Genome-Wide Transcriptome Analyses of Silicon Metabolism in Phaeodactylum tricornutum Reveal the Multilevel Regulation of Silicic Acid Transporters

BACKGROUND:Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH)(4) can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles. METHODOLOGY/PRINCIPAL FINDINGS:Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations. CONCLUSIONS/SIGNIFICANCE:Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level) to genomic (organization in clusters, dosage compensation by gene duplication), and by post-transcriptional regulation and spatial distribution of SIT proteins

Context-Scanning Strategy in Temporal Reasoning

This paper presents a method for temporal reasoning based on context-scanning rules. The method uses exclusively linguistic markers (tensed forms, temporal and non-temporal adverbials, interjections, particular syntactic structures) which allow to carry out temporal reasoning centred on the act of utterance. Due to the information extracted from the analysed texts, the method is capable to identify aspecto-temporal values in isolated utterances but also temporal structures of larger text units. The aspecto-temporal information receives formal representation in combinatory logic which allows its machine processing

Contextual Rules for Text Analysis

In this paper we describe a rule-based formalism for the analysis and labelling of texts segments. The rules are contextual rewriting rules with a restricted form of negation. They allow to underspecify text segments not considered relevant to a given task and to base decisions upon context. A parser for these rules is presented and consistence and completeness issues are discussed. Some results of an implementation of this parser with a set of rules oriented to the segmentation of texts in propositions are shown