Homoplastic microinversions and the avian tree of life

Background: Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasyfree evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution. Results: We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots. Conclusions: Microinversions can provide valuable phylogenetic information, although power analysis indicate

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems

Estudo de confiabilidade do SINAN a partir das Campanhas para a Eliminação da Sífilis Congênita no Município do Rio de Janeiro Reliability of the National Disease Surveillance Data System using Campaigns for the elimination of congenital syphilis in the City of Rio de Janeiro

A partir da construção da base de dados das Campanhas para a Eliminação da Sífilis Congênita, realizadas no Município do Rio de Janeiro em 1999 e 2000, estabeleceu-se a confiabilidade dos dados informados ao Sistema Nacional de Agravos de Notificação (SINAN). Procedeu-se também a um estudo da qualidade do preenchimento das variáveis, que são as informações solicitadas para a notificação do caso. O percentual de concordância simples para a variável número de consultas de pré-natal foi de 91% e 92,1% e para a variável sífilis na gravidez foi de 62,7% e 76,3%, para os anos de 1999 e 2000, respectivamente. A concordância para as variáveis idade da mãe, data do tratamento e tipo de tratamento foi estabelecida pelo coeficiente kappa. A variável idade apresentou excelente concordância. Contudo, as outras duas resultaram em baixa concordância para os dois anos estudados. Em relação à qualidade, variáveis importantes como realização do primeiro VDRL, do segundo VDRL e a idade gestacional no tratamento, apresentaram percentuais de caselas vazias/ignoradas superiores a 20%. O estudo da confiabilidade entre a base primária das campanhas e o SINAN-SC corrobora a necessidade de desenvolver estratégias para aprimorar a qualidade do último nos vários níveis dos sistemas de saúde. A mudança da definição de caso de sífilis congênita, realizada em 2004, e a introdução do Curso Básico de Vigilância Epidemiológica para sífilis na gestação e sífilis congênita devem contribuir para o aprimoramento do sistema.<br>Using the database obtained from the Campaigns for the elimination of congenital syphilis in the City of Rio de Janeiro in 1999 and 2000, we performed a reliability study on the National Disease Surveillance Data System (SINAN). We also evaluated the quality of the data provided. The percentage of agreement for the variable number of consultations in prenatal care was 91.0% in 1999 and 92.1% in 2000, and for syphilis during pregnancy was 62.7% in 1999 and 76.3% in 2000. Kappa statistics for the variables age of mother, date of treatment and therapy regimen provided an almost perfect agreement for age, in both years, but a slight to fair agreement for the other two. Looking at the quality of data, important variables as first VDRL during pregnancy, second VDRL and gestational age at syphilis treatment had more than 20% of blank or unknown answers. The reliability study of the SINAN using the campaigns' primary databases corroborates the need of establishing strategies to increase the quality of the SINAN at the various levels of the health systems. The 2004 change in case definition and the implementation of the Basic Course in Epidemiological Surveillance on syphilis in pregnancy and congenital syphilis will contribute to the improvement of the system

Caractérisation et modélisation de la « fonction symbiotique » de Buchnera aphidicola chez le puceron du pois Acyrthosiphon pisum

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