Dynamic Bayesian networks in molecular plant science: inferring gene regulatory networks from multiple gene expression time series

To understand the processes of growth and biomass production in plants, we ultimately need to elucidate the structure of the underlying regulatory networks at the molecular level. The advent of high-throughput postgenomic technologies has spurred substantial interest in reverse engineering these networks from data, and several techniques from machine learning and multivariate statistics have recently been proposed. The present article discusses the problem of inferring gene regulatory networks from gene expression time series, and we focus our exposition on the methodology of Bayesian networks. We describe dynamic Bayesian networks and explain their advantages over other statistical methods. We introduce a novel information sharing scheme, which allows us to infer gene regulatory networks from multiple sources of gene expression data more accurately. We illustrate and test this method on a set of synthetic data, using three different measures to quantify the network reconstruction accuracy. The main application of our method is related to the problem of circadian regulation in plants, where we aim to reconstruct the regulatory networks of nine circadian genes in Arabidopsis thaliana from four gene expression time series obtained under different experimental conditions

Heterogeneous continuous dynamic Bayesian networks with flexible structure and inter-time segment information sharing

Classical dynamic Bayesian networks (DBNs) are based on the homogeneous Markov assumption and cannot deal with heterogeneity and non-stationarity in temporal processes. Various approaches to relax the homogeneity assumption have recently been proposed. The present paper aims to improve the shortcomings of three recent versions of heterogeneous DBNs along the following lines: (i) avoiding the need for data discretization, (ii) increasing the flexibility over a time-invariant network structure, (iii) avoiding over-flexibility and overfitting by introducing a regularization scheme based in inter-time segment information sharing. The improved method is evaluated on synthetic data and compared with alternative published methods on gene expression time series from Drosophila melanogaster. 1

V39: an unusual object in the field of IC 1613

The variable star V39 in the field of IC 1613 is discussed in the light of the available photometric and new spectroscopic data. It has strong emission Balmer lines, and the observed characteristics could be explained by a W Vir pulsating star with a period of 14.341 d, located at more than 115 kpc, that is in the very outer halo of our Galaxy. It should have an apparent companion, a long period (1118d) red variable, belonging to IC 1613. The main uncertainty in this interpretation is an emission feature at 668.4 nm, which we tentatively identified as a He I line.Comment: 5 pages; accepted for publication in Astronomy & Astrophysic

Morphological and biochemical changes in trisomy 21

Introdução: A Trissomia 21 (T21) é a aneuploidia mais comum, apresentando uma prevalência de 1/670 nascimentos. É a principal causa de défice intelectual moderado a grave, e está associada a diversas anomalias congénitas, sendo as malformações cardiovasculares as mais frequentes. O objetivo deste trabalho é caracterizar as alterações morfológicas e bioquímicas nos casos de T21. Material e Métodos: Estudo prospetivo, realizado no nosso Hospital entre 1998 e 2008, de avaliação dos casos com rastreio bioquímico considerado positivo para T21. Foram também analisados os resultados dos exames invasivos realizados no mesmo período e revistos os processos com diagnóstico de T21 neste exame, assim como os processos das mães cujos recém-nascidos foram codificados com diagnóstico de T21 na alta. Resultados: Neste período foram efetuados 12163 rastreios. Foram identificados 18 casos de T21. Houve 2 resultados falsos-negativos, representando uma taxa de deteção do rastreio de 88,9%. A mediana das MoM's dos marcadores bioquímicos nas grávidas com fetos afetados foi: 0,735 de AFP, 0,685 de µE3 e 2,54 de βHCG. Quinze dos 18 casais optaram por interromper a gravidez. Nasceram 3 recém-nascidos com T21. As anomalias presentes nos fetos afetados foram essencialmente alterações do hábito externo, nomeadamente a existência de pregas palmares transversais em uma ou ambas as mãos e alterações craniofaciais. Quanto às alterações do hábito interno as mais comuns foram as malformações cardiovasculares, nomeadamente a comunicação interventricular (CIV). Discussão: Neste estudo a taxa de deteção do rastreio foi elevada. A maioria dos casais optou por interromper a gravidez. A maioria dos fetos e recém-nascidos afetados apresentou alterações morfológicas subtis, difíceis de detetar ecograficamente, salientando a importância do rastreio bioquímico.info:eu-repo/semantics/publishedVersio

Echelle long-slit optical spectroscopy of evolved stars

We present echelle long-slit optical spectra of a sample of objects evolving off the AGB, most of them in the pre-planetary nebula (pPN) phase, obtained with the ESI and MIKE spectrographs at Keck-II and Magellan-I, respectively. The total wavelength range covered with ESI (MIKE) is ~3900 to 10900 A (~3600 to 7200A). In this paper, we focus our analysis mainly on the Halpha profiles. Prominent Halpha emission is detected in half of the objects, most of which show broad Halpha wings (up to ~4000 km/s). In the majority of the Halpha-emission sources, fast, post-AGB winds are revealed by P-Cygni profiles. In ~37% of the objects Halpha is observed in absorption. In almost all cases, the absorption profile is partially filled with emission, leading to complex, structured profiles that are interpreted as an indication of incipient post-AGB mass-loss. All sources in which Halpha is seen mainly in absorption have F-G type central stars, whereas sources with intense Halpha emission span a larger range of spectral types from O to G. Shocks may be an important excitation agent of the close stellar surroundings for objects with late type central stars. Sources with pure emission or P Cygni Halpha profiles have larger J-K color excess than objects with Halpha mainly in absorption, which suggests the presence of warm dust near the star in the former. The two classes of profile sources also segregate in the IRAS color-color diagram in a way that intense Halpha-emitters have dust grains with a larger range of temperatures. (abridged)Comment: 68 pages, 14 figures, accepted for publication in ApJS (abstract abridged

Amphipoda (Crustacea) Associados a “Bostrychietum” em uma Área de Manguezal na Região Norte do Estado de São Paulo

O manguezal é um sistema ecológico tropical que se restringe a estreitas faixas costeiras, apresentando condições propícias para alimentação, proteção e reprodução de muitas espécies de animais. Nos manguezais ocorrem importantes associações de macroalgas aderidas em pneumatóforos, rizóforos e troncos das árvores dos gêneros Avicennia L., Rhizophora L. e Laguncularia Gaertn denominadas como “Bostrychietum”. Essas associações incluem cianobactérias e clorofíceas, contudo há imensa dominância de rodofïceas, mais precisamente dos gêneros Bostrychia Mont., Caloglossa (Harv.) G. Martens e Catenella Grev. Os Amphipoda são muito comuns em ambientes de manguezal ao redor do mundo, no entanto não há nenhum estudo faunístico abrangente sobre este grupo para manguezais brasileiros. A área de estudo é uma região de manguezal localizada no Município de São Vicente, Baixada Santista, região norte do estado de São Paulo. A comunidade de “Bostrychietum” é coletada por meio de raspagem dos substratos (pneumatóforos, rizóforos e troncos). Os anfípodes são anestesiados por meio de submerssão em etanol 5-10%. Posteriormente, os anfípodes são triados em laboratório, fixados em etanol 70% e identificados com base em literatura especializada. As amostras de “Bostrychietum” foram depositadas na coleção de algas da Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Campus do Litoral Paulista. Todo o material de Amphipoda está conservado em etanol 70% na coleção do Laboratório de Zoologia do UniFOA. Após a realização do estudo todo o material será depositado em coleções zoológicas de referência. Este projeto está em fase intermediária e parte das amostras já foi analisada. Uma lista preliminar da fauna Amphipoda identificada será apresentada

Exposure to diesel exhaust particles increases susceptibility to invasive pneumococcal disease.

BACKGROUND: The World Health Organization estimates that air pollution is responsible for 7 million deaths per annum, with 7% of these attributable to pneumonia. Many of these fatalities have been linked to exposure to high levels of airborne particulates, such as diesel exhaust particles (DEPs). OBJECTIVES: We sought to determine whether exposure to DEPs could promote the progression of asymptomatic nasopharyngeal carriage of Streptococcus pneumoniae to invasive pneumococcal disease. METHODS: We used mouse models and in vitro assays to provide a mechanistic understanding of the link between DEP exposure and pneumococcal disease risk, and we confirmed our findings by using induced sputum macrophages isolated from healthy human volunteers. RESULTS: We demonstrate that inhaled exposure to DEPs disrupts asymptomatic nasopharyngeal carriage of S pneumoniae in mice, leading to dissemination to lungs and blood. Pneumococci are transported from the nasopharynx to the lungs following exposure to DEPs, leading to increased proinflammatory cytokine production, reduced phagocytic function of alveolar macrophages, and consequently, increased pneumococcal loads within the lungs and translocation into blood. These findings were confirmed by using DEP-exposed induced sputum macrophages isolated from healthy volunteers, demonstrating that impaired innate immune mechanisms following DEP exposure are also at play in humans. CONCLUSION: Lung inhaled DEPs increase susceptibility to pneumococcal disease by leading to loss of immunological control of pneumococcal colonisation, increased inflammation, tissue damage, and systemic bacterial dissemination