: Mínimos, Intermediários, Alta dependência, Semi-intensivo e Intensivo. A validação das categorias de cuidado subsidiou a construção de um sistema de classificação de pacientes pediátricos que poderá contribuir para o processo de tomada de decisão do enfermeiro na prática gerencial e assistencial.

Genetik der essentiellen arteriellen Hypertonie [Essential hypertension - which genes can be held responsible for it?].

Hypertension is a common heritable cardiovascular risk factor. Some rare monogenic forms of hypertension have been described, but the majority of patients suffer from essential hypertension, for whom the underlying genetic mechanisms are not clear. Essential hypertension is a complex trait, involving multiple genes and environmental factors. Recently, progress in the identification of common genetic variants associated with essential hypertension has been made due to large-scale international collaborative projects. In this article we review the new research methods used as well as selected recent findings in this field.

Repeated exposure to Lutzomyia intermedia sand fly saliva induces local expression of interferon-inducible genes both at the site of injection in mice and in human blood.

During a blood meal, Lutzomyia intermedia sand flies transmit Leishmania braziliensis, a parasite causing tegumentary leishmaniasis. In experimental leishmaniasis, pre-exposure to saliva of most blood-feeding sand flies results in parasite establishment in absence of any skin damages in mice challenged with dermotropic Leishmania species together with saliva. In contrast, pre-immunization with Lu. intermedia salivary gland sonicate (SGS) results in enhanced skin inflammatory exacerbation upon co-inoculation of Lu. intermedia SGS and L. braziliensis. These data highlight potential unique features of both L. braziliensis and Lu. intermedia. In this study, we investigated the genes modulated by Lu. intermedia SGS immunization to understand their potential impact on the subsequent cutaneous immune response following inoculation of both SGS and L. braziliensis. The cellular recruitment and global gene expression profile was analyzed in mice repeatedly inoculated or not with Lu. intermedia. Microarray gene analysis revealed the upregulation of a distinct set of IFN-inducible genes, an immune signature not seen to the same extent in control animals. Of note this INF-inducible gene set was not induced in SGS pre-immunized mice subsequently co-inoculated with SGS and L. braziliensis. These data suggest the parasite prevented the upregulation of this Lu. intermedia saliva-related immune signature. The presence of these IFN-inducible genes was further analyzed in peripheral blood mononuclear cells (PBMCs) sampled from uninfected human individuals living in a L. braziliensis-endemic region of Brazil thus regularly exposed to Lu. intermedia bites. PBMCs were cultured in presence or absence of Lu. intermedia SGS. Using qRT-PCR we established that the IFN-inducible genes induced in the skin of SGS pre-immunized mice, were also upregulated by SGS in PBMCs from human individuals regularly exposed to Lu. intermedia bites, but not in PBMCs of control subjects. These data demonstrate that repeated exposure to Lu. intermedia SGS induces the expression of potentially host-protective IFN-inducible genes.

Classificação Internacional das Práticas de Enfermagem em Saúde Coletiva - CIPESC®: instrumento pedagógico de investigação epidemiológica

A CIPESC® é um instrumento de trabalho do enfermeiro em Saúde Coletiva, que visa apoiar a sistematização de sua prática assistencial, gerencial e de investigação. É também, instrumental pedagógico potente para a formação e qualificação de enfermeiros comprometidos com o SUS. No ensino das doenças transmissíveis, o uso da CIPESC® auxilia a análise sobre as intervenções, ao estimular o raciocínio clínico e epidemiológico do processo saúde-doença e das necessidades de saúde dos indivíduos, famílias e grupos sociais. Com o propósito de desenvolver recursos didáticos para graduação de enfermagem e estimular a reflexão sobre o processo de trabalho de enfermagem, este artigo apresenta o relato de uma experiência de aplicação da CIPESC®, tomando como exemplo a meningite meningocócica.

Avaliação de um instrumento para classificação de pacientes pediátricos oncológicos

Este estudo teve como objetivos avaliar a reprodutibilidade interavaliadores do instrumento para a classificação de pacientes pediátricos portadores de câncer; verificar se o instrumento de classificação de pacientes é adequado a pacientes pediátricos portadores de câncer e elaborar uma proposta de modificação do instrumento, permitindo a adaptação para pacientes pediátricos oncológicos. Foram avaliados, na unidade de internação pediátrica de um Hospital de câncer, 34 pacientes pelas equipes de médicos, enfermeiros e técnicos de enfermagem. Para a avaliação do grau de concordância entre os escores obtidos pelos avaliadores foi utilizado o coeficiente Kappa, que revelou um valor intermediário/alto nas classificações objetivas, e um valor baixo nas subjetivas. Conclui-se que o instrumento é confiável e reprodutível, porém, para classificação do paciente pediátrico oncológico, sugere-se a complementação de itens para atingir um resultado mais compatível com a realidade dessa população.

Association of candidate genes with phenotypic traits relevant to anorexia nervosa.

This analysis is a follow-up to an earlier investigation of 182 genes selected as likely candidate genetic variations conferring susceptibility to anorexia nervosa (AN). As those initial case-control results revealed no statistically significant differences in single nucleotide polymorphisms, herein, we investigate alternative phenotypes associated with AN. In 1762 females, using regression analyses, we examined the following: (i) lowest illness-related attained body mass index; (ii) age at menarche; (iii) drive for thinness; (iv) body dissatisfaction; (v) trait anxiety; (vi) concern over mistakes; and (vii) the anticipatory worry and pessimism versus uninhibited optimism subscale of the harm avoidance scale. After controlling for multiple comparisons, no statistically significant results emerged. Although results must be viewed in the context of limitations of statistical power, the approach illustrates a means of potentially identifying genetic variants conferring susceptibility to AN because less complex phenotypes associated with AN are more proximal to the genotype and may be influenced by fewer genes. Copyright © 2011 John Wiley & Sons, Ltd and Eating Disorders Association.

Identifying protein-coding genes in genomic sequences.

The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets.

Ferripyochelin uptake genes are involved in pyochelin-mediated signalling in Pseudomonas aeruginosa.

In response to iron starvation, Pseudomonas aeruginosa produces the siderophore pyochelin. When secreted to the extracellular environment, pyochelin chelates iron and transports it to the bacterial cytoplasm via its specific outer-membrane receptor FptA and the inner-membrane permease FptX. Exogenously added pyochelin also acts as a signal which induces the expression of the pyochelin biosynthesis and uptake genes by activating PchR, a cytoplasmic regulatory protein of the AraC/XylS family. The importance of ferripyochelin uptake genes in this regulation was evaluated. The fptA and fptX genes were shown to be part of the fptABCX ferripyochelin transport operon, which is conserved in Burkholderia sp. and Rhodospirillum rubrum. The fptB and fptC genes were found to be dispensable for utilization of pyochelin as an iron source, for signalling and for pyochelin production. By contrast, mutations in fptA and fptX not only interfered with pyochelin utilization, but also affected signalling and diminished siderophore production. It is concluded from this that pyochelin-mediated signalling operates to a large extent via the ferripyochelin transport system.

Association study of 182 candidate genes in anorexia nervosa.

We performed association studies with 5,151 SNPs that were judged as likely candidate genetic variations conferring susceptibility to anorexia nervosa (AN) based on location under reported linkage peaks, previous results in the literature (182 candidate genes), brain expression, biological plausibility, and estrogen responsivity. We employed a case-control design that tested each SNP individually as well as haplotypes derived from these SNPs in 1,085 case individuals with AN diagnoses and 677 control individuals. We also performed separate association analyses using three increasingly restrictive case definitions for AN: all individuals with any subtype of AN (All AN: n = 1,085); individuals with AN with no binge eating behavior (AN with No Binge Eating: n = 687); and individuals with the restricting subtype of AN (Restricting AN: n = 421). After accounting for multiple comparisons, there were no statistically significant associations for any individual SNP or haplotype block with any definition of illness. These results underscore the importance of large samples to yield appropriate power to detect genotypic differences in individuals with AN and also motivate complementary approaches involving Genome-Wide Association (GWA) studies, Copy Number Variation (CNV) analyses, sequencing-based rare variant discovery assays, and pathway-based analysis in order to make up for deficiencies in traditional candidate gene approaches to AN.

Sex chromosomes and male functions: where do new genes go?

The position of a gene in the genome may have important consequences for its function. Therefore, when a new duplicate gene arises, its location may be critical in determining its fate. Our recent work in humans, mouse, and Drosophila provided a test by studying the patterns of duplication in sex chromosome evolution. We revealed a bias in the generation and recruitment of new gene copies involving the X chromosome that has been shaped largely by selection for male germline functions. The gene movement patterns we observed reflect an ongoing process as some of the new genes are very young while others were present before the divergence of humans and mouse. This suggests a continuing redistribution of male-related genes to achieve a more efficient allocation of male functions. This notion should be further tested in organisms employing other sex determination systems or in organisms differing in germline sex chromosome inactivation. It is likely that the selective forces that were detected in these studies are also acting on other types of duplicate genes. As a result, future work elucidating sex chromosome differentiation by other mutational mechanisms will shed light on this important process.