Differential Network Analysis of Anti-sense Regulation

A challenging task in systems biology is to decipher cell regulation mechanisms. By comparing networks observed in two different situations, the differential network analysis approach enables to highlight interaction differences that reveal specific cellular responses. The aim of our work is to study the role of natural anti-sense transcription on cellular regulation mechanisms. Our proposal is to build and compare networks obtained from two different sets of actors: the “usual” sense actors on one hand and the sense and anti-sense actors on the other hand. Our study only considers the most significant interactions, called an Extended Core Network; therefore our differential analysis identifies important interactions that are impacted by anti-sense transcription. This paper first introduces our inference method of an Extended Core Network; this method is inspired by C3NET, but whereas C3NET only computes one interaction per gene, we propose to consider the most significant interactions for each gene. Secondly, we define the differential network analysis of two extended core networks inferred with and without anti-sense actors. On a local view, this analysis relies on change motifs that describe which genes have their most important interactions modified when the anti-sense transcripts are considered; they are called AS-impacted genes. Then from a more global view, we consider how the relationships between these AS-impacted genes are rewired in the network with anti-sense actors. Our analysis is performed by computing Steiner trees that represent minimal subnetworks connecting the AS-impacted genes. We show that the visualisation of these results help the biologists to identify interesting parts of the networks

Differential Functional Analysis and Change Motifs in Gene Networks to Explore the Role of Anti-sense Transcription

Several transcriptomic studies have shown the widespread existence of anti-sense transcription in cell. Anti-sense RNAs may be important actors in transcriptional control, especially in stress response processes. The aim of our work is to study gene networks, with the particularity to integrate in the process anti-sense transcripts. In this paper, we first present a method that highlights the importance of taking into account anti-sense data into functional enrichment analysis. Secondly, we propose the differential analysis of gene networks built with and without anti-sense actors in order to discover interesting change motifs that involve the anti-sense transcripts. For more reliability, our network comparison only studies the conservative causal part of a network, inferred by the C3NET method. Our work is realized on transcriptomic data from apple fruit

Inference and Differential Analysis of Extended Core Networks: a way to study Anti-Sense Regulation

A key issue in bioinformatics is to decipher cell regulation mechanisms. By comparing networks observed in two different situations, differential network analysis enables to highlight differences that reveal specific cellular responses. The aim of our work is to study the role of natural anti-sense transcription on cellular regulation mechanisms. Our proposal is to build and compare networks obtained from two different sets of actors: the “usual” sense actors on one hand and the sense and anti-sense actors on the other hand. Our study only considers themost significant interactions, called an Extended Core Network; therefore our differential analysis identifies important interactions that are on the influence of anti-sense transcription. Our inference method of an Extended Core Network is inspired by C3NET, but whereas C3NET only computes one interaction per gene, we propose to consider the most significant interactions for each gene. We define the differential network analysis of two extended core networks inferred with and without anti-sense actors. This relies on change motifs that describe which gene-gene interactions of the extended core network are modified when we integrate anti-sense actors in the data. As our method ocuses on the most significant interactions, these motifs highlight the impact of anti-sense transcription. The networks motifs obtained by our workflow are then compared with assessed biological knowledge. The study reported in this paper is realized on transcriptional data from apple fruit in a context of fruit ripening; the change motifs revealed by our analysis are matched on a protein-protein interaction network and give a small set of interesting actors thatdeserve further biological investigation

A Singular Conformal Spacetime

The infinite cosmological "constant" limit of the de Sitter solutions to Einstein's equation is studied. The corresponding spacetime is a singular, four-dimensional cone-space, transitive under proper conformal transformations, which constitutes a new example of maximally-symmetric spacetime. Grounded on its geometric and thermodynamic properties, some speculations are made in connection with the primordial universe.Comment: RevTeX4, 10 pages, 1 eps figure. Presentation changes, including a new title; section II.E, on the thermodynamic properties of the de Sitter horizon, completely revised. Version to be published in Journal of Geometry and Physic

Methyl coprogen B, a new potential marker of colonization of the airways of CF patients by Scedosporium apiospermum

Date du colloque&nbsp;: 06/2009</p

Hydroxamate siderophores of Scedosporium apiospermum

Scedosporium apiospermum is an emerging pathogen colonizing the airways of patients with cystic fibrosis and causing severe infections in immunocompromised hosts. In order to improve our knowledge on the pathogenic mechanisms of this fungus, we investigated the production of siderophores. Cultivation on CAS medium and specific assays for different classes of siderophores suggested the secretion of hydroxamates. A maximal production was obtained by cultivation of the fungus at alkaline pH in an iron-restricted liquid culture medium. Siderophores were then extracted from the culture filtrate by liquid/liquid extraction, and separated by reverse phase high performance liquid chromatography. Two siderophores, dimerumic acid and N α-methyl coprogen B, were identified by electrospray ionization-mass spectrometry and MS–MS fragmentation. Finally, comparison of various strains suggested a higher production of N α-methyl coprogen B by clinical isolates of respiratory origin. Studies are initiated in order to determine the potential usefulness of these siderophores as diagnostic markers of scedosporiosis

Continuum limit of amorphous elastic bodies: A finite-size study of low frequency harmonic vibrations

The approach of the elastic continuum limit in small amorphous bodies formed by weakly polydisperse Lennard-Jones beads is investigated in a systematic finite-size study. We show that classical continuum elasticity breaks down when the wavelength of the sollicitation is smaller than a characteristic length of approximately 30 molecular sizes. Due to this surprisingly large effect ensembles containing up to N=40,000 particles have been required in two dimensions to yield a convincing match with the classical continuum predictions for the eigenfrequency spectrum of disk-shaped aggregates and periodic bulk systems. The existence of an effective length scale \xi is confirmed by the analysis of the (non-gaussian) noisy part of the low frequency vibrational eigenmodes. Moreover, we relate it to the {\em non-affine} part of the displacement fields under imposed elongation and shear. Similar correlations (vortices) are indeed observed on distances up to \xi~30 particle sizes.Comment: 28 pages, 13 figures, 3 table