Interactive visualisation and exploration of biological data

International audienceno abstrac

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/

A case study in model-driven synthetic biology

We report on a case study in synthetic biology, demonstrating the modeldriven design of a self-powering electrochemical biosensor. An essential result of the design process is a general template of a biosensor, which can be instantiated to be adapted to specific pollutants. This template represents a gene expression network extended by metabolic activity. We illustrate the model-based analysis of this template using qualitative, stochastic and continuous Petri nets and related analysis techniques, contributing to a reliable and robust design

Representing and analysing molecular and cellular function in the computer

Determining the biological function of a myriad of genes, and understanding how they interact to yield a living cell, is the major challenge of the post genome-sequencing era. The complexity of biological systems is such that this cannot be envisaged without the help of powerful computer systems capable of representing and analysing the intricate networks of physical and functional interactions between the different cellular components. In this review we try to provide the reader with an appreciation of where we stand in this regard. We discuss some of the inherent problems in describing the different facets of biological function, give an overview of how information on function is currently represented in the major biological databases, and describe different systems for organising and categorising the functions of gene products. In a second part, we present a new general data model, currently under development, which describes information on molecular function and cellular processes in a rigorous manner. The model is capable of representing a large variety of biochemical processes, including metabolic pathways, regulation of gene expression and signal transduction. It also incorporates taxonomies for categorising molecular entities, interactions and processes, and it offers means of viewing the information at different levels of resolution, and dealing with incomplete knowledge. The data model has been implemented in the database on protein function and cellular processes 'aMAZE' (http://www.ebi.ac.uk/research/pfbp/), which presently covers metabolic pathways and their regulation. Several tools for querying, displaying, and performing analyses on such pathways are briefly described in order to illustrate the practical applications enabled by the model

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

A study on the structure and vibrations of diphenylamine by resonance-enhanced multiphoton ionization spectroscopy and ab initio calculations

Laser‐desorption jet‐cooling has been applied in combination with mass‐selective gas‐phase spectroscopic techniques to study the structure and low‐frequency vibrations of diphenylamine (DPA). Two‐color (1+1′) resonance‐enhanced multiphoton ionization has been used to measure the vibrationally resolved excitation spectrum of the S1←S0 transition in the 305–309 nm region. Ion‐dip measurements have been performed to determine the vibrational structure in the electronic ground state. The electronic spectra of DPA are dominated by long progressions in low‐frequency vibrations involving the motion of the phenyl rings as a whole. For the interpretation of the experimental data ab initio calculations have been performed at the Hartree–Fock level for the S0‐state and using single‐excitation configuration interaction for the S1‐state. The DPA molecule is found to change from a pyramidal geometry around the N‐atom with unequal torsional angles of the phenyl groups in the S0‐state to a planar geometry with equal torsional angles in the S1‐state. The two most prominent vibrational motions are the in‐phase wagging and the in‐phase torsion of the phenyl rings. In addition, the resonance‐enhanced multiphoton ionization spectra of the S1←S0 transition in the DPA‐Ar, DPA‐Kr, and DPA‐Xe van der Waals complexes have been measured. From these spectra it is inferred that there is a coupling between the van der Waals modes and the low‐frequency intra‐molecular modes of DPA

Critical Casimir forces in colloidal suspensions on chemically patterned surfaces

We investigate the behavior of colloidal particles immersed in a binary liquid mixture of water and 2,6-lutidine in the presence of a chemically patterned substrate. Close to the critical point of the mixture, the particles are subjected to critical Casimir interactions with force components normal and parallel to the surface. Because the strength and sign of these interactions can be tuned by variations in the surface properties and the mixtures temperature, critical Casimir forces allow the formation of highly ordered monolayers but also extend the use of colloids as model systems.Comment: 4 papges, 4 figures, accepted at Phys. Rev. Let

ReSolVe : restaurer la fertilité des sols viticoles en agriculture biologique

Le projet ReSolVe (programme Core Organic Plus) regroupe 6 pays dans l’objectif de restaurer la fertilité des sols viticoles par des méthodes alternatives dans des parcelles conduites en agriculture biologique présentant des zones caractérisées par des déficiences de vigueur, de récolte ou encore de qualité. L’objectif est de tester des techniques compatibles avec l’agriculture biologique afin de rétablir la fertilité et le fonctionnement du sol dans ces zones dégradées : ajout de compost, semis d’engrais verts, et semis d’un enherbement géré en mulch. 6 parcelles d'essai ont été mises en place en France. Les relations entre caractéristiques des sols, biodiversité (dont mésofaune), décomposition de la matière organique et conséquences sur la productivité de la vigne ont été évaluées lors d'une première année témoin en 2015 et les effets de la mise en place des modalités commencent à être évalués en 2016