Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: new insights into anti-mineralogenic effect of vanadate

<p>Abstract</p> <p>Background</p> <p>Fish has been deemed suitable to study the complex mechanisms of vertebrate skeletogenesis and gilthead seabream (<it>Sparus aurata</it>), a marine teleost with acellular bone, has been successfully used in recent years to study the function and regulation of bone and cartilage related genes during development and in adult animals. Tools recently developed for gilthead seabream, <it>e.g. </it>mineralogenic cell lines and a 4 × 44K Agilent oligo-array, were used to identify molecular determinants of <it>in vitro </it>mineralization and genes involved in anti-mineralogenic action of vanadate.</p> <p>Results</p> <p>Global analysis of gene expression identified 4,223 and 4,147 genes differentially expressed (fold change - FC > 1.5) during <it>in vitro </it>mineralization of VSa13 (pre-chondrocyte) and VSa16 (pre-osteoblast) cells, respectively. Comparative analysis indicated that nearly 45% of these genes are common to both cell lines and gene ontology (GO) classification is also similar for both cell types. Up-regulated genes (FC > 10) were mainly associated with transport, matrix/membrane, metabolism and signaling, while down-regulated genes were mainly associated with metabolism, calcium binding, transport and signaling. Analysis of gene expression in proliferative and mineralizing cells exposed to vanadate revealed 1,779 and 1,136 differentially expressed genes, respectively. Of these genes, 67 exhibited reverse patterns of expression upon vanadate treatment during proliferation or mineralization.</p> <p>Conclusions</p> <p>Comparative analysis of expression data from fish and data available in the literature for mammalian cell systems (bone-derived cells undergoing differentiation) indicate that the same type of genes, and in some cases the same orthologs, are involved in mechanisms of <it>in vitro </it>mineralization, suggesting their conservation throughout vertebrate evolution and across cell types. Array technology also allowed identification of genes differentially expressed upon exposure of fish cell lines to vanadate and likely involved in its anti-mineralogenic activity. Many were found to be unknown or they were never associated to bone homeostasis previously, thus providing a set of potential candidates whose study will likely bring insights into the complex mechanisms of tissue mineralization and bone formation.</p

The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation

Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. Conjugation allows the broadest range and the highest gene transfer input per transfer event. While conjugative plasmids have been studied for decades, the number and diversity of integrative conjugative elements (ICE) in prokaryotes remained unknown. We defined a large set of protein profiles of the conjugation machinery to scan over 1,000 genomes of prokaryotes. We found 682 putative conjugative systems among all major phylogenetic clades and showed that ICEs are the most abundant conjugative elements in prokaryotes. Nearly half of the genomes contain a type IV secretion system (T4SS), with larger genomes encoding more conjugative systems. Surprisingly, almost half of the chromosomal T4SS lack co-localized relaxases and, consequently, might be devoted to protein transport instead of conjugation. This class of elements is preponderant among small genomes, is less commonly associated with integrases, and is rarer in plasmids. ICEs and conjugative plasmids in proteobacteria have different preferences for each type of T4SS, but all types exist in both chromosomes and plasmids. Mobilizable elements outnumber self-conjugative elements in both ICEs and plasmids, which suggests an extensive use of T4SS in trans. Our evolutionary analysis indicates that switch of plasmids to and from ICEs were frequent and that extant elements began to differentiate only relatively recently. According to the present results, ICEs are the most abundant conjugative elements in practically all prokaryotic clades and might be far more frequently domesticated into non-conjugative protein transport systems than previously thought. While conjugative plasmids and ICEs have different means of genomic stabilization, their mechanisms of mobility by conjugation show strikingly conserved patterns, arguing for a unitary view of conjugation in shaping the genomes of prokaryotes by horizontal gene transfer

Studies on the effectiveness of diarylheptanoids derivatives against Leishmania amazonensis

In a previous work we demonstrated that diarylheptanoids extracted from Centrolobium sclerophyllum are very active against Leishmania amazonensis promastigotes. In order to continue our studies with these class of compounds, we decided to evaluate the activity of several diarylheptanoids derived from curcumin (diferuloyl methane) against the extracellular form (promastigotes) of L. amazonensis. Furthermore, an experiment against the intracellular form of the parasite (amastigotes) was carried out, comparing the most active compound among the curcumin derivatives (the methylcurcumin) with des-O-methylcentrolobine, the most active diarylheptanoid derived from C. sclerophyllum

Avaliação de políticas públicas de segurança alimentar e combate à fome no período de 1995-2002: 1 - Abordagem metodológica Evaluation of public policies for food security and hunger control in Brazil, 1995-2002: 1 - Methodological framework

Descrevem-se a adaptação e aplicação de uma metodologia multidimensional baseada na tríade estrutura-processo-resultado ao contexto da avaliação de programas de segurança alimentar e combate à fome. Segundo a proposta, o estudo da estrutura analisa os instrumentos físicos e discursivos dos programas; a dimensão processo, as atividades e intervenções desenvolvidas e a dimensão resultado, além da cobertura, focalização e controle social, poderia contemplar os efeitos das intervenções sobre a segurança alimentar e nutrição dos beneficiários. A metodologia foi empregada para avaliar programas implementados no Brasil no período de 1995-2002. Além disso, foi realizado um estudo de caso em 45 municípios da Bahia, envolvendo pesquisa documental, entrevistas com informantes-chave e pesquisa domiciliar em 1.750 famílias de baixa renda no interior e 760 famílias na capital. Espera-se que os resultados contribuam para a discussão sobre os fatores facilitadores e os obstáculos que são enfrentados no nível local para a implementação de programas dessa natureza, tanto quanto para o desenvolvimento metodológico no campo da avaliação de políticas de alimentação, nutrição e combate à fome.<br>The authors describe the adaptation and application of a multidimensional methodology based on structure-process-outcome for evaluating food security and hunger control programs. According to the proposal, study of the structure dimension analyzes the programs' material and discursive instruments; the process dimension focuses on the activities and interventions; and the outcome dimension includes coverage, targeting, and social control, and also potentially the effects of the interventions on the beneficiaries' food security and nutrition. The methodology was used to evaluate programs implemented in Brazil from 1995 to 2002. A case study was also done including 45 municipalities in the State of Bahia, involving documental research, interviews with key informants, and a household survey including 1,750 low-income families in the rural area and 760 in the capital city. The results are expected to contribute to the discussion on facilitating factors and obstacles at the local level for the implementation of such programs, and to methodological development in the field of food security, nutrition, and hunger control policies