Building and analysing genome-wide gene disruption networks.

MOTIVATION: Microarray experiments comparing expression levels of all genes in yeast for hundreds of mutants allow us to examine properties of gene regulatory networks on a genomic scale. We can investigate questions such as network modularity, connectivity, and look for genes with particular roles in the network structure. RESULTS: We have built genome-wide disruption networks for yeast, using a representation of gene expression data as directed labelled graphs. Nodes represent genes and arcs connect nodes if the disruption of the source gene significantly alters the expression of the target gene. We are interested in features of the resulting disruption networks that are robust over a range of significance cutoffs. The networks show a significant overlap with analogous networks constructed from scientific literature. In disruption networks the number of arcs adjacent to different nodes are distributed roughly according to a power-law, like in many complex systems where the robustness against perturbations is important. The networks are dominated by a single large component and do not have an obvious modular structure. Genes with the highest outdegrees often encode proteins with regulatory functions, whereas genes with the highest indegrees are predominantly involved in metabolism. The local structure of the networks is meaningful, genes involved in the same cellular processes are close together in the network. AVAILABILITY: http://www.ebi.ac.uk/microarray/networks

General measures for signal-noise separation in nonlinear dynamical systems.

We propose the straight phi divergences from statistics and information theory (IT) as a set of separation indices between signal and noise in stochastic nonlinear dynamical systems (SNDS). The straight phi divergences provide a more informative alternative to the signal-to-noise ratio (SNR) and have the advantage of being applicable to virtually any kind of stochastic system. Moreover, straight phi divergences are intimately connected to various fundamental limits in IT. Using the properties of straight phi divergences, we show that the classical stochastic resonance (SR) curve can be interpreted as the performance of a nonoptimal, or mismatched, detector applied to the output of a SNDS. Indeed, for a prototype double-well system with forcing in the form of white Gaussian noise plus a possible embedded signal, the whole information loss can be attributed to this mismatch; an optimal detection procedure (for the signal) gives the same performance when based on the output as when based on the input of the system. More generally, it follows that, when characterizing signal-noise separation (or system performance) of SNDS in terms of criteria that do not correspond to IT limits, the choice of criterion can be crucial. The indicated figure of merit will then not be universal and will be relevant only to some family of applications, such as the classical (narrow-band SNR) SR criterion, which is relevant for narrow-band post processing. We illustrate the theory using simple SNDS excited by both wide- and narrow-band signals; however, we stress that the results are applicable to a much larger class of signals and systems.

Database "SIGMA Pro" information system and bibliographical management of active substances of plant protection products and biocides.

In order to satisfy its obligations as stipulated in European legislative, in 1998, the Management of Surface Waters in the Walloon Region modified its monitoring of plant protection products in surface waters in co-operation with the Regional Phyto Committee (LLN). Notably, this monitoring network takes into account the agricultural specifics of the main watersheds in Wallonia. It has led to the publication of a specific decree (A.G.W. of June 29th, 2000), which, among others, specifies the list of dangerous relevant substances in Walloon Region as well as their investigation methods (quality, monitoring network, action programmes). Together with the implementation of Directive 76/464/EEC concerning the pollution caused by some dangerous substances in aquatic environment, the Management of Surface Waters is also finalizing a database connected with plant production products. It contains technical data on active ingredients and relevant metabolites (nomenclature, toxicology, physico-chemical properties, ...), bibliographical information referring to these (synthesis of documents, table with results, ...) and some Internet connections. It has been elaborated so as to help Walloon public authorities make their decision.

Structure and heterologous expression of a gene encoding fructose-6-phosphate,2-kinase/fructose-2,6-bisphosphatase from Arabidopsis thaliana.

A full-length cDNA clone encoding fructose-6-phosphate, 2-kinase/fructose-2,6-bisphosphatase from Arabidopsis thaliana (AtF2KP) was isolated. The encoded protein is composed of two different regions: (i) a 400 amino acid COOH-terminal region, covering the catalytic region of the protein which is homologous to enzymes from other eukaryotes. This region is highly conserved among plant species (88% identity to spinach F2KP). (ii) A 345 amino acid plant-specific NH(2)-terminal region, with 59% identity to spinach F2KP, which is composed of homologous motifs and intermittent variable sequences. Western blots show that F2KP from several plant species migrates in sodium dodecyl sulphate-polyacrylamide gel electrophoresis as a similar sized (93 kDa) protein. AtF2KP was expressed in Escherichia coli as a full length and a truncated (without the NH(2)-terminal region) fusion protein. Both forms had kinase as well as phosphatase activity, but presence of the NH(2)-terminal region influenced the ratio between the two activities. It is suggested that the NH(2)-terminal region represents a regulatory region, which defines specific properties of the plant enzymes. A genomic clone for the corresponding gene, AtF2KP, was isolated. The clone (9519 bp) included 23 exons, 22 introns and the promoter sequence. Southern blot analysis showed only one copy of the gene in the A. thaliana genome.