Application of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data

We present two complementary approaches for the interpretation of clusters of co-regulated genes, such as those obtained from DNA chips and related methods. Starting from a cluster of genes with similar expression profiles, two basic questions can be asked: 1. Which mechanism is responsible for the coordinated transcriptional response of the genes? This question is approached by extracting motifs that are shared between the upstream sequences of these genes. The motifs extracted are putative cis-acting regulatory elements. 2. What is the physiological meaning for the cell to express together these genes? One way to answer the question is to search for potential metabolic pathways that could be catalyzed by the products of the genes. This can be done by selecting the genes from the cluster that code for enzymes, and trying to assemble the catalyzed reactions to form metabolic pathways. We present tools to answer these two questions, and we illustrate their use with selected examples in the yeast Saccharomyces cerevisiae. The tools are available on the web (http://ucmb.ulb.ac.be/bioinformatics/rsa-tools/; http://www.ebi.ac.uk/research/pfbp/; http://www.soi.city.ac.uk/~msch/)

RSAT 2011: regulatory sequence analysis tools

RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), a 100-times faster version of matrix-scan enabling the scanning of genome-scale sequence sets, and a series of facilities for random model generation and statistical evaluation (random-genome-fragments, random-motifs, random-sites, implant-sites, sequence-probability, permute-matrix). Our most recent work also focused on motif comparison (compare-matrices) and evaluation of motif quality (matrix-quality) by combining theoretical and empirical measures to assess the predictive capability of position-specific scoring matrices. To process large collections of peak sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict transcription factor binding motifs, match them against motif databases and predict their binding sites. Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/

RSAT: regulatory sequence analysis tools

The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published

Use and non-use of accounting information: The case of controversial projects in public and non-profit settings

This paper investigates whether and how accounting information is used in debates and decision-making processes about controversial projects in public sector and non-profit settings in the Netherlands and Italy. The research is based on two case studies and relies on multiple methods of qualitative data collection, including documents, interviews with key actors and media reports. The research finds a more limited extent of accounting information use than expected given the controversiality of the projects. It raises various types of explanations for this limited accounting information use, especially that ruling groups of actors supporting the project do not give room to the opposing minority for putting forward their concerns and preferences. The power position of the ruling majority thus matters in mitigating opportunities for a dialogic use of accounting information leading to the decision-making about the projects. So, controversiality is a determining factor, but insufficient as an explanation for the extent to which accounting information is used. In addition, the type of accounting information use is depending on the actors’ appreciation of the project. Advocates and opponents concerning both projects were in general inclined to an ammunition type of accounting information use, whereas actors holding a neutral position used available accounting information in a more rational way.This paper investigates whether and how accounting information is used in debates and decision-making processes about controversial projects in public sector and non-profit settings in the Netherlands and Italy. The research is based on two case studies and relies on multiple methods of qualitative data collection, including documents, interviews with key actors and media reports. The research finds a more limited extent of accounting information use than expected given the controversiality of the projects. It raises various types of explanations for this limited accounting information use, especially that ruling groups of actors supporting the project do not give room to the opposing minority for putting forward their concerns and preferences. The power position of the ruling majority thus matters in mitigating opportunities for a dialogic use of accounting information leading to the decision-making about the projects. So, controversiality is a determining factor, but insufficient as an explanation for the extent to which accounting information is used. In addition, the type of accounting information use is depending on the actors’ appreciation of the project. Advocates and opponents concerning both projects were in general inclined to an ammunition type of accounting information use, whereas actors holding a neutral position used available accounting information in a more rational way

Evidence of the dominant production mechanism of ammonia in a hydrogen plasma with parts per million of nitrogen

Absolute ground state atomic hydrogen densities were measured, by the utilization of two-photon absorption laser induced fluorescence, in a low-pressure electron cyclotron resonance plasma as a function of nitrogen admixtures - 0 to 5000 ppm. At nitrogen admixtures of 1500 ppm and higher, the spectral distribution of the fluorescence changes from a single Gaussian to a double Gaussian distribution; this is due to a separate, nascent contribution arising from the photolysis of an ammonia molecule. At nitrogen admixtures of 5000 ppm, the nascent contribution becomes the dominant contribution at all investigated pressures. Thermal loading experiments were conducted by heating the chamber walls to different temperatures; this showed a decrease in the nascent contributions with increasing temperature. This is explained by considering how the temperature influences recombination coefficients, and from which, it can be stated that the Langmuir-Hinshelwood recombination mechanism is dominant over the Eley-Rideal mechanism

Downregulation of Fzd6 and Cthrc1 and upregulation of olfactory receptors and protocadherins by dietary beta-carotene in lungs of Bcmo1-/- mice.

An ongoing controversy exists on beneficial versus harmful effects of high beta-carotene (BC) intake, especially for the lung. To elucidate potential mechanisms, we studied effects of BC on lung gene expression. We used a beta-carotene 15,15'-monooxygenase 1 (Bcmo1) knockout mouse (Bcmo1-/-) model, unable to convert BC to retinoids, and wild-type mice (Bcmo1+/+) mice to dissect the effects of intact BC from effects of BC metabolites. As expected, BC supplementation resulted in a higher BC accumulation in lungs of Bcmo1-/- mice than in lungs of Bcmo1+/+ mice. Whole mouse genome transcriptome analysis on lung tissue revealed that more genes were regulated in Bcmo1-/- mice than Bcmo1+/+ mice upon BC supplementation. Frizzled homolog 6 (Fzd6) and collagen triple helix repeat containing 1 (Cthrc1) were significantly downregulated (fold changes -2.99 and -2.60, respectively, false discovery rate <0.05) by BC in Bcmo1-/-. Moreover, many olfactory receptors and many members of the protocadherin family were upregulated. Since both olfactory receptors and protocadherins have an important function in sensory nerves and Fzd6 and Cthrc1 are important in stem cell development, we hypothesize that BC might have an effect on the highly innervated pulmonary neuroendocrine cell (PNEC) cluster. PNECs are highly associated with sensory nerves and are important cells in the control of stem cells. A role for BC in the innervated PNEC cluster might be of particular importance in smoke-induced carcinogenesis since PNEC-derived lung cancer is highly associated with tobacco smoke

Downregulation of Fzd6 and Cthrc1 and upregulation of olfactory receptors and protocadherins by dietary beta-carotene in lungs of Bcmo1-/- mice.

An ongoing controversy exists on beneficial versus harmful effects of high beta-carotene (BC) intake, especially for the lung. To elucidate potential mechanisms, we studied effects of BC on lung gene expression. We used a beta-carotene 15,15'-monooxygenase 1 (Bcmo1) knockout mouse (Bcmo1-/-) model, unable to convert BC to retinoids, and wild-type mice (Bcmo1+/+) mice to dissect the effects of intact BC from effects of BC metabolites. As expected, BC supplementation resulted in a higher BC accumulation in lungs of Bcmo1-/- mice than in lungs of Bcmo1+/+ mice. Whole mouse genome transcriptome analysis on lung tissue revealed that more genes were regulated in Bcmo1-/- mice than Bcmo1+/+ mice upon BC supplementation. Frizzled homolog 6 (Fzd6) and collagen triple helix repeat containing 1 (Cthrc1) were significantly downregulated (fold changes -2.99 and -2.60, respectively, false discovery rate <0.05) by BC in Bcmo1-/-. Moreover, many olfactory receptors and many members of the protocadherin family were upregulated. Since both olfactory receptors and protocadherins have an important function in sensory nerves and Fzd6 and Cthrc1 are important in stem cell development, we hypothesize that BC might have an effect on the highly innervated pulmonary neuroendocrine cell (PNEC) cluster. PNECs are highly associated with sensory nerves and are important cells in the control of stem cells. A role for BC in the innervated PNEC cluster might be of particular importance in smoke-induced carcinogenesis since PNEC-derived lung cancer is highly associated with tobacco smoke

Incidence of heat-labile enterotoxin-producing Escherichia coli detected by means of polymerase chain reaction amplification

CITATION: Winterbach, R. et al. 1994. Incidence of heat-labile enterotoxin-producing Escherichia coli detected by means of polymerase chain reaction amplification. South African Medical Journal, 84:85-87.The original publication is available at http://www.samj.org.zaDiarrhoea can be caused by many different organisms, some of which are notoriously difficult to identify. One of these is enterotoxin-producing Escherichia coli. Recently a new diagnostic technique that uses polymerase chain reaction DNA amplification was developed for detection of the 'A' subunit of the labile enterotoxin-producing E. coli gene. This technique was used to evaluate the incidence of heat-labile (LT+) enterotoxin-producing E. coli in the causation of diarrhoea. The results from this study showed that LT+ E. coli is a cause of diarrhoea in the western Cape and that 5,3% of non-diagnosed diarrhoea patients in Tygerberg Hospital were infected with this pathogen. This represented less than 1% of the total number of cases of diarrhoea investigated in this hospital. The peak coincides with the wetter months in this locality and the infection rate is lower than that reported in most other countries. Given the low incidence of occurrence of this organism we do not recommend routine implementation of the diagnostic procedure. However, this test may be useful at times, e.g. to ascertain the source of a diarrhoea epidemic.Publisher’s versio